Solution conformation of a cohesin module and its scaffoldin linker from a prototypical cellulosome.

PubMed

Galera-Prat, Albert; Pantoja-Uceda, David; Laurents, Douglas V; Carrión-Vázquez, Mariano

2018-04-15

Bacterial cellulases are drawing increased attention as a means to obtain plentiful chemical feedstocks and fuels from renewable lignocellulosic biomass sources. Certain bacteria deploy a large extracellular multi-protein complex, called the cellulosome, to degrade cellulose. Scaffoldin, a key non-catalytic cellulosome component, is a large protein containing a cellulose-specific carbohydrate-binding module and several cohesin modules which bind and organize the hydrolytic enzymes. Despite the importance of the structure and protein/protein interactions of the cohesin module in the cellulosome, its structure in solution has remained unknown to date. Here, we report the backbone 1 H, 13 C and 15 N NMR assignments of the Cohesin module 5 from the highly stable and active cellulosome from Clostridium thermocellum. These data reveal that this module adopts a tightly packed, well folded and rigid structure in solution. Furthermore, since in scaffoldin, the cohesin modules are connected by linkers we have also characterized the conformation of a representative linker segment using NMR spectroscopy. Analysis of its chemical shift values revealed that this linker is rather stiff and tends to adopt extended conformations. This suggests that the scaffoldin linkers act to minimize interactions between cohesin modules. These results pave the way towards solution studies on cohesin/dockerin's fascinating dual-binding mode. Copyright © 2018 Elsevier Inc. All rights reserved.

Harmonic Analysis and Free Field Realization of the Takiff Supergroup of GL(1|1)

NASA Astrophysics Data System (ADS)

Babichenko, Andrei; Creutzig, Thomas

2015-08-01

Takiff superalgebras are a family of non semi-simple Lie superalgebras that are believed to give rise to a rich structure of indecomposable representations of associated conformal field theories. We consider the Takiff superalgebra of gl(1\\vert 1), especially we perform harmonic analysis for the corresponding supergroup. We find that every simple module appears as submodule of an infinite-dimensional indecomposable but reducible module. We lift our results to two free field realizations for the corresponding conformal field theory and construct some modules.

Low Phase Noise Fiber Optics Links for Space Applications

DTIC Science & Technology

2005-07-13

photo- oscillateur intégré pour 17 dB de pertes optiques Liaison active à 874,2 MHz avec photo- oscillateur intégré pour 18 dB de pertes optiques Liaison...active à 874,2 MHz avec photo- oscillateur intégré pour 20 dB de pertes optiques Liaison active à 874,2 MHz avec photo- oscillateur intégré pour 23 dB...de pertes optiques Liaison active à 874,2 MHz avec photo- oscillateur intégré pour 25 dB de pertes optiques Liaison active à 874,2 MHz avec photo

Stabilisation de l'etat de polarisation d'un laser par la conception et fabrication d'un miroir polarisant fait de couches minces nanostructurees

NASA Astrophysics Data System (ADS)

Doucet, Alexandre

Ce manuscrit presente la conception et la fabrication d'un miroir polarisant fabrique avec la methode de deposition par incidence oblique communement appelee en anglais GLAD (GLancing Angle Deposition). Cette methode de deposition par GLAD permet de changer la nanostructure des revetements avec l'inclinaison et la rotation du substrat par rapport au flux de materiau evapore. Ceci nous permet d'ajuster l'indice de refraction et d'obtenir des revetements birefringents avec un materiau intrinsequement isotrope. Puisque l'indice de refraction peut etre change, les miroirs sont fabriques avec un seul materiau contrairement aux methodes usuelles qui necessite deux materiaux. Les proprietes optiques des echantillons sont mesurees avec l'aide de l'ellipsometrie. Des images avec un microscope electronique a balayage par transmission permettent de verifier Ia structure des revetements deposes. Les miroirs sont utilises comme coupleurs de sortie du resonateur d'un laser avec un milieu actif d'(Yb3+0.1 Y 0.9)3Al5O12, ou plus simplement Yb: YAG, pompe optiquement avec une diode laser. Ces cristaux presentent des proprietes optiques interessantes pour leur utilisation comme milieu actif, mais avec une structure cristalline cubique, ils donnent lieu a des faisceaux polarises aleatoirement. Les miroirs que nous fabriquons permettent d'obtenir une emission polarisee lineairement sans avoir a ajouter d'autres elements au resonateur. Les tests sont faits en regime continu et pulse avec un absorbant saturable de Cr : Y AG. Deux materiaux sont etudies, soit le WO3 et le TiO2, et ils nous permettent d'obtenir une emission polarisee lineairement dans le mode TEM 00 avec un rapport d'extinction de 1000 (30 dB), mais seuls les miroirs de TiO2 permettent une emission pulsee periodique avec une densite de puissance crete pres de 700+/-80 MW/cm2. En etudiant le rapport d'extinction en fonction du temps de pompage, nous remarquons que l'etat de polarisation est beaucoup plus stable que celui obtenu avec un miroir isotrope. Des mesures du spectre d'emission avec un spectrometre de haute resolution permettent de constater le caractere multimode longitudinal en regime continu et une emission monomode longitudinale en regime pulse. None None None None None None None None None None None None None None None None None None None None None None None

Bladder radiotherapy treatment: A retrospective comparison of 3-dimensional conformal radiotherapy, intensity-modulated radiation therapy, and volumetric-modulated arc therapy plans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pasciuti, Katia, E-mail: k.pasciuti@virgilio.it; Kuthpady, Shrinivas; Anderson, Anne

To examine tumor's and organ's response when different radiotherapy plan techniques are used. Ten patients with confirmed bladder tumors were first treated using 3-dimensional conformal radiotherapy (3DCRT) and subsequently the original plans were re-optimized using the intensity-modulated radiation treatment (IMRT) and volumetric-modulated arc therapy (VMAT)-techniques. Targets coverage in terms of conformity and homogeneity index, TCP, and organs' dose limits, including integral dose analysis were evaluated. In addition, MUs and treatment delivery times were compared. Better minimum target coverage (1.3%) was observed in VMAT plans when compared to 3DCRT and IMRT ones confirmed by a statistically significant conformity index (CI) results.more » Large differences were observed among techniques in integral dose results of the femoral heads. Even if no statistically significant differences were reported in rectum and tissue, a large amount of energy deposition was observed in 3DCRT plans. In any case, VMAT plans provided better organs and tissue sparing confirmed also by the normal tissue complication probability (NTCP) analysis as well as a better tumor control probability (TCP) result. Our analysis showed better overall results in planning using VMAT techniques. Furthermore, a total time reduction in treatment observed among techniques including gantry and collimator rotation could encourage using the more recent one, reducing target movements and patient discomfort.« less

Anharmonic longitudinal motion of bases and dynamics of nonlinear excitation in DNA.

PubMed

Di Garbo, Angelo

2016-01-01

The dynamics of the transcription bubble in DNA is studied by using a nonlinear model in which torsional and longitudinal conformations of the biomolecule are coupled. In the absence of forcing and dissipation the torsional dynamics is described by a perturbed kink of the Sine-Gordon DNA model, while the longitudinal conformational energy propagate as phonons. It was found that for random initial conditions of the longitudinal conformational field the presence of the kink promotes the creation of phonons propagating along the chain axis. Moreover, the presence of forcing, describing the active role of RNA polymerase, determines in agreement to the experimental data a modulation of the velocity of the transcription bubble. Lastly, it was shown that the presence of dissipation impacts the dynamic of the phonon by reducing the amplitude of the corresponding conformational field. On the contrary, dissipation and forcing modulate the velocity of the transcription bubble alone.

Worming our way to novel drug discovery with the Caenorhabditis elegans proteostasis network, stress response and insulin-signaling pathways.

PubMed

O'Reilly, Linda P; Benson, Joshua A; Cummings, Erin E; Perlmutter, David H; Silverman, Gary A; Pak, Stephen C

2014-09-01

Many human diseases result from a failure of a single protein to achieve the correct folding and tertiary conformation. These so-called 'conformational diseases' involve diverse proteins and distinctive cellular pathologies. They all engage the proteostasis network (PN), to varying degrees in an attempt to mange cellular stress and restore protein homeostasis. The insulin/insulin-like growth factor signaling (IIS) pathway is a master regulator of cellular stress response, which is implicated in regulating components of the PN. This review focuses on novel approaches to target conformational diseases. The authors discuss the evidence supporting the involvement of the IIS pathway in modulating the PN and regulating proteostasis in Caenorhabditis elegans. Furthermore, they review previous PN and IIS drug screens and explore the possibility of using C. elegans for whole organism-based drug discovery for modulators of IIS-proteostasis pathways. An alternative approach to develop individualized therapy for each conformational disease is to modulate the global PN. The involvement of the IIS pathway in regulating longevity and response to a variety of stresses is well documented. Increasing data now provide evidence for the close association between the IIS and the PN pathways. The authors believe that high-throughput screening campaigns, which target the C. elegans IIS pathway, may identify drugs that are efficacious in treating numerous conformational diseases.

Fast, clash-free RNA conformational morphing using molecular junctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus

Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less

Fast, clash-free RNA conformational morphing using molecular junctions

DOE PAGES

Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus; ...

2017-03-13

Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less

Modulation of the Conformational Dynamics of Apo-Adenylate Kinase through a π-Cation Interaction.

PubMed

Halder, Ritaban; Manna, Rabindra Nath; Chakraborty, Sandipan; Jana, Biman

2017-06-15

Large-scale conformational transition from open to closed state of adenylate kinase (ADK) is essential for its catalytic cycle. Apo-ADK undergoes conformational transition in a way that closely resembles an open-to-closed conformational transition. Here, equilibrium simulations, free-energy simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations in combination with several bioinformatics approaches have been used to explore the molecular origin of this conformational transition in apo-ADK. In addition to its conventional open state, Escherichia coli apo-ADK adopts conformations that resemble a closed-like intermediate, the "half-open-half-closed" (HOHC) state, and a π-cation interaction can account for the stability of this HOHC state. Energetics and the electronic properties of this π-cation interaction have been explored using QM/MM calculations. Upon rescinding the π-cation interaction, the conformational landscape of the apo-ADK changes completely. The apo-ADK population is shifted completely toward the open state. This π-cation interaction is highly conserved in bacterial ADK; the cationic guanidinium moiety of a conserved ARG interacts with the delocalized π-electron cloud of either PHE or TYR. Interestingly, this study demonstrates the modulation of a principal protein dynamics by a conserved specific π-cation interaction across different organisms.

Detection of Mutant Huntingtin Aggregation Conformers and Modulation of SDS-Soluble Fibrillar Oligomers by Small Molecules

PubMed Central

Sontag, Emily Mitchell; Lotz, Gregor P.; Yang, Guocheng; Sontag, Christopher J.; Cummings, Brian J.; Glabe, Charles G.; Muchowski, Paul J.; Thompson, Leslie Michels

2012-01-01

The Huntington’s disease (HD) mutation leads to a complex process of Huntingtin (Htt) aggregation into multimeric species that eventually form visible inclusions in cytoplasm, nuclei and neuronal processes. One hypothesis is that smaller, soluble forms of amyloid proteins confer toxic effects and contribute to early cell dysfunction. However, analysis of mutant Htt aggregation intermediates to identify conformers that may represent toxic forms of the protein and represent potential drug targets remains difficult. We performed a detailed analysis of aggregation conformers in multiple in vitro, cell and ex vivo models of HD. Conformation-specific antibodies were used to identify and characterize aggregation species, allowing assessment of multiple conformers present during the aggregation process. Using a series of assays together with these antibodies, several forms could be identified. Fibrillar oligomers, defined as having a β-sheet rich conformation, are observed in vitro using recombinant protein and in protein extracts from cells in culture or mouse brain and shown to be globular, soluble and non-sedimentable structures. Compounds previously described to modulate visible inclusion body formation and reduce toxicity in HD models were also tested and consistently found to alter the formation of fibrillar oligomers. Interestingly, these compounds did not alter the rate of visible inclusion formation, indicating that fibrillar oligomers are not necessarily the rate limiting step of inclusion body formation. Taken together, we provide insights into the structure and formation of mutant Htt fibrillar oligomers that are modulated by small molecules with protective potential in HD models. PMID:24086178

Trajectory modulated prone breast irradiation: a LINAC-based technique combining intensity modulated delivery and motion of the couch.

PubMed

Fahimian, Benjamin; Yu, Victoria; Horst, Kathleen; Xing, Lei; Hristov, Dimitre

2013-12-01

External beam radiation therapy (EBRT) provides a non-invasive treatment alternative for accelerated partial breast irradiation (APBI), however, limitations in achievable dose conformity of current EBRT techniques have been correlated to reported toxicity. To enhance the conformity of EBRT APBI, a technique for conventional LINACs is developed, which through combined motion of the couch, intensity modulated delivery, and a prone breast setup, enables wide-angular coronal arc irradiation of the ipsilateral breast without irradiating through the thorax and contralateral breast. A couch trajectory optimization technique was developed to determine the trajectories that concurrently avoid collision with the LINAC and maintain the target within the MLC apertures. Inverse treatment planning was performed along the derived trajectory. The technique was experimentally implemented by programming the Varian TrueBeam™ STx in Developer Mode. The dosimetric accuracy of the delivery was evaluated by ion chamber and film measurements in phantom. The resulting optimized trajectory was shown to be necessarily non-isocentric, and contain both translation and rotations of the couch. Film measurements resulted in 93% of the points in the measured two-dimensional dose maps passing the 3%/3mm Gamma criterion. Preliminary treatment plan comparison to 5-field 3D-conformal, IMRT, and VMAT demonstrated enhancement in conformity, and reduction of the normal tissue V50% and V100% parameters that have been correlated with EBRT toxicity. The feasibility of wide-angular intensity modulated partial breast irradiation using motion of the couch has been demonstrated experimentally on a standard LINAC for the first time. For patients eligible for a prone setup, the technique may enable improvement of dose conformity and associated dose-volume parameters correlated with toxicity. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Protein Conformational Populations and Functionally Relevant Sub-states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agarwal, Pratul K; Burger, Virginia; Savol, Andrej

2013-01-01

Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates with dynamic and structural features that support the designated function of themore » protein. Nuclear magnetic resonance (NMR) experiments provide information about conformational ensembles of proteins. X-ray crystallography allows researchers to identify the most populated states along the landscape, and computational simulations give atom-level information about the conformational substates of different proteins. This ability to characterize and obtain quantitative information about the conformational substates and the populations of proteins within them is allowing researchers to better understand the relationship between protein structure and dynamics and the mechanisms of protein function. In this Account, we discuss recent developments and challenges in the characterization of functionally relevant conformational populations and substates of proteins. In some enzymes, the sampling of functionally relevant conformational substates is connected to promoting the overall mechanism of catalysis. For example, the conformational landscape of the enzyme dihydrofolate reductase has multiple substates, which facilitate the binding and the release of the cofactor and substrate and catalyze the hydride transfer. For the enzyme cyclophilin A, computational simulations reveal that the long time scale conformational fluctuations enable the enzyme to access conformational substates that allow it to attain the transition state, therefore promoting the reaction mechanism. In the long term, this emerging view of proteins with conformational substates has broad implications for improving our understanding of enzymes, enzyme engineering, and better drug design. Researchers have already used photoactivation to modulate protein conformations as a strategy to develop a hypercatalytic enzyme. In addition, the alteration of the conformational substates through binding of ligands at locations other than the active site provides the basis for the design of new medicines through allosteric modulation.« less

47 CFR 73.128 - AM stereophonic broadcasting.

Code of Federal Regulations, 2010 CFR

2010-10-01

... stereophonic transmissions conform to the modulation characteristics specified in paragraphs (b) and (c) of... occupied bandwidth specifications of § 73.44 under all possible conditions of program modulation. Compliance with requirement shall be demonstrated either by the following specific modulation tests or other...

Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques

PubMed Central

Provasi, Davide; Artacho, Marta Camacho; Negri, Ana; Mobarec, Juan Carlos; Filizola, Marta

2011-01-01

Extensive experimental information supports the formation of ligand-specific conformations of G protein-coupled receptors (GPCRs) as a possible molecular basis for their functional selectivity for signaling pathways. Taking advantage of the recently published inactive and active crystal structures of GPCRs, we have implemented an all-atom computational strategy that combines different adaptive biasing techniques to identify ligand-specific conformations along pre-determined activation pathways. Using the prototypic GPCR β2-adrenergic receptor as a suitable test case for validation, we show that ligands with different efficacies (either inverse agonists, neutral antagonists, or agonists) modulate the free-energy landscape of the receptor by shifting the conformational equilibrium towards active or inactive conformations depending on their elicited physiological response. Notably, we provide for the first time a quantitative description of the thermodynamics of the receptor in an explicit atomistic environment, which accounts for the receptor basal activity and the stabilization of different active-like states by differently potent agonists. Structural inspection of these metastable states reveals unique conformations of the receptor that may have been difficult to retrieve experimentally. PMID:22022248

Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts.

PubMed

Chen, Haorong; Zhang, Hanyu; Pan, Jing; Cha, Tae-Gon; Li, Shiming; Andréasson, Joakim; Choi, Jong Hyun

2016-05-24

DNA origami has received enormous attention for its ability to program complex nanostructures with a few nanometer precision. Dynamic origami structures that change conformation in response to environmental cues or external signals hold great promises in sensing and actuation at the nanoscale. The reconfiguration mechanism of existing dynamic origami structures is mostly limited to single-stranded hinges and relies almost exclusively on DNA hybridization or strand displacement. Here, we show an alternative approach by demonstrating on-demand conformation changes with DNA-binding molecules, which intercalate between base pairs and unwind DNA double helices. The unwinding effect modulates the helicity mismatch in DNA origami, which significantly influences the internal stress and the global conformation of the origami structure. We demonstrate the switching of a polymerized origami nanoribbon between different twisting states and a well-constrained torsional deformation in a monomeric origami shaft. The structural transformation is shown to be reversible, and binding isotherms confirm the reconfiguration mechanism. This approach provides a rapid and reversible means to change DNA origami conformation, which can be used for dynamic and progressive control at the nanoscale.

Modulation of phase transition of thermosensitive liposomes with leucine zipper-structured lipopeptides.

PubMed

Xu, Xiejun; Xiao, Xingqing; Wang, Yiming; Xu, Shouhong; Liu, Honglai

2018-06-13

Targeted therapy for cancer requires thermosensitive components in drug carriers for controlled drug release against viral cells. The conformational transition characteristic of leucine zipper-structured lipopeptides is utilized in our lab to modulate the phase transition temperature of liposomes, thus achieving temperature-responsive control. In this study, we computationally examined the conformational transition behaviors of leucine zipper-structured lipopeptides that were modified at the N-terminus by distinct functional groups. The conformational transition temperatures of these lipopeptides were determined by structural analysis of the implicit-solvent replica exchange molecular dynamics simulation trajectories using the dihedral angle principal component analysis and the dictionary of protein secondary structure method. Our calculations revealed that the computed transition temperatures of the lipopeptides are in good agreement with the experimental measurements. The effect of hydrogen bonds on the conformational stability of the lipopeptide dimers was examined in conventional explicit-solvent molecular dynamics simulations. A quantitative correlation of the degree of structural dissociation of the dimers and their binding strength is well described by an exponential fit of the binding free energies to the conformation transition temperatures of the lipopeptides.

Structural basis for the ATP-independent proteolytic activity of LonB proteases and reclassification of their AAA+ modules.

PubMed

An, Young Jun; Na, Jung-Hyun; Kim, Myung-Il; Cha, Sun-Shin

2015-10-01

Lon proteases degrade defective or denature proteins as well as some folded proteins for the control of cellular protein quality. There are two types of Lon proteases, LonA and LonB. Each consists of two functional components: a protease component and an ATPase associated with various cellular activities (AAA+ module). Here, we report the 2.03 -resolution crystal structure of the isolated AAA+ module (iAAA+ module) of LonB from Thermococcus onnurineus NA1 (TonLonB). The iAAA+ module, having no bound nucleotide, adopts a conformation virtually identical to the ADP-bound conformation of AAA+ modules in the hexameric structure of TonLonB; this provides insights into the ATP-independent proteolytic activity observed in a LonB protease. Structural comparison of AAA+ modules between LonA and LonB revealed that the AAA+ modules of Lon proteases are separated into two distinct clades depending on their structural features. The AAA+ module of LonB belongs to the -H2 & Ins1 insert clade (HINS clade)- defined for the first time in this study, while the AAA+ module of LonA is a member of the HCLR clade.

Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding

PubMed Central

Koenig, Patrick; Lee, Chingwei V.; Walters, Benjamin T.; Janakiraman, Vasantharajan; Stinson, Jeremy; Patapoff, Thomas W.; Fuh, Germaine

2017-01-01

Somatic mutations within the antibody variable domains are critical to the immense capacity of the immune repertoire. Here, via a deep mutational scan, we dissect how mutations at all positions of the variable domains of a high-affinity anti-VEGF antibody G6.31 impact its antigen-binding function. The resulting mutational landscape demonstrates that large portions of antibody variable domain positions are open to mutation, and that beneficial mutations can be found throughout the variable domains. We determine the role of one antigen-distal light chain position 83, demonstrating that mutation at this site optimizes both antigen affinity and thermostability by modulating the interdomain conformational dynamics of the antigen-binding fragment. Furthermore, by analyzing a large number of human antibody sequences and structures, we demonstrate that somatic mutations occur frequently at position 83, with corresponding domain conformations observed for G6.31. Therefore, the modulation of interdomain dynamics represents an important mechanism during antibody maturation in vivo. PMID:28057863

Hidden supersymmetry and quadratic deformations of the space-time conformal superalgebra

NASA Astrophysics Data System (ADS)

Yates, L. A.; Jarvis, P. D.

2018-04-01

We analyze the structure of the family of quadratic superalgebras, introduced in Jarvis et al (2011 J. Phys. A: Math. Theor. 44 235205), for the quadratic deformations of N  =  1 space-time conformal supersymmetry. We characterize in particular the ‘zero-step’ modules for this case. In such modules, the odd generators vanish identically, and the quadratic superalgebra is realized on a single irreducible representation of the even subalgebra (which is a Lie algebra). In the case under study, the quadratic deformations of N  =  1 space-time conformal supersymmetry, it is shown that each massless positive energy unitary irreducible representation (in the standard classification of Mack), forms such a zero-step module, for an appropriate parameter choice amongst the quadratic family (with vanishing central charge). For these massless particle multiplets therefore, quadratic supersymmetry is unbroken, in that the supersymmetry generators annihilate all physical states (including the vacuum state), while at the same time, superpartners do not exist.

Epitope analysis of the malaria surface antigen pfs48/45 identifies a subdomain that elicits transmission blocking antibodies.

PubMed

Outchkourov, Nikolay; Vermunt, Adriaan; Jansen, Josephine; Kaan, Anita; Roeffen, Will; Teelen, Karina; Lasonder, Edwin; Braks, Anneke; van de Vegte-Bolmer, Marga; Qiu, Li Yan; Sauerwein, Robert; Stunnenberg, Hendrik G

2007-06-08

Pfs48/45, a member of a Plasmodium-specific protein family, displays conformation-dependent epitopes and is an important target for malaria transmission-blocking (TB) immunity. To design a recombinant Pfs48/45-based TB vaccine, we analyzed the conformational TB epitopes of Pfs48/45. The Pfs48/45 protein was found to consist of a C-terminal six-cysteine module recognized by anti-epitope I antibodies, a middle four-cysteine module recognized by anti-epitopes IIb and III, and an N-terminal module recognized by anti-epitope V antibodies. Refolding assays identified that a fragment of 10 cysteines (10C), comprising the middle four-cysteine and the C-terminal six-cysteine modules, possesses superior refolding capacity. The refolded and partially purified 10C conformer elicited antibodies in mice that targeted at least two of the TB epitopes (I and III). The induced antibodies could block the fertilization of Plasmodium falciparum gametes in vivo in a concentration-dependent manner. Our results provide important insight into the structural organization of the Pfs48/45 protein and experimental support for a Pfs48/45-based subunit vaccine.

Recent advances in intensity modulated radiotherapy and proton therapy for esophageal cancer.

PubMed

Xi, Mian; Lin, Steven H

2017-07-01

Radiotherapy is an important component of the standard of care for esophageal cancer. In the past decades, significant improvements in the planning and delivery of radiation techniques have led to better dose conformity to the target volume and improved normal tissue sparing. Areas covered: This review focuses on the advances in radiotherapy techniques and summarizes the availably dosimetric and clinical outcomes of intensity-modulated radiation therapy (IMRT), volumetric modulated arc therapy, proton therapy, and four-dimensional radiotherapy for esophageal cancer, and discusses the challenges and future development of proton therapy. Expert commentary: Although three-dimensional conformal radiotherapy is the standard radiotherapy technique in esophageal cancer, the retrospectively comparative studies strongly suggest that the dosimetric advantage of IMRT over three-dimensional conformal radiotherapy can translate into improved clinical outcomes, despite the lack of prospective randomized evidence. As a novel form of conventional IMRT technique, volumetric modulated arc therapy can produce equivalent or superior dosimetric quality with significantly higher treatment efficiency in esophageal cancer. Compared with photon therapy, proton therapy has the potential to achieve further clinical improvement due to their physical properties; however, prospective clinical data, long-term results, and cost-effectiveness are needed.

General Conformity Training Modules: Appendix A Sample Emissions Calculations

EPA Pesticide Factsheets

Appendix A of the training modules gives example calculations for external and internal combustion sources, construction, fuel storage and transfer, on-road vehicles, aircraft operations, storage piles, and paved roads.

Quantum/molecular mechanics study of firefly bioluminescence on luciferase oxidative conformation

NASA Astrophysics Data System (ADS)

Pinto da Silva, Luís; Esteves da Silva, Joaquim C. G.

2014-07-01

This is the first report of a computational study of the color tuning mechanism of firefly bioluminescence, using the oxidative conformation of luciferase. The results of these calculations demonstrated that the electrostatic field generated by luciferase is fundamental both for the emission shift and efficiency. Further calculations indicated that a shift in emission is achieved by modulating the energy, at different degrees, of the emissive and ground states. These differences in energy modulation will then lead to changes in the energy gap between the states.

Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs

NASA Astrophysics Data System (ADS)

Dror, Ron O.; Green, Hillary F.; Valant, Celine; Borhani, David W.; Valcourt, James R.; Pan, Albert C.; Arlow, Daniel H.; Canals, Meritxell; Lane, J. Robert; Rahmani, Raphaël; Baell, Jonathan B.; Sexton, Patrick M.; Christopoulos, Arthur; Shaw, David E.

2013-11-01

The design of G-protein-coupled receptor (GPCR) allosteric modulators, an active area of modern pharmaceutical research, has proved challenging because neither the binding modes nor the molecular mechanisms of such drugs are known. Here we determine binding sites, bound conformations and specific drug-receptor interactions for several allosteric modulators of the M2 muscarinic acetylcholine receptor (M2 receptor), a prototypical family A GPCR, using atomic-level simulations in which the modulators spontaneously associate with the receptor. Despite substantial structural diversity, all modulators form cation-π interactions with clusters of aromatic residues in the receptor extracellular vestibule, approximately 15Å from the classical, `orthosteric' ligand-binding site. We validate the observed modulator binding modes through radioligand binding experiments on receptor mutants designed, on the basis of our simulations, either to increase or to decrease modulator affinity. Simulations also revealed mechanisms that contribute to positive and negative allosteric modulation of classical ligand binding, including coupled conformational changes of the two binding sites and electrostatic interactions between ligands in these sites. These observations enabled the design of chemical modifications that substantially alter a modulator's allosteric effects. Our findings thus provide a structural basis for the rational design of allosteric modulators targeting muscarinic and possibly other GPCRs.

77 FR 4853 - In the Matter of Airbee Wireless, Inc., Axial Vector Engine Corp. (n/k/a Avec Corporation), and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-31

... Vector Engine Corp. (n/k/a Avec Corporation), and Exploration Drilling International, Inc.; Order of... securities of Axial Vector Engine Corp. (n/k/a Avec Corporation) because it has not filed any periodic...(k) of the Securities Exchange Act of 1934, that trading in the securities of the above-listed...

Conformal superalgebras via tractor calculus

NASA Astrophysics Data System (ADS)

Lischewski, Andree

2015-01-01

We use the manifestly conformally invariant description of a Lorentzian conformal structure in terms of a parabolic Cartan geometry in order to introduce a superalgebra structure on the space of twistor spinors and normal conformal vector fields formulated in purely algebraic terms on parallel sections in tractor bundles. Via a fixed metric in the conformal class, one reproduces a conformal superalgebra structure that has been considered in the literature before. The tractor approach, however, makes clear that the failure of this object to be a Lie superalgebra in certain cases is due to purely algebraic identities on the spinor module and to special properties of the conformal holonomy representation. Moreover, it naturally generalizes to higher signatures. This yields new formulas for constructing new twistor spinors and higher order normal conformal Killing forms out of existing ones, generalizing the well-known spinorial Lie derivative. Moreover, we derive restrictions on the possible dimension of the space of twistor spinors in any metric signature.

GHSR-D2R heteromerization modulates dopamine signaling through an effect on G protein conformation.

PubMed

Damian, Marjorie; Pons, Véronique; Renault, Pedro; M'Kadmi, Céline; Delort, Bartholomé; Hartmann, Lucie; Kaya, Ali I; Louet, Maxime; Gagne, Didier; Ben Haj Salah, Khoubaib; Denoyelle, Séverine; Ferry, Gilles; Boutin, Jean A; Wagner, Renaud; Fehrentz, Jean-Alain; Martinez, Jean; Marie, Jacky; Floquet, Nicolas; Galès, Céline; Mary, Sophie; Hamm, Heidi E; Banères, Jean-Louis

2018-04-24

The growth hormone secretagogue receptor (GHSR) and dopamine receptor (D2R) have been shown to oligomerize in hypothalamic neurons with a significant effect on dopamine signaling, but the molecular processes underlying this effect are still obscure. We used here the purified GHSR and D2R to establish that these two receptors assemble in a lipid environment as a tetrameric complex composed of two each of the receptors. This complex further recruits G proteins to give rise to an assembly with only two G protein trimers bound to a receptor tetramer. We further demonstrate that receptor heteromerization directly impacts on dopamine-mediated Gi protein activation by modulating the conformation of its α-subunit. Indeed, association to the purified GHSR:D2R heteromer triggers a different active conformation of Gαi that is linked to a higher rate of GTP binding and a faster dissociation from the heteromeric receptor. This is an additional mechanism to expand the repertoire of GPCR signaling modulation that could have implications for the control of dopamine signaling in normal and physiopathological conditions.

Carcinoma of the anal canal: Intensity modulated radiation therapy (IMRT) versus three-dimensional conformal radiation therapy (3DCRT).

PubMed

Sale, Charlotte; Moloney, Phillip; Mathlum, Maitham

2013-12-01

Patients with anal canal carcinoma treated with standard conformal radiotherapy frequently experience severe acute and late toxicity reactions to the treatment area. Roohipour et al. (Dis Colon Rectum 2008; 51: 147-53) stated a patient's tolerance of chemoradiation to be an important prediction of treatment success. A new intensity modulated radiation therapy (IMRT) technique for anal carcinoma cases has been developed at the Andrew Love Cancer Centre aimed at reducing radiation to surrounding healthy tissue. A same-subject repeated measures design was used for this study, where five anal carcinoma cases at the Andrew Love Cancer Centre were selected. Conformal and IMRT plans were generated and dosimetric evaluations were performed. Each plan was prescribed a total of 54 Gray (Gy) over a course of 30 fractions to the primary site. The IMRT plans resulted in improved dosimetry to the planning target volume (PTV) and reduction in radiation to the critical structures (bladder, external genitalia and femoral heads). Statistically there was no difference between the IMRT and conformal plans in the dose to the small and large bowel; however, the bowel IMRT dose-volume histogram (DVH) doses were consistently lower. The IMRT plans were superior to the conformal plans with improved dose conformity and reduced radiation to the surrounding healthy tissue. Anecdotally it was found that patients tolerated the IMRT treatment better than the three-dimensional (3D) conformal radiation therapy. This study describes and compares the planning techniques.

Carcinoma of the anal canal: Intensity modulated radiation therapy (IMRT) versus three-dimensional conformal radiation therapy (3DCRT)

PubMed Central

Sale, Charlotte; Moloney, Phillip; Mathlum, Maitham

2013-01-01

Introduction Patients with anal canal carcinoma treated with standard conformal radiotherapy frequently experience severe acute and late toxicity reactions to the treatment area. Roohipour et al. (Dis Colon Rectum 2008; 51: 147–53) stated a patient's tolerance of chemoradiation to be an important prediction of treatment success. A new intensity modulated radiation therapy (IMRT) technique for anal carcinoma cases has been developed at the Andrew Love Cancer Centre aimed at reducing radiation to surrounding healthy tissue. Methods A same-subject repeated measures design was used for this study, where five anal carcinoma cases at the Andrew Love Cancer Centre were selected. Conformal and IMRT plans were generated and dosimetric evaluations were performed. Each plan was prescribed a total of 54 Gray (Gy) over a course of 30 fractions to the primary site. Results The IMRT plans resulted in improved dosimetry to the planning target volume (PTV) and reduction in radiation to the critical structures (bladder, external genitalia and femoral heads). Statistically there was no difference between the IMRT and conformal plans in the dose to the small and large bowel; however, the bowel IMRT dose–volume histogram (DVH) doses were consistently lower. Conclusion The IMRT plans were superior to the conformal plans with improved dose conformity and reduced radiation to the surrounding healthy tissue. Anecdotally it was found that patients tolerated the IMRT treatment better than the three-dimensional (3D) conformal radiation therapy. This study describes and compares the planning techniques. PMID:26229623

Carcinoma of the anal canal: Intensity modulated radiation therapy (IMRT) versus three-dimensional conformal radiation therapy (3DCRT)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sale, Charlotte; Moloney, Phillip; Mathlum, Maitham

Patients with anal canal carcinoma treated with standard conformal radiotherapy frequently experience severe acute and late toxicity reactions to the treatment area. Roohipour et al. (Dis Colon Rectum 2008; 51: 147–53) stated a patient's tolerance of chemoradiation to be an important prediction of treatment success. A new intensity modulated radiation therapy (IMRT) technique for anal carcinoma cases has been developed at the Andrew Love Cancer Centre aimed at reducing radiation to surrounding healthy tissue. A same-subject repeated measures design was used for this study, where five anal carcinoma cases at the Andrew Love Cancer Centre were selected. Conformal and IMRTmore » plans were generated and dosimetric evaluations were performed. Each plan was prescribed a total of 54 Gray (Gy) over a course of 30 fractions to the primary site. The IMRT plans resulted in improved dosimetry to the planning target volume (PTV) and reduction in radiation to the critical structures (bladder, external genitalia and femoral heads). Statistically there was no difference between the IMRT and conformal plans in the dose to the small and large bowel; however, the bowel IMRT dose–volume histogram (DVH) doses were consistently lower. The IMRT plans were superior to the conformal plans with improved dose conformity and reduced radiation to the surrounding healthy tissue. Anecdotally it was found that patients tolerated the IMRT treatment better than the three-dimensional (3D) conformal radiation therapy. This study describes and compares the planning techniques.« less

CEF1/CDC5 alleles modulate transitions between catalytic conformations of the spliceosome

PubMed Central

Query, Charles C.; Konarska, Maria M.

2012-01-01

Conformational change within the spliceosome is required between the first and second catalytic steps of pre-mRNA splicing. A prior genetic screen for suppressors of an intron mutant that stalls between the two steps yielded both prp8 and non-prp8 alleles that suppressed second-step splicing defects. We have now identified the strongest non-prp8 suppressors as alleles of the NTC (Prp19 complex) component, CEF1. These cef1 alleles generally suppress second-step defects caused by a variety of intron mutations, mutations in U6 snRNA, or deletion of the second-step protein factor Prp17, and they can activate alternative 3′ splice sites. Genetic and functional interactions between cef1 and prp8 alleles suggest that they modulate the same event(s) in the first-to-second-step transition, most likely by stabilization of the second-step spliceosome; in contrast, alleles of U6 snRNA that also alter this transition modulate a distinct event, most likely by stabilization of the first-step spliceosome. These results implicate a myb-like domain of Cef1/CDC5 in interactions that modulate conformational states of the spliceosome and suggest that alteration of these events affects splice site use, resulting in alternative splicing-like patterns in yeast. PMID:22408182

Media effects in modulating the conformational equilibrium of a model compound for tumor necrosis factor converting enzyme inhibition

NASA Astrophysics Data System (ADS)

Banchelli, Martina; Guardiani, Carlo; Sandberg, Robert B.; Menichetti, Stefano; Procacci, Piero; Caminati, Gabriella

2015-07-01

Small-molecule inhibitors of Tumor Necrosis Factor α Converting Enzyme (TACE) are a promising therapeutic tool for Rheumatoid Arthritis, Multiple Sclerosis and other autoimmune diseases. Here we report on an extensive chemical-physical analysis of the media effects in modulating the conformational landscape of MBET306, the common scaffold and a synthetic precursor of a family of recently discovered tartrate-based TACE inhibitors. The structural features of this molecule with potential pharmaceutical applications have been disclosed by interpreting extensive photophysical measurements in various solvents with the aid of enhanced sampling molecular dynamics simulations and time dependent density functional calculations. Using a combination of experimental and computational techniques, the paper provides a general protocol for studying the structure in solution of molecular systems characterized by the existence of conformational metastable states.

First Experiences in Intensity Modulated Radiation Surgery at the National Institute of Neurology and Neurosurgery: A Dosimetric Point of View

NASA Astrophysics Data System (ADS)

Lárraga-Gutiérrez, José M.; Celis-López, Miguel A.

2003-09-01

The National Institute of Neurology and Neurosurgery in Mexico City has acquired a Novalis® shaped beam radiosurgery unit. The institute is pioneer in the use of new technologies for neuroscience. The Novalis® unit allows the use of conformal beam radiosurgery/therapy and the more advanced modality of conformal therapy: Intensity Modulated Radiation Therapy (IMRT). In the present work we present the first cases of treatments that use the IMRT technique and show its ability to protect organs at risk, such as brainstem and optical vias.

A disulfide-stabilized conformer of methionine synthase reveals an unexpected role for the histidine ligand of the cobalamin cofactor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Datta, Supratim; Koutmos, Markos; Pattridge, Katherine A.

2008-07-08

B{sub 12}-dependent methionine synthase (MetH) from Escherichia coli is a large modular protein that is alternately methylated by methyltetrahydrofolate to form methylcobalamin and demethylated by homocysteine to form cob(I)alamin. Major domain rearrangements are required to allow cobalamin to react with three different substrates: homocysteine, methyltetrahydrofolate, and S-adenosyl-l-methionine (AdoMet). These same rearrangements appear to preclude crystallization of the wild-type enzyme. Disulfide cross-linking was used to lock a C-terminal fragment of the enzyme into a unique conformation. Cysteine point mutations were introduced at Ile-690 and Gly-743. These cysteine residues span the cap and the cobalamin-binding module and form a cross-link that reducesmore » the conformational space accessed by the enzyme, facilitating protein crystallization. Here, we describe an x-ray structure of the mutant fragment in the reactivation conformation; this conformation enables the transfer of a methyl group from AdoMet to the cobalamin cofactor. In the structure, the axial ligand to the cobalamin, His-759, dissociates from the cobalamin and forms intermodular contacts with residues in the AdoMet-binding module. This unanticipated intermodular interaction is expected to play a major role in controlling the distribution of conformers required for the catalytic and the reactivation cycles of the enzyme.« less

47 CFR 73.128 - AM stereophonic broadcasting.

Code of Federal Regulations, 2013 CFR

2013-10-01

... negative peaks of 100%. (ii) Stereophonic (L−R) modulated with audio tones of the same amplitude at the... characteristics: (1) The audio response of the main (L+R) channel shall conform to the requirements of the ANSI... (NRSC-1). (2) The left and right channel audio signals shall conform to frequency response limitations...

Facteurs de risque dans le trouble déficitaire de l’attention et de l’hyperactivité: étude familiale

PubMed Central

Poissant, Hélène; Rapin, Lucile

2012-01-01

Résumé Objectif: Notre étude a pour but d’évaluer les facteurs de risque associés au trouble déficitaire de l’attention et de l’hyperactivité (TDAH) en termes de comorbidités et de facteurs d’adversité à l’intérieur des familles avec un TDAH. Méthodologie: 137 parents de 104 enfants avec un TDAH et 40 parents de 34 enfants contrôles ont répondu aux items d’un questionnaire. Des tests Chi-carrés et des tests de Student ont mesuré l’association de chaque item avec les groupes et les différences entre les groupes. Résultats: Les enfants avec un TDAH avaient des performances scolaires plus faibles et une plus forte prévalence des troubles d’apprentissage, oppositionnel, des conduites et anxieux que celle des enfants contrôles. Des difficultés d’apprentissage étaient plus souvent rapportées chez les pères d’enfants avec un TDAH. Par ailleurs, l’isolement social et les accidents de la route étaient davantage présents chez les mères d’enfants avec un TDAH. Ces dernières souffraient plus de dépression et de trouble anxieux et prenaient davantage de médicaments que les mères contrôles. Conclusion: L’étude de facteurs de risque révèle un lien entre les parents et les enfants, spécifiquement la présence de dépression parmi les mères d’enfants avec un TDAH et de difficultés d’apprentissage chez les pères, suggérant une composante familiale dans le trouble. La sous-représentation du TDAH chez les pères d’enfants avec un TDAH est discutée. PMID:23133459

SU-F-T-184: 3D Range-Modulator for Scanned Particle Therapy: Development, Monte Carlo Simulations and Measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simeonov, Y; Penchev, P; Ringbaek, T Printz

2016-06-15

Purpose: Active raster scanning in particle therapy results in highly conformal dose distributions. Treatment time, however, is relatively high due to the large number of different iso-energy layers used. By using only one energy and the so called 3D range-modulator irradiation times of a few seconds only can be achieved, thus making delivery of homogeneous dose to moving targets (e.g. lung cancer) more reliable. Methods: A 3D range-modulator consisting of many pins with base area of 2.25 mm2 and different lengths was developed and manufactured with rapid prototyping technique. The form of the 3D range-modulator was optimised for a sphericalmore » target volume with 5 cm diameter placed at 25 cm in a water phantom. Monte Carlo simulations using the FLUKA package were carried out to evaluate the modulating effect of the 3D range-modulator and simulate the resulting dose distribution. The fine and complicated contour form of the 3D range-modulator was taken into account by a specially programmed user routine. Additionally FLUKA was extended with the capability of intensity modulated scanning. To verify the simulation results dose measurements were carried out at the Heidelberg Ion Therapy Center (HIT) with a 400.41 MeV 12C beam. Results: The high resolution measurements show that the 3D range-modulator is capable of producing homogeneous 3D conformal dose distributions, simultaneously reducing significantly irradiation time. Measured dose is in very good agreement with the previously conducted FLUKA simulations, where slight differences were traced back to minor manufacturing deviations from the perfect optimised form. Conclusion: Combined with the advantages of very short treatment time the 3D range-modulator could be an alternative to treat small to medium sized tumours (e.g. lung metastasis) with the same conformity as full raster-scanning treatment. Further simulations and measurements of more complex cases will be conducted to investigate the full potential of the 3D range-modulator.« less

Diagnostic tardif d'une hyperoxalurie primitive au stade d'insuffisance rénale chronique terminale avec hypoparathyroïdie sévère

PubMed Central

El Ghali, Zineb; Lahcen, Zineb Ait; Fadili, Wafaa; Kaitouni, Abderrahim Idrissi; Hakkou, Mohamed; Hamdaoui, Abderrachid; Laouad, Inass

2014-01-01

L'hyperoxalurie primitive est une anomalie métabolique congénitale rare caractérisée par un excès de production avec accumulation d'oxalate secondaire à un déficit enzymatique hépatique. Nous rapportons le cas d'un patient de 18 ans qui avait comme antécédent des lithiases rénales récidivantes depuis l'enfance évoluant vers l'insuffisance rénale chronique terminale, mis en hémodialyse périodique depuis 4 ans avec apparition d'une anémie résistante à l’érythropoïétine pour laquelle il a été multitransfusé et qui était admis pour prise en charge de douleurs osseuses invalidantes d'aggravation progressive associées à un syndrome tumoral fait d'adénopathies périphériques et de splénomégalie avec dyspnée et altération de l’état général. Le bilan réalisé avait objectivé de multiples images lytiques lacunaires et condensantes au niveau des poignets et des mains avec des petits reins calcifiés, une pleurésie avec péricardite de grande abondance drainée, une ascite de moyenne abondance avec splénomégalie homogène, une anémie normochrome normocytaire à 7.2 g/dl avec hyperferritinémie à 1129 μg/l et un syndrome inflammatoire biologique. La calcémie était spontanément normale à 97 mg/l avec hyperphosphorémie à 83 mg/l et hypoparathyroïdie à 74,85 pg/ml. Les PAL étaient à 136 UI/l, l'aluminium sérique à 13μg/l et la Vitamine D native à 20,87ng/ml. Le diagnostic d'hyperoxalurie a été retenu sur les données de la biopsie ostéomédullaire objectivant des dépôts de cristaux d'oxalate de calcium avec fibrose médullaire et réaction macrophagique à corps étranger. L’évolution a été marquée par la survenue de fractures spontanées récidivantes au niveau de l’épaule et des 2 hanches. PMID:25328593

Design of a novel freeform lens for LED uniform illumination and conformal phosphor coating.

PubMed

Hu, Run; Luo, Xiaobing; Zheng, Huai; Qin, Zong; Gan, Zhiqiang; Wu, Bulong; Liu, Sheng

2012-06-18

A conformal phosphor coating can realize a phosphor layer with uniform thickness, which could enhance the angular color uniformity (ACU) of light-emitting diode (LED) packaging. In this study, a novel freeform lens was designed for simultaneous realization of LED uniform illumination and conformal phosphor coating. The detailed algorithm of the design method, which involves an extended light source and double refractions, was presented. The packaging configuration of the LED modules and the modeling of the light-conversion process were also presented. Monte Carlo ray-tracing simulations were conducted to validate the design method by comparisons with a conventional freeform lens. It is demonstrated that for the LED module with the present freeform lens, the illumination uniformity and ACU was 0.89 and 0.9283, respectively. The present freeform lens can realize equivalent illumination uniformity, but the angular color uniformity can be enhanced by 282.3% when compared with the conventional freeform lens.

The Role of Cholesterol in the Activation of Nicotinic Acetylcholine Receptors.

PubMed

Baenziger, John E; Domville, Jaimee A; Therien, J P Daniel

2017-01-01

Cholesterol is a potent modulator of the nicotinic acetylcholine receptor (nAChR) from Torpedo. Here, we review current understanding of the mechanisms underlying cholesterol-nAChR interactions in the context of increasingly available high-resolution structural and functional data. Cholesterol and other lipids influence function by conformational selection and kinetic mechanisms, stabilizing varying proportions of activatable vs nonactivatable conformations, as well as influencing the rates of transitions between conformational states. In the absence of cholesterol and anionic lipids, the nAChR adopts an uncoupled conformation that binds agonist but does not undergo agonist-induced conformational transitions-unless the nAChR is located in a relatively thick lipid bilayer, such as that found in cholesterol-rich lipid rafts. We highlight different sites of cholesterol action, including the lipid-exposed M4 transmembrane α-helix. Cholesterol and other lipids likely alter function by modulating interactions between M4 and the adjacent transmembrane α-helices, M1 and M3. These same interactions have been implicated in both the folding and trafficking of nAChRs to the cell surface. We evaluate the nature of cholesterol-nAChR interactions, considering the evidence supporting the roles of both direct binding to allosteric sites and cholesterol-induced changes in bulk membrane physical properties. © 2017 Elsevier Inc. All rights reserved.

Bisecting GlcNAc restricts conformations of branches in model N-glycans with GlcNAc termini.

PubMed

Hanashima, Shinya; Suga, Akitsugu; Yamaguchi, Yoshiki

2018-02-01

Bisected N-glycans play significant roles in tumor migration and Alzheimer's disease through modulating the action and localization of their carrier proteins. Such biological functions are often discussed in terms of the conformation of the attached N-glycans with or without bisecting GlcNAc. To obtain insights into the effects of bisecting GlcNAc on glycan conformation, a systematic NMR structural analysis was performed on two pairs of synthetic N-glycans, with and without bisecting GlcNAc. The analysis reveals that terminal GlcNAcs and bisecting GlcNAc cooperate to restrict the conformations of both the α1-3 and α1-6 branches of N-glycans. 1 H and 13 C chemical shift comparisons suggest that bisecting GlcNAc directly modulates local conformation. Unique NOE correlations between core-mannose and the α1-3 branch mannose as well as the 3 J C-H constant of the glycoside linkage indicate that bisecting GlcNAc restricts the conformation of the 1-3 branch. The angles of the glycosidic bonds between core-mannose and α1-6 branch mannose derived from 3 J C-H and 3 J H-H coupling constants show that terminal GlcNAcs restrict the distribution of the ψ angle to 180° and the bisecting GlcNAc increases the distribution of the ω angle +60° in the presence of terminal GlcNAcs. It is feasible that restriction of branch conformations by bisecting GlcNAc has important consequences for protein-glycan interplay and following biological events. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation des indicateurs d’alerte précoce de la résistance du VIH aux ARV en Côte d’Ivoire en 2011

PubMed Central

Yao, Kouadio Jean; Damey, Néto Florence; Konan, Diby Jean Paul; Aka, Joseph; Aka-Konan, Sandrine; Ani, Alex; Bonle, Marguerite Te; Kouassi, Dinard

2016-01-01

Introduction En 2001, l'Organisation des Nations Unies recommandait de rendre disponible les médicaments antirétroviraux dans les pays à ressources limitées. Cependant, l'utilisation de ces médicaments à grande échelle s'accompagne du développement de résistance du virus. En Côte d'Ivoire, plusieurs sites prescrivent les antirétroviraux. Cette étude avait pour objectif d'évaluer les facteurs programmatiques associés à un risque élevé d'émergence de résistance du VIH aux antirétroviraux. Méthodes Il s'agit d'une cohorte rétrospective sur 20 sites de prise en charge des personnes vivant avec le VIH. La population d'étude était constituée des personnes ayant initié leur traitement antirétroviral sur les sites en 2008-2009. L'estimation de la taille de l'échantillon a été faite à partir de la stratégie d'échantillonnage de l'OMS. Résultats Sur 20 sites, 98% des prescriptions initiales étaient conformes aux directives nationales et 20% des sites avaient 100% de prescriptions conformes. Au total, 33% des patients étaient perdus de vue au cours des 12 premiers mois de traitement antirétroviral et 20% des sites avaient moins de 20% de perdus de vue. A 12 mois, 51% des patients demeuraient sous traitement de première intention approprié et 11% des sites ont atteint le seuil d'au moins 70% de patients sous traitement de première intention approprié. Un seul site n'a pas connu de rupture d'antirétroviraux sur les 12 mois. Conclusion Des insuffisances relevées dans la prise en charge des personnes vivant avec le VIH traduisent l'existence d'un risque important de résistance du virus aux antirétroviraux en 2008-2009. Pour minimiser ce risque les pratiques de prescription devraient être améliorées, un système de recherche des absents aux rendez-vous devrait être mis en place et la disponibilité constante des antirétroviraux devraient être assurée. PMID:28250876

QUELS FUTURS TRAITEMENTS POUR LA DEPENDANCE AU TABAC ET AU CANNABIS?

PubMed Central

LE FOLL, Bernard; JUSTINOVA, Zuzana; TANDA, Gianlugi; GOLDBERG, Steven R.

2009-01-01

RESUME Plus de trois millions de morts sont attribués au tabagisme dans le monde par an, et l’usage de tabac est en progression dans les pays en voie de développement. L’usage de tabac est donc une des rares causes de mortalité qui augmente, avec une prévision de plus de 10 millions de morts par an dans 30–40 ans. Le cannabis ou marijuana est la drogue illicite la plus consommée dans le monde et il n’y a actuellement pas de traitement disponible. Bien que les systèmes dopaminergiques jouent un rôle central dans les effets renforçants des drogues, d’autres systèmes sont impliqués. Nous présentons ici des résultats récents obtenus avec des antagonistes des récepteurs cannabinoides CB1, des récepteurs D3 de la dopamine et des récepteurs opioïdes. Ces antagonistes qui modulent de façon directe ou indirecte la transmission dopaminergique cérébrale représentent des approches prometteuses pour le traitement du tabagisme ou de la dépendance au cannabis. Ces approches sont à valider dans des essais cliniques. PMID:18663981

Food as a way to convey masculinities: How conformity to hegemonic masculinity norms influences men's and women's food consumption.

PubMed

Campos, Lúcia; Bernardes, Sónia; Godinho, Cristina

2018-05-01

This study investigated how conformity to hegemonic masculinity norms affects men's and women's food consumption and whether such influence was contextually modulated. A total of 519 individuals (65% women; M = 44 years old) participated in a 2 (gender salience: low vs high) × 2 (participants' sex: male vs female) quasi-experimental between-subjects design, completing the Conformity to Masculinity Norms Inventory (Portuguese version) and reporting their past week's food consumption. Gender salience moderated the relation between men's conformity to masculinity norms and food consumption; sex-related differences in food consumption were partially mediated by conformity to masculinity norms. Implications for food consumption interventions are discussed.

Analysis of calcium-induced effects on the conformation of fengycin.

PubMed

Nasir, Mehmet Nail; Laurent, Pascal; Flore, Christelle; Lins, Laurence; Ongena, Marc; Deleu, Magali

2013-06-01

Fengycin is a natural lipopeptide with antifungal and eliciting properties and able to inhibit the activity of phospholipase A2. A combination of CD, FT-IR, NMR and fluorescence spectroscopic techniques was applied to elucidate its conformation in a membrane-mimicking environment and to investigate the effect of calcium ions on it. We mainly observed that fengycin adopts a turn conformation. Our results showed that calcium ions are bound by the two charged glutamates. The calcium binding has an influence on the fengycin conformation and more particularly, on the environment of the tyrosine residues. The modulation of the fengycin conformation by the environmental conditions may influence its biological properties. Copyright © 2013 Elsevier B.V. All rights reserved.

Bioactive focus in conformational ensembles: a pluralistic approach

NASA Astrophysics Data System (ADS)

Habgood, Matthew

2017-12-01

Computational generation of conformational ensembles is key to contemporary drug design. Selecting the members of the ensemble that will approximate the conformation most likely to bind to a desired target (the bioactive conformation) is difficult, given that the potential energy usually used to generate and rank the ensemble is a notoriously poor discriminator between bioactive and non-bioactive conformations. In this study an approach to generating a focused ensemble is proposed in which each conformation is assigned multiple rankings based not just on potential energy but also on solvation energy, hydrophobic or hydrophilic interaction energy, radius of gyration, and on a statistical potential derived from Cambridge Structural Database data. The best ranked structures derived from each system are then assembled into a new ensemble that is shown to be better focused on bioactive conformations. This pluralistic approach is tested on ensembles generated by the Molecular Operating Environment's Low Mode Molecular Dynamics module, and by the Cambridge Crystallographic Data Centre's conformation generator software.

Probing RNA Native Conformational Ensembles with Structural Constraints.

PubMed

Fonseca, Rasmus; van den Bedem, Henry; Bernauer, Julie

2016-05-01

Noncoding ribonucleic acids (RNA) play a critical role in a wide variety of cellular processes, ranging from regulating gene expression to post-translational modification and protein synthesis. Their activity is modulated by highly dynamic exchanges between three-dimensional conformational substates, which are difficult to characterize experimentally and computationally. Here, we present an innovative, entirely kinematic computational procedure to efficiently explore the native ensemble of RNA molecules. Our procedure projects degrees of freedom onto a subspace of conformation space defined by distance constraints in the tertiary structure. The dimensionality reduction enables efficient exploration of conformational space. We show that the conformational distributions obtained with our method broadly sample the conformational landscape observed in NMR experiments. Compared to normal mode analysis-based exploration, our procedure diffuses faster through the experimental ensemble while also accessing conformational substates to greater precision. Our results suggest that conformational sampling with a highly reduced but fully atomistic representation of noncoding RNA expresses key features of their dynamic nature.

Ulcérations buccales et péri-anales: un mode de révélation inhabituel d'une granulomatose avec polyangéite - à propos d'un cas

PubMed Central

Jaafoura, Neirouz Ghannouchi; Thaljaoui, Wathek; Atig, Amira; Bouker, Ahmed; Khalifa, Mabrouk; Bahri, Fathi

2014-01-01

La granulomatose avec polyangéite, est une vascularite systémique rare qui touche avec prédilection les voies aériennes supérieures, les poumons et les reins. L'atteinte cutanéo-muqueuse ainsi que l'atteinte digestive ne sont pas inhabituelles mais elles sont rarement inaugurales de la maladie. Nous rapportons l'observation d'une femme âgée de 57 ans, ayant une granulomatose avec polyangéite multi-systémique avec comme premières manifestations une atteinte cutanéo-muqueuse à type de nécrose de la langue et d'ulcérations péri-anales ainsi que des rectorragies. La présence de signes radiologiques orientant vers une hémmorragie intra-alvéolaire, l'atteinte rénale, l'atteinte neurologique périphérique ainsi que la positivité des C-ANCA de type anti-PR3 ont permis de rattacher les manifestations dermatologiques à cette vascularite. Des manifestations cutanéo-muqueuses atypiques, au cours d'une granulomateuse avec polyangéite, doivent être connues par le clinicien pour un diagnostic et une prise en charge adéquate. PMID:25404981

Catalysis-Enhancement via Rotary Fluctuation of F1-ATPase

PubMed Central

Watanabe, Rikiya; Hayashi, Kumiko; Ueno, Hiroshi; Noji, Hiroyuki

2013-01-01

Protein conformational fluctuations modulate the catalytic powers of enzymes. The frequency of conformational fluctuations may modulate the catalytic rate at individual reaction steps. In this study, we modulated the rotary fluctuation frequency of F1-ATPase (F1) by attaching probes with different viscous drag coefficients at the rotary shaft of F1. Individual rotation pauses of F1 between rotary steps correspond to the waiting state of a certain elementary reaction step of ATP hydrolysis. This allows us to investigate the impact of the frequency modulation of the rotary fluctuation on the rate of the individual reaction steps by measuring the duration of rotation pauses. Although phosphate release was significantly decelerated, the ATP-binding and hydrolysis steps were less sensitive or insensitive to the viscous drag coefficient of the probe. Brownian dynamics simulation based on a model similar to the Sumi-Marcus theory reproduced the experimental results, providing a theoretical framework for the role of rotational fluctuation in F1 rate enhancement. PMID:24268150

Methods in Enzymology: “Flexible backbone sampling methods to model and design protein alternative conformations”

PubMed Central

Ollikainen, Noah; Smith, Colin A.; Fraser, James S.; Kortemme, Tanja

2013-01-01

Sampling alternative conformations is key to understanding how proteins work and engineering them for new functions. However, accurately characterizing and modeling protein conformational ensembles remains experimentally and computationally challenging. These challenges must be met before protein conformational heterogeneity can be exploited in protein engineering and design. Here, as a stepping stone, we describe methods to detect alternative conformations in proteins and strategies to model these near-native conformational changes based on backrub-type Monte Carlo moves in Rosetta. We illustrate how Rosetta simulations that apply backrub moves improve modeling of point mutant side chain conformations, native side chain conformational heterogeneity, functional conformational changes, tolerated sequence space, protein interaction specificity, and amino acid co-variation across protein-protein interfaces. We include relevant Rosetta command lines and RosettaScripts to encourage the application of these types of simulations to other systems. Our work highlights that critical scoring and sampling improvements will be necessary to approximate conformational landscapes. Challenges for the future development of these methods include modeling conformational changes that propagate away from designed mutation sites and modulating backbone flexibility to predictively design functionally important conformational heterogeneity. PMID:23422426

Dosimetric comparison between modulated arc therapy and static intensity modulated radiotherapy in thoracic esophageal cancer: a single institutional experience.

PubMed

Choi, Kyu Hye; Kim, Jina; Lee, Sea-Won; Kang, Young-Nam; Jang, HongSeok

2018-03-01

The objective of this study was to compare dosimetric characteristics of three-dimensional conformal radiotherapy (3D-CRT) and two types of intensity-modulated radiotherapy (IMRT) which are step-and-shoot intensity modulated radiotherapy (s-IMRT) and modulated arc therapy (mARC) for thoracic esophageal cancer and analyze whether IMRT could reduce organ-at-risk (OAR) dose. We performed 3D-CRT, s-IMRT, and mARC planning for ten patients with thoracic esophageal cancer. The dose-volume histogram for each plan was extracted and the mean dose and clinically significant parameters were analyzed. Analysis of target coverage showed that the conformity index (CI) and conformation number (CN) in mARC were superior to the other two plans (CI, p = 0.050; CN, p = 0.042). For the comparison of OAR, lung V 5 was lowest in s-IMRT, followed by 3D-CRT, and mARC (p = 0.033). s-IMRT and mARC had lower values than 3D-CRT for heart V 30 (p = 0.039), V 40 (p = 0.040), and V 50 (p = 0.032). Effective conservation of the lung and heart in thoracic esophageal cancer could be expected when using s-IMRT. The mARC was lower in lung V 10 , V 20 , and V 30 than in 3D-CRT, but could not be proven superior in lung V 5 . In conclusion, low-dose exposure to the lung and heart were expected to be lower in s-IMRT, reducing complications such as radiation pneumonitis or heart-related toxicities.

Two intermediate states of the conformational switch in dual specificity phosphatase 13a.

PubMed

Wei, Chun Hwa; Min, Hee Gyeong; Kim, Myeongbin; Kim, Gwan Hee; Chun, Ha-Jung; Ryu, Seong Eon

2018-02-01

Dual specificity phosphatases (DUSPs) include MAP kinase phosphatases and atypical dual specificity phosphatases and mediate cell growth and differentiation, brain function, and immune responses. They serve as targets for drug development against cancers, diabetes and depression. Several DUSPs have non-canonical conformation of the central β-sheet and active site loops, suggesting that they may have conformational switch that is related to the regulation of enzyme activity. Here, we determined the crystal structure of DUSP13a, and identified two different structures that represent intermediates of the postulated conformational switch. Amino acid sequence of DUSP13a is not significantly homologous to DUSPs with conformational switch, indicating that the conformational switch is not sequence-dependent, but rather determined by ligand interaction. The sequence-independency suggests that other DUSPs with canonical conformation may have the conformational switch during specific cellular regulation. The conformational switch leads to significant changes in the protein surface, including a hydrophobic surface and pockets, which can be exploited for development of allosteric modulators of drug target DUSPs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparison of heart and coronary artery doses associated with intensity-modulated radiotherapy versus three-dimensional conformal radiotherapy for distal esophageal cancer.

PubMed

Kole, Thomas P; Aghayere, Osarhieme; Kwah, Jason; Yorke, Ellen D; Goodman, Karyn A

2012-08-01

To compare heart and coronary artery radiation exposure using intensity-modulated radiotherapy (IMRT) vs. four-field three-dimensional conformal radiotherapy (3D-CRT) treatment plans for patients with distal esophageal cancer undergoing chemoradiation. Nineteen patients with distal esophageal cancers treated with IMRT from March 2007 to May 2008 were identified. All patients were treated to 50.4 Gy with five-field IMRT plans. Theoretical 3D-CRT plans with four-field beam arrangements were generated. Dose-volume histograms of the planning target volume, heart, right coronary artery, left coronary artery, and other critical normal tissues were compared between the IMRT and 3D-CRT plans, and selected parameters were statistically evaluated using the Wilcoxon rank-sum test. Intensity-modulated radiotherapy treatment planning showed significant reduction (p < 0.05) in heart dose over 3D-CRT as assessed by average mean dose (22.9 vs. 28.2 Gy) and V30 (24.8% vs. 61.0%). There was also significant sparing of the right coronary artery (average mean dose, 23.8 Gy vs. 35.5 Gy), whereas the left coronary artery showed no significant improvement (mean dose, 11.2 Gy vs. 9.2 Gy), p = 0.11. There was no significant difference in percentage of total lung volume receiving at least 10, 15, or 20 Gy or in the mean lung dose between the planning methods. There were also no significant differences observed for the kidneys, liver, stomach, or spinal cord. Intensity-modulated radiotherapy achieved a significant improvement in target conformity as measured by the conformality index (ratio of total volume receiving 95% of prescription dose to planning target volume receiving 95% of prescription dose), with the mean conformality index reduced from 1.56 to 1.30 using IMRT. Treatment of patients with distal esophageal cancer using IMRT significantly decreases the exposure of the heart and right coronary artery when compared with 3D-CRT. Long-term studies are necessary to determine how this will impact on development of coronary artery disease and other cardiac complications. Copyright © 2012 Elsevier Inc. All rights reserved.

Conformer-specific microwave spectroscopy of 3-phenylpropionitrile by strong field coherence breaking

NASA Astrophysics Data System (ADS)

Fritz, Sean M.; Hernandez-Castillo, A. O.; Abeysekera, Chamara; Hays, Brian M.; Zwier, Timothy S.

2018-07-01

Strong field coherence breaking (SFCB) was used with a chirped-pulse Fourier Transform microwave spectrometer to obtain conformer-specific rotational spectra of 3-phenylpropionitrile in the 8-18 GHz region. Transitions belonging to anti and gauche conformers were identified and assigned and accurate experimental rotational constants were determined to provide insight to the molecular structure. Experimental rotational transitions provided relative abundances in the supersonic expansion. A modified line picking scheme was developed in the process to modulate more transitions and improve the overall efficiency of the SFCB multiple selective excitation technique.

Structural insights into selective agonist actions of tamoxifen on human estrogen receptor alpha.

PubMed

Chakraborty, Sandipan; Biswas, Pradip Kumar

2014-08-01

Tamoxifen-an anti-estrogenic ligand in breast tissues used as a first-line treatment in estrogen receptor (ER)-positive breast cancers-is associated with the development of resistance followed by resumption of tumor growth in about 30 % of cases. Whether tamoxifen assists in proliferation in such cases or whether any ligand-independent pathway to transcription exists is not fully understood; also, no ERα mutants have been detected so far that could lead to tamoxifen resistance. Using in silico conformational analysis of the ERα ligand binding domain (LBD), in the absence and presence of selective agonist (diethylstilbestrol; DES), antagonist (Faslodex; ICI), and selective estrogen receptor modulator (SERM; 4-hydroxy tamoxifen; 4-OHT) ligands, we have elucidated ligand-responsive structural modulations of the ERα-LBD dimer in its agonist and antagonist complexes to address the issue of "tamoxifen resistance". DES and ICI were found to stabilize the dimer in their agonist and antagonist conformations, respectively. The ERα-LBD dimer without the presence of any bound ligand also led to a stable structure in agonist conformation. However, binding of 4-OHT to the antagonist structure led to a flexible conformation allowing the protein to visit conformations populated by agonists as was evident from principal component analysis and radius of gyration plots. Further, the relaxed conformations of the 4-OHT bound protein exhibited a diminished size of the co-repressor binding pocket in the LBD, thus signaling a partial blockage of the co-repressor binding motif. Thus, the ability of 4-OHT-bound ERα-LBD to assume flexible conformations visited by agonists and reduced co-repressor binding surface at the LBD provide crucial structural insights into tamoxifen-resistance that complement our existing understanding.

Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation

PubMed Central

Śledź, Paweł; Unverdorben, Pia; Beck, Florian; Pfeifer, Günter; Schweitzer, Andreas; Förster, Friedrich; Baumeister, Wolfgang

2013-01-01

The 26S proteasome is a 2.5-MDa, ATP-dependent multisubunit proteolytic complex that processively destroys proteins carrying a degradation signal. The proteasomal ATPase heterohexamer is a key module of the 19S regulatory particle; it unfolds substrates and translocates them into the 20S core particle where degradation takes place. We used cryoelectron microscopy single-particle analysis to obtain insights into the structural changes of 26S proteasome upon the binding and hydrolysis of ATP. The ATPase ring adopts at least two distinct helical staircase conformations dependent on the nucleotide state. The transition from the conformation observed in the presence of ATP to the predominant conformation in the presence of ATP-γS induces a sliding motion of the ATPase ring over the 20S core particle ring leading to an alignment of the translocation channels of the ATPase and the core particle gate, a conformational state likely to facilitate substrate translocation. Two types of intersubunit modules formed by the large ATPase domain of one ATPase subunit and the small ATPase domain of its neighbor exist. They resemble the contacts observed in the crystal structures of ClpX and proteasome-activating nucleotidase, respectively. The ClpX-like contacts are positioned consecutively and give rise to helical shape in the hexamer, whereas the proteasome-activating nucleotidase-like contact is required to close the ring. Conformational switching between these forms allows adopting different helical conformations in different nucleotide states. We postulate that ATP hydrolysis by the regulatory particle ATPase (Rpt) 5 subunit initiates a cascade of conformational changes, leading to pulling of the substrate, which is primarily executed by Rpt1, Rpt2, and Rpt6. PMID:23589842

SU-F-T-635: Lung SBRT: Dosimetric and Treatment Time Comparison of Volumetric-Modulated Arc Therapy and Three-Dimensional Conformal Radiotherapy in Clinically Treated Cases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, J; Xu, Z; Baker, J

Purpose: To compare three-dimensional conformal radiotherapy (3D CRT) and volumetric-modulated arc therapy (VMAT) in lung stereotactic body radiation therapy (SBRT) Methods: A retrospective study of clinically treated lung SBRT cases treated between 2010 and 2015 at our hospital was performed. All treatment modalities were included in this evaluation (VMAT, 3D CRT, static IMRT, and dynamic conformal arc therapy). However, the majority of treatment modalities were either VMAT or 3D CRT. Treatment times of patients and dosimetric plan quality metrics were compared. Treatment times were calculated based on the time the therapist opened and closed the patient’s treatment plan. This treatmentmore » time closely approximates the utilization time of the treatment room. The dosimetric plan quality metrics evaluated include ICRU conformity index, the volume of 105% prescribed dose outside PTV, the ratio of volume of 50% prescribed dose to the volume of PTV, the percentage of maximum dose at 2 cm away from PTV to the prescribed dose, and the V20 (percentage of lung volume receiving 20 Gy or more). Results: Treatment time comparisons show that on average VMAT has shorter treatment times than 3D CRT. Dose conformity, defined by the ICRU conformity index, and high dose spillage, defined by the volume of 105% dose outside the PTV, is reduced when using VMAT compared to 3D CRT. V20 and intermediate dose spillage/fall-off metrics of VMAT and 3D are not significantly different. Conclusion: Clinically treated lung SBRT cases indicate VMAT is superior to 3D with regard to shorter treatment times, plan dose conformity, and plan high dose spillage.« less

Membrane cholesterol effect on the 5-HT2A receptor: Insights into the lipid-induced modulation of an antipsychotic drug target.

PubMed

Ramírez-Anguita, Juan Manuel; Rodríguez-Espigares, Ismael; Guixà-González, Ramon; Bruno, Agostino; Torrens-Fontanals, Mariona; Varela-Rial, Alejandro; Selent, Jana

2018-01-01

The serotonin 5-hydroxytryptamine 2A (5-HT 2A ) receptor is a G-protein-coupled receptor (GPCR) relevant for the treatment of CNS disorders. In this regard, neuronal membrane composition in the brain plays a crucial role in the modulation of the receptor functioning. Since cholesterol is an essential component of neuronal membranes, we have studied its effect on the 5-HT 2A receptor dynamics through all-atom MD simulations. We find that the presence of cholesterol in the membrane increases receptor conformational variability in most receptor segments. Importantly, detailed structural analysis indicates that conformational variability goes along with the destabilization of hydrogen bonding networks not only within the receptor but also between receptor and lipids. In addition to increased conformational variability, we also find receptor segments with reduced variability. Our analysis suggests that this increased stabilization is the result of stabilizing effects of tightly bound cholesterol molecules to the receptor surface. Our finding contributes to a better understanding of membrane-induced alterations of receptor dynamics and points to cholesterol-induced stabilizing and destabilizing effects on the conformational variability of GPCRs. © 2017 International Union of Biochemistry and Molecular Biology, Inc.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmandt, Nicolaus; Velisetty, Phanindra; Chalamalasetti, Sreevatsa V.

Recent high resolution structures of several pentameric ligand–gated ion channels have provided unprecedented details of their molecular architecture. However, the conformational dynamics and structural rearrangements that underlie gating and allosteric modulation remain poorly understood. We used a combination of electrophysiology, double electron–electron resonance (DEER) spectroscopy, and x-ray crystallography to investigate activation mechanisms in a novel functional chimera with the extracellular domain (ECD) of amine-gated Erwinia chrysanthemi ligand–gated ion channel, which is activated by primary amines, and the transmembrane domain of Gloeobacter violaceus ligand–gated ion channel, which is activated by protons. We found that the chimera was independently gated by primarymore » amines and by protons. The crystal structure of the chimera in its resting state, at pH 7.0 and in the absence of primary amines, revealed a closed-pore conformation and an ECD that is twisted with respect to the transmembrane region. Amine- and pH-induced conformational changes measured by DEER spectroscopy showed that the chimera exhibits a dual mode of gating that preserves the distinct conformational changes of the parent channels. Collectively, our findings shed light on both conserved and divergent features of gating mechanisms in this class of channels, and will facilitate the design of better allosteric modulators.« less

Immirzi parameter without Immirzi ambiguity: Conformal loop quantization of scalar-tensor gravity

NASA Astrophysics Data System (ADS)

Veraguth, Olivier J.; Wang, Charles H.-T.

2017-10-01

Conformal loop quantum gravity provides an approach to loop quantization through an underlying conformal structure i.e. conformally equivalent class of metrics. The property that general relativity itself has no conformal invariance is reinstated with a constrained scalar field setting the physical scale. Conformally equivalent metrics have recently been shown to be amenable to loop quantization including matter coupling. It has been suggested that conformal geometry may provide an extended symmetry to allow a reformulated Immirzi parameter necessary for loop quantization to behave like an arbitrary group parameter that requires no further fixing as its present standard form does. Here, we find that this can be naturally realized via conformal frame transformations in scalar-tensor gravity. Such a theory generally incorporates a dynamical scalar gravitational field and reduces to general relativity when the scalar field becomes a pure gauge. In particular, we introduce a conformal Einstein frame in which loop quantization is implemented. We then discuss how different Immirzi parameters under this description may be related by conformal frame transformations and yet share the same quantization having, for example, the same area gaps, modulated by the scalar gravitational field.

Modulation of Cell Proliferation and Differentiation through Substrate-dependent Changes in Fibronectin Conformation

PubMed Central

García, Andrés J.; Vega, María D.; Boettiger, David

1999-01-01

Integrin-mediated cell adhesion to extracellular matrices provides signals essential for cell cycle progression and differentiation. We demonstrate that substrate-dependent changes in the conformation of adsorbed fibronectin (Fn) modulated integrin binding and controlled switching between proliferation and differentiation. Adsorption of Fn onto bacterial polystyrene (B), tissue culture polystyrene (T), and collagen (C) resulted in differences in Fn conformation as indicated by antibody binding. Using a biochemical method to quantify bound integrins in cultured cells, we found that differences in Fn conformation altered the quantity of bound α5 and β1 integrin subunits but not αv or β3. C2C12 myoblasts grown on these Fn-coated substrates proliferated to different levels (B > T > C). Immunostaining for muscle-specific myosin revealed minimal differentiation on B, significant levels on T, and extensive differentiation on C. Differentiation required binding to the RGD cell binding site in Fn and was blocked by antibodies specific for this site. Switching between proliferation and differentiation was controlled by the levels of α5β1 integrin bound to Fn, and differentiation was inhibited by anti-α5, but not anti-αv, antibodies, suggesting distinct integrin-mediated signaling pathways. Control of cell proliferation and differentiation through conformational changes in extracellular matrix proteins represents a versatile mechanism to elicit specific cellular responses for biological and biotechnological applications. PMID:10069818

A comparison between cobalt and linear accelerator-based treatment plans for conformal and intensity-modulated radiotherapy.

PubMed

Adams, E J; Warrington, A P

2008-04-01

The simplicity of cobalt units gives them the advantage of reduced maintenance, running costs and downtime when compared with linear accelerators. However, treatments carried out on such units are typically limited to simple techniques. This study has explored the use of cobalt beams for conformal and intensity-modulated radiotherapy (IMRT). Six patients, covering a range of treatment sites, were planned using both X-ray photons (6/10 MV) and cobalt-60 gamma rays (1.17 and 1.33 MeV). A range of conformal and IMRT techniques were considered, as appropriate. Conformal plans created using cobalt beams for small breast, meningioma and parotid cases were found to compare well with those created using X-ray photons. By using additional fields, acceptable conformal plans were also created for oesophagus and prostate cases. IMRT plans were found to be of comparable quality for meningioma, parotid and thyroid cases on the basis of dose-volume histogram analysis. We conclude that it is possible to plan high-quality radical radiotherapy treatments for cobalt units. A well-designed beam blocking/compensation system would be required to enable a practical and efficient alternative to multileaf collimator (MLC)-based linac treatments to be offered. If cobalt units were to have such features incorporated into them, they could offer considerable benefits to the radiotherapy community.

47 CFR 73.128 - AM stereophonic broadcasting.

Code of Federal Regulations, 2012 CFR

2012-10-01

... channel reversed. (iii) Left and Right Channel only, under all conditions of modulation for the... (NRSC-1). (2) The left and right channel audio signals shall conform to frequency response limitations...)=audio signal left channel, R(t)=audio signal right channel, m=modulation factor, and mpeak(L(t)+R(t))=1...

Use of hydrostatic pressure for modulation of protein chemical modification and enzymatic selectivity.

PubMed

Makarov, Alexey A; Helmy, Roy; Joyce, Leo; Reibarkh, Mikhail; Maust, Mathew; Ren, Sumei; Mergelsberg, Ingrid; Welch, Christopher J

2016-05-11

Using hydrostatic pressure to induce protein conformational changes can be a powerful tool for altering the availability of protein reactive sites and for changing the selectivity of enzymatic reactions. Using a pressure apparatus, it has been demonstrated that hydrostatic pressure can be used to modulate the reactivity of lysine residues of the protein ubiquitin with a water-soluble amine-specific homobifunctional coupling agent. Fewer reactive lysine residues were observed when the reaction was carried out under elevated pressure of 3 kbar, consistent with a pressure-induced conformational change of ubiquitin that results in fewer exposed lysine residues. Additionally, modulation of the stereoselectivity of an enzymatic transamination reaction was observed at elevated hydrostatic pressure. In one case, the minor diasteromeric product formed at atmospheric pressure became the major product at elevated pressure. Such pressure-induced alterations of protein reactivity may provide an important new tool for enzymatic reactions and the chemical modification of proteins.

High dose bystander effects in spatially fractionated radiation therapy

PubMed Central

Asur, Rajalakshmi; Butterworth, Karl T.; Penagaricano, Jose A.; Prise, Kevin M.; Griffin, Robert J.

2014-01-01

Traditional radiotherapy of bulky tumors has certain limitations. Spatially fractionated radiation therapy (GRID) and intensity modulated radiotherapy (IMRT) are examples of advanced modulated beam therapies that help in significant reductions in normal tissue damage. GRID refers to the delivery of a single high dose of radiation to a large treatment area that is divided into several smaller fields, while IMRT allows improved dose conformity to the tumor target compared to conventional three-dimensional conformal radiotherapy. In this review, we consider spatially fractionated radiotherapy approaches focusing on GRID and IMRT, and present complementary evidence from different studies which support the role of radiation induced signaling effects in the overall radiobiological rationale for these treatments. PMID:24246848

Variabilite temporelle des naines T et construction d'une camera infrarouge a grand champ

NASA Astrophysics Data System (ADS)

Artigau, Etienne

Le travail de thèse décrit ici se divise en deux sections distinctes: la première porte sur une étude de la variabilité temporelle des naines T et la seconde sur la construction et les performances de la Caméra PAnoramique Proche InfraRouge (CPAPIR). Les naines brunes sont des objets qui se forment comme les étoiles, lors de l'effondrement gravitationnel d'un nuage de gaz moléculaire, mais dont la masse est trop faible pour leur permettre d'entretenir des réactions de fusion nucléaire. Environ 70% des naines brunes de type L, qui ont des températures comprises entre 2200 K et 1500 K, présentent une variabilité temporelle dont les mécanismes exacts font toujours l'objet de débats. Nous avons étendu la recherche de variabilité temporelle aux naines brunes ayant des températures inférieures à ~1500 K et qui présentent les signatures du méthane, soit les naines T. Nos observations menées à l'Observatoire du mont Mégantic montrent qu'une fraction importante des naines T sont variables à 1.2 mm et 1.6 mm à des niveaux allant de 17 mmag à 53 mmag RMS. Les propriétés photométriques de cette variabilité sont consistantes avec une évolution de la couverture de nuages de poussière à la surface de plusieurs naines T. Des observations complémentaires menées en spectroscopie au télescope Canada-France-Hawaii montrent, pour une naine T, une variabilité spectroscopique dans le proche infrarouge qui est aussi consistante avec l'évolution de tels nuages de poussière. CPAPIR est une caméra infrarouge con=E7ue pour être utilisée à l'Observatoire du mont Mégantic. Elle possède un champ de 30' × 30', soit le plus grand champ de vue parmi les caméras infrarouges astronomiques actuellement en service. CPAPIR est équipé d'un détecteur de type Hawaii-II sensible de 0.8 mm à 2.4 mm avec 2048×2048 pixels. L'optique cryogénique de CPAPIR comprend 8 lentilles cryogéniques et 10 filtres disposés dans deux roues à filtres. Les observations menées au télescope avec CPAPIR montrent que la qualité d'image obtenue et la transmission globale sont conformes aux prédictions faites à partir du design optique et des courbes de transmission des revêtements utilisées pour ses différentes composantes optiques. Mots-clefs . astronomie, naines brunes, naines T, instrumentation, caméra, relevé, infrarouge

Retrospective evaluation of dosimetric quality for prostate carcinomas treated with 3D conformal, intensity modulated and volumetric modulated arc radiotherapy

PubMed Central

Crowe, Scott B; Kairn, Tanya; Middlebrook, Nigel; Hill, Brendan; Christie, David R H; Knight, Richard T; Kenny, John; Langton, Christian M; Trapp, Jamie V

2013-01-01

Introduction This study examines and compares the dosimetric quality of radiotherapy treatment plans for prostate carcinoma across a cohort of 163 patients treated across five centres: 83 treated with three-dimensional conformal radiotherapy (3DCRT), 33 treated with intensity modulated radiotherapy (IMRT) and 47 treated with volumetric modulated arc therapy (VMAT). Methods Treatment plan quality was evaluated in terms of target dose homogeneity and organs at risk (OAR), through the use of a set of dose metrics. These included the mean, maximum and minimum doses; the homogeneity and conformity indices for the target volumes; and a selection of dose coverage values that were relevant to each OAR. Statistical significance was evaluated using two-tailed Welch's T-tests. The Monte Carlo DICOM ToolKit software was adapted to permit the evaluation of dose metrics from DICOM data exported from a commercial radiotherapy treatment planning system. Results The 3DCRT treatment plans offered greater planning target volume dose homogeneity than the other two treatment modalities. The IMRT and VMAT plans offered greater dose reduction in the OAR: with increased compliance with recommended OAR dose constraints, compared to conventional 3DCRT treatments. When compared to each other, IMRT and VMAT did not provide significantly different treatment plan quality for like-sized tumour volumes. Conclusions This study indicates that IMRT and VMAT have provided similar dosimetric quality, which is superior to the dosimetric quality achieved with 3DCRT. PMID:26229621

Heparin-induced conformational changes of fibronectin within the extracellular matrix promote hMSC osteogenic differentiation.

PubMed

Li, Bojun; Lin, Zhe; Mitsi, Maria; Zhang, Yang; Vogel, Viola

2015-01-01

An increasing body of evidence suggests important roles of extracellular matrix (ECM) in regulating stem cell fate. This knowledge can be exploited in tissue engineering applications for the design of ECM scaffolds appropriate to direct stem cell differentiation. By probing the conformation of fibronectin (Fn) using fluorescence resonance energy transfer (FRET), we show here that heparin treatment of the fibroblast-derived ECM scaffolds resulted in more extended conformations of fibrillar Fn in ECM. Since heparin is a highly negatively charged molecule while fibronectin contains segments of positively charged modules, including FnIII13, electrostatic interactions between Fn and heparin might interfere with residual quaternary structure in relaxed fibronectin fibers thereby opening up buried sites. The conformation of modules FnIII12-14 in particular, which contain one of the heparin binding sites as well as binding sites for many growth factors, may be activated by heparin, resulting in alterations in growth factor binding to Fn. Indeed, upregulated osteogenic differentiation was observed when hMSCs were seeded on ECM scaffolds that had been treated with heparin and were subsequently chemically fixed. In contrast, either rigidifying relaxed fibers by fixation alone, or heparin treatment without fixation had no effect. We hypothesize that fibronectin's conformations within the ECM are activated by heparin such as to coordinate with other factors to upregulate hMSC osteogenic differentiation. Thus, the conformational changes of fibronectin within the ECM could serve as a 'converter' to tune hMSC differentiation in extracellular matrices. This knowledge could also be exploited to promote osteogenic stem cell differentiation on biomedical surfaces.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liang, Xiaodong, E-mail: lxdctopone@sina.com; Ni, Lingqin; Hu, Wei

The objective of this study was to evaluate the dose conformity and feasibility of whole-brain radiotherapy with a simultaneous integrated boost by forward intensity-modulated radiation therapy in patients with 1 to 3 brain metastases. Forward intensity-modulated radiation therapy plans were generated for 10 patients with 1 to 3 brain metastases on Pinnacle 6.2 Treatment Planning System. The prescribed dose was 30 Gy to the whole brain (planning target volume [PTV]{sub wbrt}) and 40 Gy to individual brain metastases (PTV{sub boost}) simultaneously, and both doses were given in 10 fractions. The maximum diameters of individual brain metastases ranged from 1.6 tomore » 6 cm, and the summated PTVs per patient ranged from 1.62 to 69.81 cm{sup 3}. Conformity and feasibility were evaluated regarding conformation number and treatment delivery time. One hundred percent volume of the PTV{sub boost} received at least 95% of the prescribed dose in all cases. The maximum doses were less than 110% of the prescribed dose to the PTV{sub boost}, and all of the hot spots were within the PTV{sub boost}. The volume of the PTV{sub wbrt} that received at least 95% of the prescribed dose ranged from 99.2% to 100%. The mean values of conformation number were 0.682. The mean treatment delivery time was 2.79 minutes. Ten beams were used on an average in these plans. Whole-brain radiotherapy with a simultaneous integrated boost by forward intensity-modulated radiation therapy in 1 to 3 brain metastases is feasible, and treatment delivery time is short.« less

ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

PubMed

Parvatikar, Akash; Vacaliuc, Gabriel S; Ramanathan, Arvind; Chennubhotla, S Chakra

2018-05-08

Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Conformal Galilei algebras, symmetric polynomials and singular vectors

NASA Astrophysics Data System (ADS)

Křižka, Libor; Somberg, Petr

2018-01-01

We classify and explicitly describe homomorphisms of Verma modules for conformal Galilei algebras cga_ℓ (d,C) with d=1 for any integer value ℓ \\in N. The homomorphisms are uniquely determined by singular vectors as solutions of certain differential operators of flag type and identified with specific polynomials arising as coefficients in the expansion of a parametric family of symmetric polynomials into power sum symmetric polynomials.

Separation of photoactive conformers based on hindered diarylethenes: efficient modulation in photocyclization quantum yields.

PubMed

Li, Wenlong; Jiao, Changhong; Li, Xin; Xie, Yongshu; Nakatani, Keitaro; Tian, He; Zhu, Weihong

2014-04-25

Endowing both solvent independency and excellent thermal bistability, the benzobis(thiadiazole)-bridged diarylethene system provides an efficient approach to realize extremely high photocyclization quantum yields (Φo-c , up to 90.6 %) by both separating completely pure anti-parallel conformer and suppressing intramolecular charge transfer (ICT). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP.

PubMed

Rozentur-Shkop, Eva; Goobes, Gil; Chill, Jordan H

2016-12-01

Intrinsically disordered proteins (IDPs) are multi-conformational polypeptides that lack a single stable three-dimensional structure. It has become increasingly clear that the versatile IDPs play key roles in a multitude of biological processes, and, given their flexible nature, NMR is a leading method to investigate IDP behavior on the molecular level. Here we present an IDP-tailored J-modulated experiment designed to monitor changes in the conformational ensemble characteristic of IDPs by accurately measuring backbone one- and two-bond J( 15 N, 13 Cα) couplings. This concept was realized using a unidirectional (H)NCO 13 C-detected experiment suitable for poor spectral dispersion and optimized for maximum coverage of amino acid types. To demonstrate the utility of this approach we applied it to the disordered actin-binding N-terminal domain of WASp interacting protein (WIP), a ubiquitous key modulator of cytoskeletal changes in a range of biological systems. One- and two-bond J( 15 N, 13 Cα) couplings were acquired for WIP residues 2-65 at various temperatures, and in denaturing and crowding environments. Under native conditions fitted J-couplings identified in the WIP conformational ensemble a propensity for extended conformation at residues 16-23 and 45-60, and a helical tendency at residues 28-42. These findings are consistent with a previous study of the based upon chemical shift and RDC data and confirm that the WIP 2-65 conformational ensemble is biased towards the structure assumed by this fragment in its actin-bound form. The effects of environmental changes upon this ensemble were readily apparent in the J-coupling data, which reflected a significant decrease in structural propensity at higher temperatures, in the presence of 8 M urea, and under the influence of a bacterial cell lysate. The latter suggests that crowding can cause protein unfolding through protein-protein interactions that stabilize the unfolded state. We conclude that J-couplings are a useful measureable in characterizing structural ensembles in IDPs, and that the proposed experiment provides a practical method for accurately performing such measurements, once again emphasizing the power of NMR in studying IDP behavior.

Innovations en vaccinologie: enjeux et perspectives pour l’Afrique

PubMed Central

Diop, Doudou; Sanicas, Melvin

2017-01-01

La vaccination est incontestablement l’une des interventions de santé publique les plus efficaces et les plus rentables qui soient. Les vaccins continuent de révolutionner notre capacité à prévenir les maladies et à améliorer la santé. Avec toutes les avancées technologiques, nous sommes en mesure d’étendre les avantages des vaccins à plus de gens et de fournir une meilleure protection contre les maladies infectieuses mortelles. Toutefois, avec le développement incessant de nouvelles souches microbiennes à travers le monde, la recherche en vaccinologie se doit d’innover continuellement. D’énormes progrès ont été réalisés pour améliorer la couverture vaccinale et introduire de nouveaux vaccins en Afrique. De nouveaux types de vaccins associés à des outils de vectorisation, d’administration et de délivrance spécifiques mais aussi des adjuvants susceptibles de moduler finement la réponse immunitaire sont attendus dans le futur. En Afrique, il est nécessaire de développer une approche régionale afin de répondre efficacement aux nombreux défis. Une meilleure information, la formation des personnels de santé en vaccinologie et des recherches bien ciblées sont les clés des futurs accomplissements dans le domaine. PMID:28690749

Structure of a pantothenate transporter and implications for ECF module sharing and energy coupling of group II ECF transporters

PubMed Central

Zhang, Minhua; Bao, Zhihao; Zhao, Qin; Guo, Hui; Xu, Ke; Wang, Chengcheng

2014-01-01

Energy-coupling factor (ECF) transporters are a unique group of ATP-binding cassette (ABC) transporters responsible for micronutrient uptake from the environment. Each ECF transporter is composed of an S component (or EcfS protein) and T/A/A′ components (or EcfT/A/A′ proteins; ECF module). Among the group II ECF transporters, several EcfS proteins share one ECF module; however, the underlying mechanism remains unknown. Here we report the structure of a group II ECF transporter–pantothenate transporter from Lactobacillus brevis (LbECF-PanT), which shares the ECF module with the folate and hydroxymethylpyrimidine transporters (LbECF-FolT and LbECF-HmpT). Structural and mutational analyses revealed the residues constituting the pantothenate-binding pocket. We found that although the three EcfS proteins PanT, FolT, and HmpT are dissimilar in sequence, they share a common surface area composed of the transmembrane helices 1/2/6 (SM1/2/6) to interact with the coupling helices 2/3 (CH2/3) of the same EcfT. CH2 interacts mainly with SM1 via hydrophobic interactions, which may modulate the sliding movement of EcfS. CH3 binds to a hydrophobic surface groove formed by SM1, SM2, and SM6, which may transmit the conformational changes from EcfA/A′ to EcfS. We also found that the residues at the intermolecular surfaces in LbECF-PanT are essential for transporter activity, and that these residues may mediate intermolecular conformational transmission and/or affect transporter complex stability. In addition, we found that the structure of EcfT is conformationally dynamic, which supports its function as a scaffold to mediate the interaction of the ECF module with various EcfS proteins to form different transporter complexes. PMID:25512487

SU-F-T-520: Dosimetric Comparison of Radiation Treatment Plans for Whole Breast Irradiation Between 3D Conformal in Prone and Supine Positions Vs. VMAT and IMRT in Supine Positions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bejarano Buele, A; Parsai, E

Purpose: The target volume for Whole Breast Irradiation (WBI) is dictated by location of tumor mass, breast tissue distribution, and involvement of lymph nodes. Dose coverage and Organs at Risk (OARs) sparing can be difficult to achieve in patients with unfavorable thoracic geometries. For these cases, inverse-planned and 3D-conformal prone treatments can be alternatives to traditional supine 3D-conformal plans. A dosimetric comparison can determine which of these techniques achieve optimal target coverage while sparing OARs. Methods: This study included simulation datasets for 8 patients, 5 of whom were simulated in both supine and prone positions. Positioning devices included breast boardsmore » and Vaclok bags for the supine position, and prone breast boards for the prone position. WBI 3-D conformal plans were created for patients simulated in both positions. Additional VMAT and IMRT WBI plans were made for all patients in the supine position. Results: Prone and supine 3D conformal plans had comparable PTV coverage. Prone 3D conformal plans received a significant 50% decrease to V20, V10, V5 and V30% for the ipsilateral lung in contrast to the supine plans. The heart also experienced a 10% decrease in maximum dose in the prone position, and V20, V10, V5 and V2 had significantly lower values than the supine plan. Supine IMRT and VMAT breast plans obtained comparable PTV coverage. The heart experienced a 10% decrease in maximum dose with inverse modulated plans when compared to the supine 3D conformal plan, while V20, V10, V5 and V2 showed higher values with inverse modulated plans than with supine 3D conformal plans. Conclusion: Prone 3D-conformal, and supine inverse planned treatments were generally superior in sparing OARs to supine plans with comparable PTV coverage. IMRT and VMAT plans offer sparing of OARs from high dose regions with an increase of irradiated volume in the low dose regions.« less

Conformational changes in the M2 muscarinic receptor induced by membrane voltage and agonist binding

PubMed Central

Navarro-Polanco, Ricardo A; Galindo, Eloy G Moreno; Ferrer-Villada, Tania; Arias, Marcelo; Rigby, J Ryan; Sánchez-Chapula, José A; Tristani-Firouzi, Martin

2011-01-01

Abstract The ability to sense transmembrane voltage is a central feature of many membrane proteins, most notably voltage-gated ion channels. Gating current measurements provide valuable information on protein conformational changes induced by voltage. The recent observation that muscarinic G-protein-coupled receptors (GPCRs) generate gating currents confirms their intrinsic capacity to sense the membrane electrical field. Here, we studied the effect of voltage on agonist activation of M2 muscarinic receptors (M2R) in atrial myocytes and how agonist binding alters M2R gating currents. Membrane depolarization decreased the potency of acetylcholine (ACh), but increased the potency and efficacy of pilocarpine (Pilo), as measured by ACh-activated K+ current, IKACh. Voltage-induced conformational changes in M2R were modified in a ligand-selective manner: ACh reduced gating charge displacement while Pilo increased the amount of charge displaced. Thus, these ligands manifest opposite voltage-dependent IKACh modulation and exert opposite effects on M2R gating charge displacement. Finally, mutations in the putative ligand binding site perturbed the movement of the M2R voltage sensor. Our data suggest that changes in voltage induce conformational changes in the ligand binding site that alter the agonist–receptor interaction in a ligand-dependent manner. Voltage-dependent GPCR modulation has important implications for cellular signalling in excitable tissues. Gating current measurement allows for the tracking of subtle conformational changes in the receptor that accompany agonist binding and changes in membrane voltage. PMID:21282291

Conformal Radiotherapy in the Treatment of Advanced Juvenile Nasopharyngeal Angiofibroma With Intracranial Extension: An Institutional Experience

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chakraborty, Santam, E-mail: drsantam@gmail.com; Ghoshal, Sushmita; Patil, Vijay Maruti

2011-08-01

Purpose: To describe the results of conformal radiotherapy in advanced juvenile nasopharyngeal angiofibroma in a tertiary care institution. Methods and Materials: Retrospective chart review was conducted for 8 patients treated with conformal radiotherapy between 2006 and 2009. The median follow-up was 17 months. All patients had Stage IIIB disease with intracranial extension. Radiotherapy was considered as treatment because patients were deemed inoperable owing to extensive intracranial/intraorbital extension or proximity to optic nerve. All but 1 patient were treated with intensity-modulated radiotherapy using seven coplanar fields. Median (range) dose prescribed was 39.6 (30-46) Gy. Actuarial analysis of local control and descriptivemore » analysis of toxicity profile was conducted. Results: Despite the large and complex target volume (median planning target volume, 292 cm{sup 3}), intensity-modulated radiotherapy achieved conformal dose distributions (median van't Reit index, 0.66). Significant sparing of the surrounding organs at risk was obtained. No significant Grade 3/4 toxicities were experienced during or after treatment. Actual local control at 2 years was 87.5%. One patient died 1 month after radiotherapy secondary to massive epistaxis. The remaining 7 patients had progressive resolution of disease and were symptom-free at last follow-up. Persistent rhinitis was the only significant toxicity, seen in 1 patient. Conclusions: Conformal radiotherapy results in good local control with minimal acute and late side effects in juvenile nasopharyngeal angiofibromas, even in the presence of advanced disease.« less

Pyranopterin conformation defines the function of molybdenum and tungsten enzymes.

PubMed

Rothery, Richard A; Stein, Benjamin; Solomonson, Matthew; Kirk, Martin L; Weiner, Joel H

2012-09-11

We have analyzed the conformations of 319 pyranopterins in 102 protein structures of mononuclear molybdenum and tungsten enzymes. These span a continuum between geometries anticipated for quinonoid dihydro, tetrahydro, and dihydro oxidation states. We demonstrate that pyranopterin conformation is correlated with the protein folds defining the three major mononuclear molybdenum and tungsten enzyme families, and that binding-site micro-tuning controls pyranopterin oxidation state. Enzymes belonging to the bacterial dimethyl sulfoxide reductase (DMSOR) family contain a metal-bis-pyranopterin cofactor, the two pyranopterins of which have distinct conformations, with one similar to the predicted tetrahydro form, and the other similar to the predicted dihydro form. Enzymes containing a single pyranopterin belong to either the xanthine dehydrogenase (XDH) or sulfite oxidase (SUOX) families, and these have pyranopterin conformations similar to those predicted for tetrahydro and dihydro forms, respectively. This work provides keen insight into the roles of pyranopterin conformation and oxidation state in catalysis, redox potential modulation of the metal site, and catalytic function.

Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

PubMed

Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

2010-03-17

Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.

A chimeric prokaryotic pentameric ligand–gated channel reveals distinct pathways of activation

DOE PAGES

Schmandt, Nicolaus; Velisetty, Phanindra; Chalamalasetti, Sreevatsa V.; ...

2015-09-28

Recent high resolution structures of several pentameric ligand–gated ion channels have provided unprecedented details of their molecular architecture. However, the conformational dynamics and structural rearrangements that underlie gating and allosteric modulation remain poorly understood. We used a combination of electrophysiology, double electron–electron resonance (DEER) spectroscopy, and x-ray crystallography to investigate activation mechanisms in a novel functional chimera with the extracellular domain (ECD) of amine-gated Erwinia chrysanthemi ligand–gated ion channel, which is activated by primary amines, and the transmembrane domain of Gloeobacter violaceus ligand–gated ion channel, which is activated by protons. We found that the chimera was independently gated by primarymore » amines and by protons. The crystal structure of the chimera in its resting state, at pH 7.0 and in the absence of primary amines, revealed a closed-pore conformation and an ECD that is twisted with respect to the transmembrane region. Amine- and pH-induced conformational changes measured by DEER spectroscopy showed that the chimera exhibits a dual mode of gating that preserves the distinct conformational changes of the parent channels. Collectively, our findings shed light on both conserved and divergent features of gating mechanisms in this class of channels, and will facilitate the design of better allosteric modulators.« less

A chimeric prokaryotic pentameric ligand–gated channel reveals distinct pathways of activation

PubMed Central

Schmandt, Nicolaus; Velisetty, Phanindra; Chalamalasetti, Sreevatsa V.; Stein, Richard A.; Bonner, Ross; Talley, Lauren; Parker, Mark D.; Mchaourab, Hassane S.; Yee, Vivien C.; Lodowski, David T.

2015-01-01

Recent high resolution structures of several pentameric ligand–gated ion channels have provided unprecedented details of their molecular architecture. However, the conformational dynamics and structural rearrangements that underlie gating and allosteric modulation remain poorly understood. We used a combination of electrophysiology, double electron–electron resonance (DEER) spectroscopy, and x-ray crystallography to investigate activation mechanisms in a novel functional chimera with the extracellular domain (ECD) of amine-gated Erwinia chrysanthemi ligand–gated ion channel, which is activated by primary amines, and the transmembrane domain of Gloeobacter violaceus ligand–gated ion channel, which is activated by protons. We found that the chimera was independently gated by primary amines and by protons. The crystal structure of the chimera in its resting state, at pH 7.0 and in the absence of primary amines, revealed a closed-pore conformation and an ECD that is twisted with respect to the transmembrane region. Amine- and pH-induced conformational changes measured by DEER spectroscopy showed that the chimera exhibits a dual mode of gating that preserves the distinct conformational changes of the parent channels. Collectively, our findings shed light on both conserved and divergent features of gating mechanisms in this class of channels, and will facilitate the design of better allosteric modulators. PMID:26415570

Dynamic Equilibrium of Cardiac Troponin C's Hydrophobic Cleft and Its Modulation by Ca2+ Sensitizers and a Ca2+ Sensitivity Blunting Phosphomimic, cTnT(T204E).

PubMed

Schlecht, William; Dong, Wen-Ji

2017-10-18

Several studies have suggested that conformational dynamics are important in the regulation of thin filament activation in cardiac troponin C (cTnC); however, little direct evidence has been offered to support these claims. In this study, a dye homodimerization approach is developed and implemented that allows the determination of the dynamic equilibrium between open and closed conformations in cTnC's hydrophobic cleft. Modulation of this equilibrium by Ca 2+ , cardiac troponin I (cTnI), cardiac troponin T (cTnT), Ca 2+ -sensitizers, and a Ca 2+ -desensitizing phosphomimic of cTnT (cTnT(T204E) is characterized. Isolated cTnC contained a small open conformation population in the absence of Ca 2+ that increased significantly upon the addition of saturating levels of Ca 2+ . This suggests that the Ca 2+ -induced activation of thin filament arises from an increase in the probability of hydrophobic cleft opening. The inclusion of cTnI increased the population of open cTnC, and the inclusion of cTnT had the opposite effect. Samples containing Ca 2+ -desensitizing cTnT(T204E) showed a slight but insignificant decrease in open conformation probability compared to samples with cardiac troponin T, wild type [cTnT(wt)], while Ca 2+ sensitizer treated samples generally increased open conformation probability. These findings show that an equilibrium between the open and closed conformations of cTnC's hydrophobic cleft play a significant role in tuning the Ca 2+ sensitivity of the heart.

Conformational transition of κ-casein in micellar environment: Insight from the tryptophan fluorescence

NASA Astrophysics Data System (ADS)

Mishra, Smruti; Meher, Geetanjali; Chakraborty, Hirak

2017-11-01

Intrinsically disordered proteins (IDPs) are under intense analysis due to their structural flexibility and importance in biological functions. Minuscule modulation in the microenvironment induces significant conformational changes in IDPs, and these non-native conformations of the IDPs often induce aggregation and cause cell death. Changes in the membrane composition often change the microenvironment, which promote conformational change and aggregation of IDPs. κ-Casein, an important milk protein, belongs to the class of IDPs containing net negative charges. In this present work, we have studied the interaction of κ-casein with cetyltrimethyl ammonium bromide (CTAB), a positively charged surfactant, utilizing various steady state fluorescence, time-resolved fluorescence and circular dichroism spectroscopy. Our results clearly indicate that κ-casein undergoes at least two conformational transitions in presence of various concentrations of CTAB. The intrinsically disordered κ-casein assumes a partially folded conformation at lower concentration of CTAB, which adopts an unstructured conformation at higher concentration of CTAB. The partially folded conformation of κ-casein at a lower CTAB concentration might be induced by the favorable electrostatic interaction between the positively charged surfactant headgroup and net negative charges of the protein, whereas surfactant nature of CTAB is being pronounced at higher concentration of CTAB.

Implementation of a volumetric modulated arc therapy treatment planning solution for kidney and adrenal stereotactic body radiation therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sonier, Marcus, E-mail: Marcus.Sonier@bccancer.bc.ca; Chu, William; Department of Radiation Oncology, University of Toronto, Toronto, ON

To develop a volumetric modulated arc therapy (VMAT) treatment planning solution in the treatment of primary renal cell carcinoma and oligometastatic adrenal lesions with stereotactic body radiation therapy. Single-arc VMAT plans (n = 5) were compared with clinically delivered step-and-shoot intensity-modulated radiotherapy (IMRT) with planning target volume coverage normalized between techniques. Target volume conformity, organ-at-risk (OAR) dose, treatment time, and monitor units were compared. A VMAT planning solution, created from a combination of arc settings and optimization constraints, auto-generated treatment plans in a single optimization. The treatment planning solution was evaluated on 15 consecutive patients receiving kidney and adrenal stereotacticmore » body radiation therapy. Treatment time was reduced from 13.0 ± 2.6 to 4.0 ± 0.9 minutes for IMRT and VMAT, respectively. The VMAT planning solution generated treatment plans with increased target homogeneity, improved 95% conformity index, and a reduced maximum point dose to nearby OARs but with increased intermediate dose to distant OARs. The conformity of the 95% isodose improved from 1.32 ± 0.39 to 1.12 ± 0.05 for IMRT and VMAT treatment plans, respectively. Evaluation of the planning solution showed clinically acceptable dose distributions for 13 of 15 cases with tight conformity of the prescription isodose to the planning target volume of 1.07 ± 0.04, delivering minimal dose to OARs. The introduction of a stereotactic body radiation therapy VMAT treatment planning solution improves the efficiency of planning and delivery time, producing treatment plans of comparable or superior quality to IMRT in the case of primary renal cell carcinoma and oligometastatic adrenal lesions.« less

Feasibility study of an intensity-modulated radiation model for the study of erectile dysfunction.

PubMed

Koontz, Bridget F; Yan, Hui; Kimura, Masaki; Vujaskovic, Zeljko; Donatucci, Craig; Yin, Fang-Fang

2011-02-01

Preclinical studies of radiotherapy (RT) induced erectile dysfunction (ED) have been limited by radiation toxicity when using large fields. To develop a protocol of rat prostate irradiation using techniques mimicking the current clinical standard of intensity modulated radiotherapy (IMRT). Quality assurance (QA) testing of plan accuracy, animal health 9 weeks after RT, and intracavernosal pressure (ICP) measurement on cavernosal nerve stimulation. Computed tomography-based planning was used to develop a stereotactic radiosurgery (SRS) treatment plan for five young adult male Sprague-Dawley rats. Two treatment planning strategies were utilized to deliver 20 Gy in a single fraction: three-dimensional dynamic conformal arc and intensity-modulated arc (RapidArc). QA testing was performed for each plan type. Treatment was delivered using a NovalisTX (Varian Medical Systems) with high-definition multi-leaf collimators using on-board imaging prior to treatment. Each animal was evaluated for ED 2 months after treatment by nerve stimulation and ICP measurement. The mean prostate volume and target volume (5 mm expansion of prostate) for the five animals was 0.36 and 0.66 cm3, respectively. Both conformal and RapidArc plans provided at least 95% coverage of the target volume, with rapid dose fall-off. QA plans demonstrated strong agreement between doses of calculated and delivered plans, although the conformal arc plan was more homogenous in treatment delivery. Treatment was well tolerated by the animals with no toxicity out to 9 weeks. Compared with control animals, significant reduction in ICP/mean arterial pressure, maximum ICP, and ICP area under the curve were noted. Tightly conformal dynamic arc prostate irradiation is feasible and results in minimal toxicity and measurable changes in erectile function. © 2010 International Society for Sexual Medicine.

Modulation of the conformational state of the SV2A protein by an allosteric mechanism as evidenced by ligand binding assays

PubMed Central

Daniels, V; Wood, M; Leclercq, K; Kaminski, R M; Gillard, M

2013-01-01

Background and Purpose Synaptic vesicle protein 2A (SV2A) is the specific binding site of the anti-epileptic drug levetiracetam (LEV) and its higher affinity analogue UCB30889. Moreover, the protein has been well validated as a target for anticonvulsant therapy. Here, we report the identification of UCB1244283 acting as a SV2A positive allosteric modulator of UCB30889. Experimental Approach UCB1244283 was characterized in vitro using radioligand binding assays with [3H]UCB30889 on recombinant SV2A expressed in HEK cells and on rat cortex. In vivo, the compound was tested in sound-sensitive mice. Key Results Saturation binding experiments in the presence of UCB1244283 demonstrated a fivefold increase in the affinity of [3H]UCB30889 for human recombinant SV2A, combined with a twofold increase of the total number of binding sites. Similar results were obtained on rat cortex. In competition binding experiments, UCB1244283 potentiated the affinity of UCB30889 while the affinity of LEV remained unchanged. UCB1244283 significantly slowed down both the association and dissociation kinetics of [3H]UCB30889. Following i.c.v. administration in sound-sensitive mice, UCB1244283 showed a clear protective effect against both tonic and clonic convulsions. Conclusions and Implications These results indicate that UCB1244283 can modulate the conformation of SV2A, thereby inducing a higher affinity state for UCB30889. Our results also suggest that the conformation of SV2A per se might be an important determinant of its functioning, especially during epileptic seizures. Therefore, agents that act on the conformation of SV2A might hold great potential in the search for new SV2A-based anticonvulsant therapies. PMID:23530581

Dosimetric effect of beam arrangement for intensity-modulated radiation therapy in the treatment of upper thoracic esophageal carcinoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Yuchuan; Deng, Min; Zhou, Xiaojuan

To evaluate the lung sparing in intensity-modulated radiation therapy (IMRT) for patients with upper thoracic esophageal tumors extending inferiorly to the thorax by different beam arrangement. Overall, 15 patient cases with cancer of upper thoracic esophagus were selected for a retrospective treatment-planning study. Intensity-modulated radiation therapy plans using 4, 5, and 7 beams (4B, 5B, and 7B) were developed for each patient by direct machine parameter optimization (DMPO). All plans were evaluated with respect to dose volumes to irradiated targets and normal structures, with statistical comparisons made between 4B with 5B and 7B intensity-modulated radiation therapy plans. Differences among plansmore » were evaluated using a two-tailed Friedman test at a statistical significance of p < 0.05. The maximum dose, average dose, and the conformity index (CI) of planning target volume 1 (PTV1) were similar for 3 plans for each case. No significant difference of coverage for planning target volume 1 and maximum dose for spinal cords were observed among 3 plans in present study (p > 0.05). The average V{sub 5}, V{sub 13}, V{sub 20}, mean lung dose, and generalized equivalent uniform dose (gEUD) for the total lung were significantly lower in 4B-plans than those data in 5B-plans and 7B-plans (p < 0.01). Although the average V{sub 30} for the total lung were significantly higher in 4B-plans than those in 5B-plans and 7B-plans (p < 0.05). In addition, when comparing with the 4B-plans, the conformity/heterogeneity index of the 5B- and 7B-plans were significantly superior (p < 0.05). The 4B-intensity-modulated radiation therapy plan has advantage to address the specialized problem of lung sparing to low- and intermediate-dose exposure in the thorax when dealing with relative long tumors extended inferiorly to the thoracic esophagus for upper esophageal carcinoma with the cost for less conformity. Studies are needed to compare the superiority of volumetric modulated arc therapy with intensity-modulated radiation therapy technique.« less

pH-Driven Ordering Transitions in Liquid Crystal Induced by Conformational Changes of Cardiolipin.

PubMed

Sidiq, Sumyra; Verma, Indu; Pal, Santanu Kumar

2015-04-28

We report an investigation of interfacial phenomena occurring at aqueous-liquid crystal (LC) interfaces that triggers an orientational ordering transition of the LC in the presence of cardiolipin (CL) by varying pH, salt concentration and valence. In particular, the effects of three different conformational isomeric forms of the CL are observed to cause the response of the LC ordering to vary significantly from one to another at those interfaces. An ordering transition of the LC was observed when the CL is mostly in undissociated (at pH 2) and/or in bicyclic (at pH 4) conformation in which LC shows changes in the optical appearance from bright to dark. By contrast, no change in the optical appearance of the LC was observed when the pH of the system increases to 8 or higher in which the CL mostly exists in the open conformation. Fluorescence microscopy measurements further suggest that pH-dependent conformational forms of the CL have different ability to self-assemble (thus different packing efficiency) at aqueous-LC interfaces leading to dissimilar orientational behavior of the LC. Specifically, we found that change in headgroup-headgroup repulsion of the central phosphatidyl groups of the CL plays a key role in tuning the lipid packing efficiency and thus responses to interfacial phenomena. Orientational ordering transition of the LC was also observed as a function of increasing the ionic strength (buffer capacity) and strongly influenced in the presence of mono and divalent cations. Langmuir-Blodgett (LB) and polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) measurements provide further insight in modulation of the lipid packing efficiency and alkyl chain conformation of the CL at different pH and ionic conditions. Overall, the results presented in this paper establish that LCs offer a promising approach to differentiate different conformations (label free detection) of the CL through ordering transition of the LC at aqueous-LC interfaces.

SU-F-T-446: Improving Craniospinal Irradiation Technique Using Volumetric Modulated Arc Therapy (VMAT) Planning and Its Dosimetric Verification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, X; Tejani, M; Jiang, X

2016-06-15

Purpose: The purpose of this study is to investigate a volumetric modulated arc therapy (VMAT) treatment planning technique for supine craniospinal irradiation (CSI). Evaluate the suitability of VMAT for CSI with dosimetric measurements and compare it to 3D conformal planning using specific plan metrics such as dose conformity, homogeneity, and dose of organs at risk (OAR). Methods: Ten CSI patients treated with conventional 3D technique were re-planned with VMAT. The PTV was contoured to include the whole contents of the brain and spinal canal with a uniform margin of 5 mm. VMAT plans were generated with two partial arcs coveringmore » the brain, two partial arcs for the superior portion of the spinal cord and two partial arcs covering the remaining inferior portion of the spinal cord. Conformity index (CI), heterogeneity indexes (HI) and max and mean doses of OAR were compared to 3D plans. VMAT plans were delivered onto an anthropomorphic phantom loaded with Gafchromic films and OSLDs placed at specific positions to evaluate the plan dose at the junctions and as well as the plan dose distributions. Results: This VMAT technique was validated with a clinical study of 10 patients. The average CI was 1.03±0.02 for VMAT plans and 1.96±0.32 for conformal plans. And the average HI was 1.15±0.01 for VMAT plans and 1.51±0.21 for conformal plans. The mean and max doses to the all OARs for VMAT plans were significantly lower than conformal plans. The measured dose in phantom for VAMT plans was comparable to the calculated dose in Eclipse and the doses at junctions were verified. Conclusion: VMAT CSI was able to achieve better dose conformity and heterogeneity as well as significantly reducing the dose to Heart, esophagus and larynx. VMAT CSI appears to be a dosimterically advantageous, faster delivery, has better reproducibility CSI treatment.« less

FRET detection of lymphocyte function–associated antigen-1 conformational extension

PubMed Central

Chigaev, Alexandre; Smagley, Yelena; Haynes, Mark K.; Ursu, Oleg; Bologa, Cristian G.; Halip, Liliana; Oprea, Tudor; Waller, Anna; Carter, Mark B.; Zhang, Yinan; Wang, Wei; Buranda, Tione; Sklar, Larry A.

2015-01-01

Lymphocyte function–associated antigen 1 (LFA-1, CD11a/CD18, αLβ2-integrin) and its ligands are essential for adhesion between T-cells and antigen-presenting cells, formation of the immunological synapse, and other immune cell interactions. LFA-1 function is regulated through conformational changes that include the modulation of ligand binding affinity and molecular extension. However, the relationship between molecular conformation and function is unclear. Here fluorescence resonance energy transfer (FRET) with new LFA-1–specific fluorescent probes showed that triggering of the pathway used for T-cell activation induced rapid unquenching of the FRET signal consistent with extension of the molecule. Analysis of the FRET quenching at rest revealed an unexpected result that can be interpreted as a previously unknown LFA-1 conformation. PMID:25378583

Structural Basis of ATP Hydrolysis and Intersubunit Signaling in the AAA+ ATPase p97.

PubMed

Hänzelmann, Petra; Schindelin, Hermann

2016-01-05

p97 belongs to the superfamily of AAA+ ATPases and is characterized by a tandem AAA module, an N-terminal domain involved in substrate and cofactor interactions, and a functionally important unstructured C-terminal tail. The ATPase activity is controlled by an intradomain communication within the same protomer and an interdomain communication between neighboring protomers. Here, we present for the first time crystal structures in which the physiologically relevant p97 hexamer constitutes the content of the asymmetric unit, namely in the apo state without nucleotide in either the D1 or D2 module and in the pre-activated state with ATPγS bound to both modules. The structures provide new mechanistic insights into the interdomain communication mediated by conformational changes of the C terminus as well as an intersubunit signaling network, which couples the nucleotide state to the conformation of the central putative substrate binding pore. Copyright © 2016 Elsevier Ltd. All rights reserved.

Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches.

PubMed

Shukla, Diwakar; Lawrenz, Morgan; Pande, Vijay S

2015-01-01

G-protein-coupled receptors (GPCRs) are a versatile family of membrane-bound signaling proteins. Despite the recent successes in obtaining crystal structures of GPCRs, much needs to be learned about the conformational changes associated with their activation. Furthermore, the mechanism by which ligands modulate the activation of GPCRs has remained elusive. Molecular simulations provide a way of obtaining detailed an atomistic description of GPCR activation dynamics. However, simulating GPCR activation is challenging due to the long timescales involved and the associated challenge of gaining insights from the "Big" simulation datasets. Here, we demonstrate how cloud-computing approaches have been used to tackle these challenges and obtain insights into the activation mechanism of GPCRs. In particular, we review the use of Markov state model (MSM)-based sampling algorithms for sampling milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2-AR. MSMs of agonist and inverse agonist-bound β2-AR reveal multiple activation pathways and how ligands function via modulation of the ensemble of activation pathways. We target this ensemble of conformations with computer-aided drug design approaches, with the goal of designing drugs that interact more closely with diverse receptor states, for overall increased efficacy and specificity. We conclude by discussing how cloud-based approaches present a powerful and broadly available tool for studying the complex biological systems routinely. © 2015 Elsevier Inc. All rights reserved.

Mediastinal irradiation in a patient affected by lung carcinoma after heart transplantation: Helical tomotherapy versus three dimensional conformal radiotherapy.

PubMed

Giugliano, Francesca M; Iorio, Vincenzo; Cammarota, Fabrizio; Toledo, Diego; Senese, Rossana; Francomacaro, Ferdinando; Muto, Matteo; Muto, Paolo

2016-04-26

Patients who have undergone solid organ transplants are known to have an increased risk of neoplasia compared with the general population. We report our experience using mediastinal irradiation with helical tomotherapy versus three-dimensional conformal radiation therapy to treat a patient with lung carcinoma 15 years after heart transplantation. Our dosimetric evaluation showed no particular difference between the techniques, with the exception of some organs. Mediastinal irradiation after heart transplantation is feasible and should be considered after evaluation of the risk. Conformal radiotherapy or intensity-modulated radiotherapy appears to be the appropriate treatment in heart-transplanted oncologic patients.

Insight into conformational changes of a single α-helix peptide molecule through stiffness measurements

NASA Astrophysics Data System (ADS)

Kageshima, Masami; Lantz, Mark A.; Jarvis, Suzanne P.; Tokumoto, Hiroshi; Takeda, Seiji; Ptak, Arkadiusz; Nakamura, Chikashi; Miyake, Jun

2001-07-01

Stiffness variations during the conformational change of a single α-helix polylysine peptide molecule were measured in a liquid environment using atomic force microscopy (AFM) with magnetic cantilever modulation. At the initial stage of the stretching process the stiffness decreased due to the breaking of hydrogen bonds and then increased due to the stretching of the helix backbone. These changes were reversible on reversal of the stretching motion. Below p K, the stiffness did not show increase on reversal, indicating that the reforming of hydrogen bonds did not take place. Conformational changes in the molecule were examined via these changes in stiffness.

Time-resolved circular dichroism: Application to the study of conformal changes in biomolecules

NASA Astrophysics Data System (ADS)

Hache, F.

2010-06-01

Circular dichroism (CD) is known to be a very sensitive probe of the conformation of molecules and biomolecules. It is therefore tempting to implement CD in a pump-probe experiment in order to measure ultrarapid conformational changes which occur in photochemical processes. We present two technical developments of such time-resolved CD experiments. The first one relies on the modulation of the probe polarization from left to right circular whereas the second one measures the pump-induced ellipticity of the probe with a Babinet-Soleil compensator. Some applications are described and extension of these techniques towards the study of elementary protein folding processes is discussed.

Structure and dynamics of AMPA receptor GluA2 in resting, pre-open and desensitized states

PubMed Central

Dürr, Katharina L.; Chen, Lei; Stein, Richard A.; De Zorzi, Rita; MihaelaFolea, I.; Walz, Thomas; Mchaourab, Hassane S.; Gouaux, Eric

2014-01-01

Summary Ionotropic glutamate receptors (iGluRs) mediate the majority of fast excitatory signaling in the nervous system. Despite the profound importance of iGluRs in the nervous system, little is known about the structures and dynamics of intact receptors in distinct functional states. Here we elucidate the structures of the intact GluA2 AMPA receptor in an apo resting/closed state, in an activated/pre-open state bound with the partial agonists and a positive allosteric modulator and in a desensitized/closed state in complex with FW alone. To probe the conformational properties of these states, we carried out double electron-electron resonance experiments on cysteine mutants and cryo-electron microscopy studies. We show how agonist binding modulates the conformation of the ligand binding domain 'layer' of the intact receptors and how, upon desensitization, the receptor undergoes large conformational rearrangements of amino-terminal and ligand-binding domains. We define mechanistic principles by which to understand antagonism, activation and desensitization in AMPA iGluRs. PMID:25109876

Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

PubMed Central

Manna, Moutusi; Niemelä, Miia; Tynkkynen, Joona; Javanainen, Matti; Kulig, Waldemar; Müller, Daniel J; Rog, Tomasz; Vattulainen, Ilpo

2016-01-01

There is evidence that lipids can be allosteric regulators of membrane protein structure and activation. However, there are no data showing how exactly the regulation emerges from specific lipid-protein interactions. Here we show in atomistic detail how the human β2-adrenergic receptor (β2AR) – a prototypical G protein-coupled receptor – is modulated by cholesterol in an allosteric fashion. Extensive atomistic simulations show that cholesterol regulates β2AR by limiting its conformational variability. The mechanism of action is based on the binding of cholesterol at specific high-affinity sites located near the transmembrane helices 5–7 of the receptor. The alternative mechanism, where the β2AR conformation would be modulated by membrane-mediated interactions, plays only a minor role. Cholesterol analogues also bind to cholesterol binding sites and impede the structural flexibility of β2AR, however cholesterol generates the strongest effect. The results highlight the capacity of lipids to regulate the conformation of membrane receptors through specific interactions. DOI: http://dx.doi.org/10.7554/eLife.18432.001 PMID:27897972

Preventing and Reporting Resident Abuse in Assisted Living: A Learning Module for Resident Assistants.

ERIC Educational Resources Information Center

McKinnon, Cole Marie

In an effort to conform to the Massachusetts Executive Office of Elder Affairs (EOEA) staff development requirement regarding elder abuse, a learning module was developed. It was designed to be administered to an individual caregiver for the purpose of self-study or to small groups of caregivers using the lecture-discussion format. Following the…

Properties of Organic Superconductors.

DTIC Science & Technology

1983-09-01

fBEDrrrF) 4 (ReO 4 ) 2 , devient supraconducteur pour des pressions suptrseures A 4 kbar avec une temperature de transition aol environs dce 2 K. A plus...coupl6es aux 6lectrons. Ces experiences sont incompatibles avec linterpr~tation expliquant lorigine /I/ du pic A 29 cm- 1 par un pseudogap supraconducteur

Hydrogen Bonded Squaramide-Based Foldable Module Induces Both β- and α-Turns in Hairpin Structures of α-Peptides in Water.

PubMed

Martínez, Luís; Martorell, Gabriel; Sampedro, Ángel; Ballester, Pablo; Costa, Antoni; Rotger, Carmen

2015-06-19

A novel tertiary squaramido-based reverse-turn module SQ is reported, and its conformational properties are evaluated. This module is easily incorporated into a α-peptide sequence by conventional solid-phase peptide synthesis. The structure characterization of the hybrid squaramido-peptide 4 is described, showing that the turn segment induces the formation of hairpin structures in water through the formation of both αSQ- and βSQ-turns.

Hydrogen-Deuterium Exchange Mass Spectrometry Reveals Calcium Binding Properties and Allosteric Regulation of Downstream Regulatory Element Antagonist Modulator (DREAM).

PubMed

Zhang, Jun; Li, Jing; Craig, Theodore A; Kumar, Rajiv; Gross, Michael L

2017-07-18

Downstream regulatory element antagonist modulator (DREAM) is an EF-hand Ca 2+ -binding protein that also binds to a specific DNA sequence, downstream regulatory elements (DRE), and thereby regulates transcription in a calcium-dependent fashion. DREAM binds to DRE in the absence of Ca 2+ but detaches from DRE under Ca 2+ stimulation, allowing gene expression. The Ca 2+ binding properties of DREAM and the consequences of the binding on protein structure are key to understanding the function of DREAM. Here we describe the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis to investigate the Ca 2+ binding properties and the subsequent conformational changes of full-length DREAM. We demonstrate that all EF-hands undergo large conformation changes upon calcium binding even though the EF-1 hand is not capable of binding to Ca 2+ . Moreover, EF-2 is a lower-affinity site compared to EF-3 and -4 hands. Comparison of HDX profiles between wild-type DREAM and two EF-1 mutated constructs illustrates that the conformational changes in the EF-1 hand are induced by long-range structural interactions. HDX analyses also reveal a conformational change in an N-terminal leucine-charged residue-rich domain (LCD) remote from Ca 2+ -binding EF-hands. This LCD domain is responsible for the direct interaction between DREAM and cAMP response element-binding protein (CREB) and regulates the recruitment of the co-activator, CREB-binding protein. These long-range interactions strongly suggest how conformational changes transmit the Ca 2+ signal to CREB-mediated gene transcription.

Study of the chain conformation of thermotropic nematic main chain polyesters

NASA Astrophysics Data System (ADS)

Li, M. H.; Brûlet, A.; Cotton, J. P.; Davidson, P.; Strazielle, C.; Keller, P.

1994-10-01

The conformation of main chain mesomorphic polyesters is studied by small angle neutron scattering (SANS) in the isotropic and in the nematic phases, by using mixtures of deuterated and undeuterated polymers. Particular attention is given to neglect the transesterification effects occurring mainly at high temperature for these LC polymers. In the isotropic phase, despite the presence of long rigid mesogenic groups, the LC polyester chains have a Gaussian conformation shown by the variation of the radius of gyration as a function of the molecular weight. This result is confirmed from the scattering variation in the intermediate range of the scattering vector. In the nematic phase, the SANS data are well fitted to a model of cylinder, in which the main chain polymer is confined. In the unoriented phase, the measurements in the intermediate range give the values of the radii of cylinders : they lie in between 10 Å and 19 Å depending on the degree of polymerization of chains. In the oriented nematic phase, the scattering patterns are highly anisotropic : they correspond to very long, thin and well-oriented cylinders. We have calculated the fully extended chain lengths using for the monomer length that measured in situ by X-ray diffraction. Then the comparison of this length with the measured height of the cylinders gives the existence of hairpins and their number per chain. For the short chain, the conformation is almost completely elongated in the nematic direction, whereas hairpin defects appear in longer chains. Their number decreases slightly with decreasing temperature. The orientational fluctuations of cylinders relatively to the nematic director are weak as shown from the high values of their order parameter (P_2 > 0.9). These results are discussed for two spacer lengths as a function of the molecular weight and of the temperature. La conformation de polyesters linéaires mésomorphes est étudiée par diffusion de neutrons aux petits angles (DNPA) dans les phases isotrope et nématique sur des mélanges de polymères hydrogénés et deutériés. Les conditions expérimentales ont été choisies afin de pouvoir négliger les effets de la transestérification obtenus à haute température avec cette famille de polymères cristaux liquides. Dans la phase isotrope, en dépit de la présence de longs et rigides groupements mésogènes, les chaînes de polymères ont une conformation gaussienne, comme le montre la variation du rayon de giration en fonction de la masse moléculaire. Ce résultat est confirmé par les mesures faites dans le domaine intermédiaire du vecteur de diffusion. Dans la phase nématique, les données de DNPA sont bien ajustées par un modèle de cylindre dans lequel la chaîne de polymère est confinée. Dans la phase non orientée, les mesures faites dans le domaine intermédiaire donnent les valeurs des rayons des cylindres (compris entre 10 Å et 19 Å selon le degré de polymérisation des chaînes). Dans la phase nématique orientée, les figures de diffusion sont très anisotropes et correspondent à de longs et étroits cylindres bien orientés. La longueur de la chaîne totalement étirée est calculée à partir de la longueur du monomère mesurée par diffraction de rayons X. Par comparaison avec la hauteur du cylindre mesurée en DNPA, nous déduisons l'existence des épingles à cheveux et leur nombre par chaîne. La conformation d'une chaîne courte est complètement étirée dans la direction du champ nématique, alors que des défauts du type épingles à cheveux apparaissent dans les chaînes plus longues. Le nombre de ces défauts décroît légèrement en diminuant la température. Les fluctuations d'orientation des cylindres autour de la direction du champ nématique sont faibles comme le montrent les valeurs élevées des paramètres d'ordre des cylindres (P_2 > 0,9). Les résultats sont discutés, pour deux longueurs d'espaceur, en fonction de la masse moléculaire et de la température.

Site-Specific Modulation of Charge Controls the Structure and Stimulus Responsiveness of Intrinsically Disordered Peptide Brushes.

PubMed

Bhagawati, Maniraj; Rubashkin, Matt G; Lee, Jessica P; Ananthanarayanan, Badriprasad; Weaver, Valerie M; Kumar, Sanjay

2016-06-14

Intrinsically disordered proteins (IDPs) are an important and emerging class of materials for tailoring biointerfaces. While the importance of chain charge and resultant electrostatic interactions in controlling conformational properties of IDPs is beginning to be explored through in silico approaches, there is a dearth of experimental studies motivated toward a systematic study of these effects. In an effort to explore this relationship, we measured the conformations of two peptides derived from the intrinsically disordered neurofilament (NF) side arm domain: one depicting the wild-type sequence with four lysine-serine-proline repeats (KSP peptide) and another in which the serine residues were replaced with aspartates (KDP peptide), a strategy sometimes used to mimic phosphorylation. Using a variety of biophysical measurements including a novel application of scanning angle interference microscopy, we demonstrate that the KDP peptide assumes comparatively more expanded conformations in solution and forms significantly thicker brushes when immobilized on planar surfaces at high densities. In both settings, the peptides respond to changes in ambient ionic strength, with each peptide showing distinct stimulus-responsive characteristics. While the KDP peptide undergoes compaction with increasing ionic strength as would be expected for a polyampholyte, the KSP peptide shows biphasic behavior, with an initial compaction followed by an expanded state at a higher ionic strength. Together these results support the notion that modulation of charge on IDPs can regulate conformational and interfacial properties.

Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation

PubMed Central

2017-01-01

Halogen bonding is a weak chemical force that has so far mostly found applications in crystal engineering. Despite its potential for use in drug discovery, as a new molecular tool in the direction of molecular recognition events, it has rarely been assessed in biopolymers. Motivated by this fact, we have developed a peptide model system that permits the quantitative evaluation of weak forces in a biologically relevant proteinlike environment and have applied it for the assessment of a halogen bond formed between two amino acid side chains. The influence of a single weak force is measured by detection of the extent to which it modulates the conformation of a cooperatively folding system. We have optimized the amino acid sequence of the model peptide on analogues with a hydrogen bond-forming site as a model for the intramolecular halogen bond to be studied, demonstrating the ability of the technique to provide information about any type of weak secondary interaction. A combined solution nuclear magnetic resonance spectroscopic and computational investigation demonstrates that an interstrand halogen bond is capable of conformational stabilization of a β-hairpin foldamer comparable to an analogous hydrogen bond. This is the first report of incorporation of a conformation-stabilizing halogen bond into a peptide/protein system, and the first quantification of a chlorine-centered halogen bond in a biologically relevant system in solution. PMID:28581720

Microwave spectroscopy and curious molecular dynamics of ethyl trifluoroacetate

NASA Astrophysics Data System (ADS)

Bohn, Robert K.; Montgomery, John A.; Harvey Michels, H.; Acharte, Christian

2017-05-01

The first ethyl ester whose structure was determined by microwave spectroscopy is ethyl formate. It exists in two conformations. In the 1970s, that study was used as a model to determine the structures of other ethyl esters, ethyl cyanoformate, chloroformate, and trifluoroacetate. They display the same conformations as ethyl formate. But under the experimental conditions used, Stark modulation with a maximum electric field, static low pressure gas, rapid sweeping, and long detector time constants, each of those esters displays bands of an additional third species. A careful, high resolution study of ethyl cyanoformate only observed two conformers. A model has been proposed that the third species derives from a dense array of torsionally excited states with broadened transitions due to short lifetimes. The present study of ethyl trifluoroacetate in a pulsed jet Fourier Transform spectrometer is intended to clarify the earlier results. Two conformers are observed including all their monosubstituted 13C and 18O isotopologs. In a pulsed jet Fourier Transform spectrometer using argon as the carrier gas, only one conformer is observed. Switching to helium as the carrier gas, another, higher energy conformer is also observed.

Conformational flexibility and packing plausibility of repaglinide polymorphs

NASA Astrophysics Data System (ADS)

Rani, Dimpy; Goyal, Parnika; Chadha, Renu

2018-04-01

The present manuscript highlights the structural insight into the repaglinide polymorphs. The experimental screening for the possible crystal forms were carried out using various solvents, which generated three forms. The crystal structure of Form II and III was determined using PXRD pattern whereas structural analysis of Form I has already been reported. Form I, II and II was found to exist in P212121, PNA21 and P21/c space groups respectively. Conformational analysis was performed to account the conformational flexibility of RPG. The obtained conformers were further utilized to obtain the information about the crystal packing pattern of RPG polymorphs by polymorph prediction module. The lattice energy landscape, depicting the relationship between lattice energy and density of the polymorphs has been obtained for various possible polymorphs. The experimentally isolated polymorphs were successfully fitted into lattice energy landscape.

Voltage-Driven Conformational Switching with Distinct Raman Signature in a Single-Molecule Junction.

PubMed

Bi, Hai; Palma, Carlos-Andres; Gong, Yuxiang; Hasch, Peter; Elbing, Mark; Mayor, Marcel; Reichert, Joachim; Barth, Johannes V

2018-04-11

Precisely controlling well-defined, stable single-molecule junctions represents a pillar of single-molecule electronics. Early attempts to establish computing with molecular switching arrays were partly challenged by limitations in the direct chemical characterization of metal-molecule-metal junctions. While cryogenic scanning probe studies have advanced the mechanistic understanding of current- and voltage-induced conformational switching, metal-molecule-metal conformations are still largely inferred from indirect evidence. Hence, the development of robust, chemically sensitive techniques is instrumental for advancement in the field. Here we probe the conformation of a two-state molecular switch with vibrational spectroscopy, while simultaneously operating it by means of the applied voltage. Our study emphasizes measurements of single-molecule Raman spectra in a room-temperature stable single-molecule switch presenting a signal modulation of nearly 2 orders of magnitude.

SU-F-P-52: A Meta-Analysis of Controlled Clinical Trials Comparing Elective Nodal Irradiation with Involved-Field Irradiation for Conformal Or Intensity-Modulated Radiotherapy in Patients with Esophageal Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bai, W; Zhang, R; Zhou, Z

Purpose: To compare elective nodal irradiation with involved-field irradiation for three-dimensional conformal radiotherapy or intensity-modulated radiotherapy in patients with esophageal cancer by a metaanalysis. Methods: Wanfang, CNKI, VIP, CBM databases, PubMed, Embase and Cochrane Library were searched to identify the controlled clinical trials of elective nodal irradiation with involved-field irradiation for three-dimensional conformal radiotherapy or intensity-modulated radiotherapy in patients with esophageal cancer. The obtained data were analyzed using Stata 11.0. The difference between two groups was estimated by calculating the odds ratio (OR) with 95% confidence interval (95% CI). Results: A total of 12 controlled clinical trials involving 1095 esophagealmore » cancer patients, which were selected according to inclusion and exclusion criteria, were included in this meta-analysis. The meta-analysis showed that the elective nodal irradiation group reduced the rates of out-field failure comparing with involved-field irradiation group (OR=3.727, P=0.007). However, the rates of ≥grades 3 acute radiation pneumonitis and esophagitis were significantly higher in the elective nodal irradiation group than in the involved-field irradiation group (OR=0.348, P=0.001, OR=0.385, P=0.000). 1-, 2-, 3-year local control rates (OR=0.966, P=0.837, OR=0.946, P=0.781; OR=0.732P=0.098) and 1-, 3-, 5-year survival rates were similar in the two groups ( OR=0.966, P=0.837; OR=0.946, P=0.781; OR=0.732, P=0.098; OR=0.952, P=0.756; OR=1.149, P=0.422; OR=0.768, P=0.120). It is the same with the rates of distant metastasis (OR=0.986, P=0.937). Conclusion: Compared with involved-field irradiation, the elective nodal irradiation can reduce the rates of out-field failure for three-dimensional conformal radiotherapy or intensity-modulated radiotherapy in patients with esophageal cancer. However, its advantage of local control and survival rates is not obvious and it increases the incidence of toxicities.« less

Logarithmic conformal field theory: beyond an introduction

NASA Astrophysics Data System (ADS)

Creutzig, Thomas; Ridout, David

2013-12-01

This article aims to review a selection of central topics and examples in logarithmic conformal field theory. It begins with the remarkable observation of Cardy that the horizontal crossing probability of critical percolation may be computed analytically within the formalism of boundary conformal field theory. Cardy’s derivation relies on certain implicit assumptions which are shown to lead inexorably to indecomposable modules and logarithmic singularities in correlators. For this, a short introduction to the fusion algorithm of Nahm, Gaberdiel and Kausch is provided. While the percolation logarithmic conformal field theory is still not completely understood, there are several examples for which the formalism familiar from rational conformal field theory, including bulk partition functions, correlation functions, modular transformations, fusion rules and the Verlinde formula, has been successfully generalized. This is illustrated for three examples: the singlet model \\mathfrak {M} (1,2), related to the triplet model \\mathfrak {W} (1,2), symplectic fermions and the fermionic bc ghost system; the fractional level Wess-Zumino-Witten model based on \\widehat{\\mathfrak {sl}} \\left( 2 \\right) at k=-\\frac{1}{2}, related to the bosonic βγ ghost system; and the Wess-Zumino-Witten model for the Lie supergroup \\mathsf {GL} \\left( 1 {\\mid} 1 \\right), related to \\mathsf {SL} \\left( 2 {\\mid} 1 \\right) at k=-\\frac{1}{2} and 1, the Bershadsky-Polyakov algebra W_3^{(2)} and the Feigin-Semikhatov algebras W_n^{(2)}. These examples have been chosen because they represent the most accessible, and most useful, members of the three best-understood families of logarithmic conformal field theories. The logarithmic minimal models \\mathfrak {W} (q,p), the fractional level Wess-Zumino-Witten models, and the Wess-Zumino-Witten models on Lie supergroups (excluding \\mathsf {OSP} \\left( 1 {\\mid} 2n \\right)). In this review, the emphasis lies on the representation theory of the underlying chiral algebra and the modular data pertaining to the characters of the representations. Each of the archetypal logarithmic conformal field theories is studied here by first determining its irreducible spectrum, which turns out to be continuous, as well as a selection of natural reducible, but indecomposable, modules. This is followed by a detailed description of how to obtain character formulae for each irreducible, a derivation of the action of the modular group on the characters, and an application of the Verlinde formula to compute the Grothendieck fusion rules. In each case, the (genuine) fusion rules are known, so comparisons can be made and favourable conclusions drawn. In addition, each example admits an infinite set of simple currents, hence extended symmetry algebras may be constructed and a series of bulk modular invariants computed. The spectrum of such an extended theory is typically discrete and this is how the triplet model \\mathfrak {W} (1,2) arises, for example. Moreover, simple current technology admits a derivation of the extended algebra fusion rules from those of its continuous parent theory. Finally, each example is concluded by a brief description of the computation of some bulk correlators, a discussion of the structure of the bulk state space, and remarks concerning more advanced developments and generalizations. The final part gives a very short account of the theory of staggered modules, the (simplest class of) representations that are responsible for the logarithmic singularities that distinguish logarithmic theories from their rational cousins. These modules are discussed in a generality suitable to encompass all the examples met in this review and some of the very basic structure theory is proven. Then, the important quantities known as logarithmic couplings are reviewed for Virasoro staggered modules and their role as fundamentally important parameters, akin to the three-point constants of rational conformal field theory, is discussed. An appendix is also provided in order to introduce some of the necessary, but perhaps unfamiliar, language of homological algebra.

A Dualistic Conformational Response to Substrate Binding in the Human Serotonin Transporter Reveals a High Affinity State for Serotonin*

PubMed Central

Bjerregaard, Henriette; Severinsen, Kasper; Said, Saida; Wiborg, Ove; Sinning, Steffen

2015-01-01

Serotonergic neurotransmission is modulated by the membrane-embedded serotonin transporter (SERT). SERT mediates the reuptake of serotonin into the presynaptic neurons. Conformational changes in SERT occur upon binding of ions and substrate and are crucial for translocation of serotonin across the membrane. Our understanding of these conformational changes is mainly based on crystal structures of a bacterial homolog in various conformations, derived homology models of eukaryotic neurotransmitter transporters, and substituted cysteine accessibility method of SERT. However, the dynamic changes that occur in the human SERT upon binding of ions, the translocation of substrate, and the role of cholesterol in this interplay are not fully elucidated. Here we show that serotonin induces a dualistic conformational response in SERT. We exploited the substituted cysteine scanning method under conditions that were sensitized to detect a more outward-facing conformation of SERT. We found a novel high affinity outward-facing conformational state of the human SERT induced by serotonin. The ionic requirements for this new conformational response to serotonin mirror the ionic requirements for translocation. Furthermore, we found that membrane cholesterol plays a role in the dualistic conformational response in SERT induced by serotonin. Our results indicate the existence of a subpopulation of SERT responding differently to serotonin binding than hitherto believed and that membrane cholesterol plays a role in this subpopulation of SERT. PMID:25614630

Investigating ion channel conformational changes using voltage clamp fluorometry.

PubMed

Talwar, Sahil; Lynch, Joseph W

2015-11-01

Ion channels are membrane proteins whose functions are governed by conformational changes. The widespread distribution of ion channels, coupled with their involvement in most physiological and pathological processes and their importance as therapeutic targets, renders the elucidation of these conformational mechanisms highly compelling from a drug discovery perspective. Thanks to recent advances in structural biology techniques, we now have high-resolution static molecular structures for members of the major ion channel families. However, major questions remain to be resolved about the conformational states that ion channels adopt during activation, drug modulation and desensitization. Patch-clamp electrophysiology has long been used to define ion channel conformational states based on functional criteria. It achieves this by monitoring conformational changes at the channel gate and cannot detect conformational changes occurring in regions distant from the gate. Voltage clamp fluorometry involves labelling cysteines introduced into domains of interest with environmentally sensitive fluorophores and inferring structural rearrangements from voltage or ligand-induced fluorescence changes. Ion channel currents are monitored simultaneously to verify the conformational status. By defining real time conformational changes in domains distant from the gate, this technique provides unexpected new insights into ion channel structure and function. This review aims to summarise the methodology and highlight recent innovative applications of this powerful technique. This article is part of the Special Issue entitled 'Fluorescent Tools in Neuropharmacology'. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantum mechanical origin of the conformational preferences of 4-thiaproline and its S-oxides

PubMed Central

Choudhary, Amit; Pua, Khian Hong

2010-01-01

The saturated ring and secondary amine of proline spawn equilibria between pyrrolidine ring puckers as well as peptide bond isomers. These conformational equilibria can be modulated by alterations to the chemical architecture of proline. For example, Cγ in the pyrrolidine ring can be replaced with sulfur, which can be oxidized either stereoselectively to yield diastereomeric S-oxides or completely to yield a sulfone. Here, the thiazolidine ring and peptide bond conformations of 4-thiaproline and its S-oxides were analyzed in an Ac-Xaa-OMe system by using NMR spectroscopy, X-ray crystallography, and hybrid density functional theory. The results indicate that the ring pucker of the S-oxides is governed by the gauche effect, and the prolyl peptide bond conformation is determined by the strength of the n→π* interaction between the amide oxygen and the ester carbonyl group. These findings, which are consistent with those for isologous 4-hydroxyprolines and 4-fluoroprolines, substantiate the importance of electron delocalization in amino-acid conformation. PMID:20221839

Conformational Preferences of α-Substituted Proline Analogues

PubMed Central

Flores-Ortega, Alejandra; Jiménez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Alemán, Carlos; Casanovas, Jordi

2009-01-01

DFT calculations at the B3LYP/6-31+G(d,p) level have been used to investigate how the replacement of the α hydrogen by a more sterically demanding group affects the conformational preferences of proline. Specifically, the N-acetyl-N’-methylamide derivatives of L-proline, L-α-methylproline and L-α-phenylproline have been calculated, with both the cis/trans isomerism of the peptide bonds and the puckering of the pyrrolidine ring being considered. The effects of solvation have been evaluated using a Self Consistent Reaction Field model. As expected, tetrasubstitution at the α carbon destabilizes the conformers with one or more peptide bonds arranged in cis. The lowest energy minimum has been found to be identical for the three compounds investigated, but important differences are observed regarding other energetically accessible backbone conformations. The results obtained provide evidence that the distinct steric requirements of the substituent at Cα may play a significant role in modulating the conformational preferences of proline. PMID:18351745

Volumetric modulated arc radiotherapy for esophageal cancer.

PubMed

Vivekanandan, Nagarajan; Sriram, Padmanaban; Kumar, S A Syam; Bhuvaneswari, Narayanan; Saranya, Kamalakannan

2012-01-01

A treatment planning study was performed to evaluate the performance of volumetric arc modulation with RapidArc (RA) against 3D conformal radiation therapy (3D-CRT) and conventional intensity-modulated radiation therapy (IMRT) techniques for esophageal cancer. Computed tomgraphy scans of 10 patients were included in the study. 3D-CRT, 4-field IMRT, and single-arc and double-arc RA plans were generated with the aim to spare organs at risk (OAR) and healthy tissue while enforcing highly conformal target coverage. The planning objective was to deliver 54 Gy to the planning target volume (PTV) in 30 fractions. Plans were evaluated based on target conformity and dose-volume histograms of organs at risk (lung, spinal cord, and heart). The monitor unit (MU) and treatment delivery time were also evaluated to measure the treatment efficiency. The IMRT plan improves target conformity and spares OAR when compared with 3D-CRT. Target conformity improved with RA plans compared with IMRT. The mean lung dose was similar in all techniques. However, RA plans showed a reduction in the volume of the lung irradiated at V(₂₀Gy) and V(₃₀Gy) dose levels (range, 4.62-17.98%) compared with IMRT plans. The mean dose and D(₃₅%) of heart for the RA plans were better than the IMRT by 0.5-5.8%. Mean V(₁₀Gy) and integral dose to healthy tissue were almost similar in all techniques. But RA plans resulted in a reduced low-level dose bath (15-20 Gy) in the range of 14-16% compared with IMRT plans. The average MU needed to deliver the prescribed dose by RA technique was reduced by 20-25% compared with IMRT technique. The preliminary study on RA for esophageal cancers showed improvements in sparing OAR and healthy tissue with reduced beam-on time, whereas only double-arc RA offered improved target coverage compared with IMRT and 3D-CRT plans. Copyright © 2012 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.

Diagnostic et traitement de la Maladie du charbon à localisation palpébrale: à propos d'un cas et revue de littérature

PubMed Central

Hafidi, Zouheir; Handor, Hanan; Laghmari, Mina; Handor, Najat; Cherkaoui, Lalla Ouafae; Tachfouti, Samira; Seffar, Myriame; Daoudi, Rajae

2013-01-01

L′anthrax est une zoonose causée par le Bacillus anthracis. les humains contractent généralement cette maladie dans des régions endémiques, par contact direct avec des animaux infectés ou avec leurs produits contaminés. Les localisations palpébrales sont rares dans la pratique clinique et posent des problèmes de diagnostic différentiel. Les auteurs rapportent l'observation d'un patient admis dans un tableau de cellulite préseptale, avec escarre noirâtre étendue de la paupière supérieure et œdème extensif de l′hémiface, faisant suspecter une localisation palpébrale de la maladie du charbon. L'examen bactériologique a permis de confirmer le diagnostic. Le patient a bénéficié d′une antibiothérapie à base de pénicilline G avec une bonne évolution. PMID:24171070

Le Laser A Argon Ionise : Applications Therapeutiques

NASA Astrophysics Data System (ADS)

Brunetaud, J. M.; Mosquet, L.; Mordon, S.; Rotteleur, G.

1984-03-01

Le laser a argon ionise est un laser a emission continue, reglee en general en multiraies de 487 a 544 nm. Le rayonnement de ce laser est bien absorbe par les tissus vivants, avec une action preferentielle au niveau des pigments rouges (hemoglobine, myoglobine) et noirs (melanine). Le laser a argon est princi-palement utilise en therapeutique pour ses effets thermiques : en fonction du choix des parametres (puissance optique, surface exposee, temps d'exposition) on peut obtenir une coagulation (temperature optimale au niveau des tissus 60° - 80°) ou une volatisation (temperature superieure a 100°). Si la zone volatilisee est tres etroite (inferieure a 0,5 mm) on obtient un effet de coupe. Par rapport aux deux autres lasers egalement utilises pour leurs effets thermiques (CO2 et Nd. YAG) l'argon a des effets intermediaires : la coagulation sera plus superficielle qu'avec le Nd. YAG et la volatisation plus profonde qu'avec le CO2. Lors de la coupe, la necrose sur les berges sera egalement plus importante qu'avec le CO2.

Not Too Old, Not Too Young: Older Women's Perceptions of Physicians.

PubMed

MacRae, Hazel

2015-12-01

RÉSUMÉ Les femmes plus âgées interagissent avec les médecins plus souvent que les hommes âgés et les personnes plus jeunes; pourtant, la connaissance et la compréhension de leurs expériences avec les médecins sont limitées. Le but de cette étude était d'étudier les perceptions des femmes âgées de leurs interactions avec les médecins et d'identifier ce que les femmes veulent de leurs médecins. Les entrevues en profondeur avec 30 femmes âgées montrent que la majorité veulent être impliquée activement dans leurs propres soins de santé. Dans la relation patient-médecin, les femmes donnent généralement la priorité aux qualités personnelles de médecins et leur comportement à l'égard du patient. Pour de nombreuses femmes, l'âge et le sexe du médecin ont aussi leur importance.

Conformational dynamics of amyloid proteins at the aqueous interface

NASA Astrophysics Data System (ADS)

Armbruster, Matthew; Horst, Nathan; Aoki, Brendy; Malik, Saad; Soto, Patricia

2013-03-01

Amyloid proteins is a class of proteins that exhibit distinct monomeric and oligomeric conformational states hallmark of deleterious neurological diseases for which there are not yet cures. Our goal is to examine the extent of which the aqueous/membrane interface modulates the folding energy landscape of amyloid proteins. To this end, we probe the dynamic conformational ensemble of amyloids (monomer prion protein and Alzheimer's Ab protofilaments) interacting with model bilayers. We will present the results of our coarse grain molecular modeling study in terms of the existence of preferential binding spots of the amyloid to the bilayer and the response of the bilayer to the interaction with the amyloid. NSF Nebraska EPSCoR First Award

In search of a consensus model of the resting state of a voltage-sensing domain.

PubMed

Vargas, Ernesto; Bezanilla, Francisco; Roux, Benoît

2011-12-08

Voltage-sensing domains (VSDs) undergo conformational changes in response to the membrane potential and are the critical structural modules responsible for the activation of voltage-gated channels. Structural information about the key conformational states underlying voltage activation is currently incomplete. Through the use of experimentally determined residue-residue interactions as structural constraints, we determine and refine a model of the Kv channel VSD in the resting conformation. The resulting structural model is in broad agreement with results that originate from various labs using different techniques, indicating the emergence of a consensus for the structural basis of voltage sensing. Copyright © 2011 Elsevier Inc. All rights reserved.

Developpement d'une commande pour une hydrolienne de riviere et optimisation =

NASA Astrophysics Data System (ADS)

Tetrault, Philippe

Suivant le developpement des energies renouvelables, la presente etude se veut une base theorique quant aux principes fondamentaux necessaires au bon fonctionnement et a l'implementation d'une hydrolienne de riviere. La problematique derriere ce nouveau type d'appareil est d'abord presentee. La machine electrique utilisee dans l'application, c'est-a-dire la machine synchrone a aimants permanents, est etudiee : ses equations dynamiques mecaniques et electriques sont developpees, introduisant en meme temps le concept de referentiel tournant. Le fonctionnement de l'onduleur utilise, soit un montage en pont complet a deux niveaux a semi-conducteurs, est explique et mit en equation pour permettre de comprendre les strategies de modulation disponibles. Un bref historique de ces strategies est fait avant de mettre l'emphase sur la modulation vectorielle qui sera celle utilisee pour l'application en cours. Les differents modules sont assembles dans une simulation Matlab pour confirmer leur bon fonctionnement et comparer les resultats de la simulation avec les calculs theoriques. Differents algorithmes permettant de traquer et maintenir un point de fonctionnement optimal sont presentes. Le comportement de la riviere est etudie afin d'evaluer l'ampleur des perturbations que le systeme devra gerer. Finalement, une nouvelle approche est presentee et comparee a une strategie plus conservatrice a l'aide d'un autre modele de simulation Matlab.

A comparative study of standard intensity-modulated radiotherapy and RapidArc planning techniques for ipsilateral and bilateral head and neck irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pursley, Jennifer, E-mail: jpursley@mgh.harvard.edu; Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA; Damato, Antonio L.

The purpose of this study was to investigate class solutions using RapidArc volumetric-modulated arc therapy (VMAT) planning for ipsilateral and bilateral head and neck (H&N) irradiation, and to compare dosimetric results with intensity-modulated radiotherapy (IMRT) plans. A total of 14 patients who received ipsilateral and 10 patients who received bilateral head and neck irradiation were retrospectively replanned with several volumetric-modulated arc therapy techniques. For ipsilateral neck irradiation, the volumetric-modulated arc therapy techniques included two 360° arcs, two 360° arcs with avoidance sectors around the contralateral parotid, two 260° or 270° arcs, and two 210° arcs. For bilateral neck irradiation, themore » volumetric-modulated arc therapy techniques included two 360° arcs, two 360° arcs with avoidance sectors around the shoulders, and 3 arcs. All patients had a sliding-window-delivery intensity-modulated radiotherapy plan that was used as the benchmark for dosimetric comparison. For ipsilateral neck irradiation, a volumetric-modulated arc therapy technique using two 360° arcs with avoidance sectors around the contralateral parotid was dosimetrically comparable to intensity-modulated radiotherapy, with improved conformity (conformity index = 1.22 vs 1.36, p < 0.04) and lower contralateral parotid mean dose (5.6 vs 6.8 Gy, p < 0.03). For bilateral neck irradiation, 3-arc volumetric-modulated arc therapy techniques were dosimetrically comparable to intensity-modulated radiotherapy while also avoiding irradiation through the shoulders. All volumetric-modulated arc therapy techniques required fewer monitor units than sliding-window intensity-modulated radiotherapy to deliver treatment, with an average reduction of 35% for ipsilateral plans and 67% for bilateral plans. Thus, for ipsilateral head and neck irradiation a volumetric-modulated arc therapy technique using two 360° arcs with avoidance sectors around the contralateral parotid is recommended. For bilateral neck irradiation, 2- or 3-arc techniques are dosimetrically comparable to intensity-modulated radiotherapy, but more work is needed to determine the optimal approaches by disease site.« less

A comparative study of standard intensity-modulated radiotherapy and RapidArc planning techniques for ipsilateral and bilateral head and neck irradiation.

PubMed

Pursley, Jennifer; Damato, Antonio L; Czerminska, Maria A; Margalit, Danielle N; Sher, David J; Tishler, Roy B

2017-01-01

The purpose of this study was to investigate class solutions using RapidArc volumetric-modulated arc therapy (VMAT) planning for ipsilateral and bilateral head and neck (H&N) irradiation, and to compare dosimetric results with intensity-modulated radiotherapy (IMRT) plans. A total of 14 patients who received ipsilateral and 10 patients who received bilateral head and neck irradiation were retrospectively replanned with several volumetric-modulated arc therapy techniques. For ipsilateral neck irradiation, the volumetric-modulated arc therapy techniques included two 360° arcs, two 360° arcs with avoidance sectors around the contralateral parotid, two 260° or 270° arcs, and two 210° arcs. For bilateral neck irradiation, the volumetric-modulated arc therapy techniques included two 360° arcs, two 360° arcs with avoidance sectors around the shoulders, and 3 arcs. All patients had a sliding-window-delivery intensity-modulated radiotherapy plan that was used as the benchmark for dosimetric comparison. For ipsilateral neck irradiation, a volumetric-modulated arc therapy technique using two 360° arcs with avoidance sectors around the contralateral parotid was dosimetrically comparable to intensity-modulated radiotherapy, with improved conformity (conformity index = 1.22 vs 1.36, p < 0.04) and lower contralateral parotid mean dose (5.6 vs 6.8Gy, p < 0.03). For bilateral neck irradiation, 3-arc volumetric-modulated arc therapy techniques were dosimetrically comparable to intensity-modulated radiotherapy while also avoiding irradiation through the shoulders. All volumetric-modulated arc therapy techniques required fewer monitor units than sliding-window intensity-modulated radiotherapy to deliver treatment, with an average reduction of 35% for ipsilateral plans and 67% for bilateral plans. Thus, for ipsilateral head and neck irradiation a volumetric-modulated arc therapy technique using two 360° arcs with avoidance sectors around the contralateral parotid is recommended. For bilateral neck irradiation, 2- or 3-arc techniques are dosimetrically comparable to intensity-modulated radiotherapy, but more work is needed to determine the optimal approaches by disease site. Copyright © 2017 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.

Dynamic Conformational Changes in MUNC18 Prevent Syntaxin Binding

PubMed Central

Bar-On, Dana; Nachliel, Esther; Gutman, Menachem; Ashery, Uri

2011-01-01

The Sec1/munc18 protein family is essential for vesicle fusion in eukaryotic cells via binding to SNARE proteins. Protein kinase C modulates these interactions by phosphorylating munc18a thereby reducing its affinity to one of the central SNARE members, syntaxin-1a. The established hypothesis is that the reduced affinity of the phosphorylated munc18a to syntaxin-1a is a result of local electrostatic repulsion between the two proteins, which interferes with their compatibility. The current study challenges this paradigm and offers a novel mechanistic explanation by revealing a syntaxin-non-binding conformation of munc18a that is induced by the phosphomimetic mutations. In the present study, using molecular dynamics simulations, we explored the dynamics of the wild-type munc18a versus phosphomimetic mutant munc18a. We focused on the structural changes that occur in the cavity between domains 3a and 1, which serves as the main syntaxin-binding site. The results of the simulations suggest that the free wild-type munc18a exhibits a dynamic equilibrium between several conformations differing in the size of its cavity (the main syntaxin-binding site). The flexibility of the cavity's size might facilitate the binding or unbinding of syntaxin. In silico insertion of phosphomimetic mutations into the munc18a structure induces the formation of a conformation where the syntaxin-binding area is rigid and blocked as a result of interactions between residues located on both sides of the cavity. Therefore, we suggest that the reduced affinity of the phosphomimetic mutant/phosphorylated munc18a is a result of the closed-cavity conformation, which makes syntaxin binding energetically and sterically unfavorable. The current study demonstrates the potential of phosphoryalation, an essential biological process, to serve as a driving force for dramatic conformational changes of proteins modulating their affinity to target proteins. PMID:21390273

Dosimetric and radiobiologic comparison of 3D conformal versus intensity modulated planning techniques for prostate bed radiotherapy.

PubMed

Koontz, Bridget F; Das, Shiva; Temple, Kathy; Bynum, Sigrun; Catalano, Suzanne; Koontz, Jason I; Montana, Gustavo S; Oleson, James R

2009-01-01

Adjuvant radiotherapy for locally advanced prostate cancer improves biochemical and clinical disease-free survival. While comparisons in intact prostate cancer show a benefit for intensity modulated radiation therapy (IMRT) over 3D conformal planning, this has not been studied for post-prostatectomy radiotherapy (RT). This study compares normal tissue and target dosimetry and radiobiological modeling of IMRT vs. 3D conformal planning in the postoperative setting. 3D conformal plans were designed for 15 patients who had been treated with IMRT planning for salvage post-prostatectomy RT. The same computed tomography (CT) and target/normal structure contours, as well as prescription dose, was used for both IMRT and 3D plans. Normal tissue complication probabilities (NTCPs) were calculated based on the dose given to the bladder and rectum by both plans. Dose-volume histogram and NTCP data were compared by paired t-test. Bladder and rectal sparing were improved with IMRT planning compared to 3D conformal planning. The volume of the bladder receiving at least 75% (V75) and 50% (V50) of the dose was significantly reduced by 28% and 17%, respectively (p = 0.002 and 0.037). Rectal dose was similarly reduced, V75 by 33% and V50 by 17% (p = 0.001 and 0.004). While there was no difference in the volume of rectum receiving at least 65 Gy (V65), IMRT planning significant reduced the volume receiving 40 Gy or more (V40, p = 0.009). Bladder V40 and V65 were not significantly different between planning modalities. Despite these dosimetric differences, there was no significant difference in the NTCP for either bladder or rectal injury. IMRT planning reduces the volume of bladder and rectum receiving high doses during post-prostatectomy RT. Because of relatively low doses given to the bladder and rectum, there was no statistically significant improvement in NTCP between the 3D conformal and IMRT plans.

HRD Motif as the Central Hub of the Signaling Network for Activation Loop Autophosphorylation in Abl Kinase.

PubMed

La Sala, Giuseppina; Riccardi, Laura; Gaspari, Roberto; Cavalli, Andrea; Hantschel, Oliver; De Vivo, Marco

2016-11-08

A number of structural factors modulate the activity of Abelson (Abl) tyrosine kinase, whose deregulation is often related to oncogenic processes. First, only the open conformation of the Abl kinase domain's activation loop (A-loop) favors ATP binding to the catalytic cleft. In this regard, the trans-autophosphorylation of the Y412 residue, which is located along the A-loop, favors the stability of the open conformation, in turn enhancing Abl activity. Another key factor for full Abl activity is the formation of active conformations of the catalytic DFG motif in the Abl kinase domain. Furthermore, binding of the SH2 domain to the N-lobe of the Abl kinase was recently demonstrated to have a long-range allosteric effect on the stabilization of the A-loop open state. Intriguingly, these distinct structural factors imply a complex signal transmission network for controlling the A-loop's flexibility and conformational preference for optimal Abl function. However, the exact dynamical features of this signal transmission network structure remain unclear. Here, we report on microsecond-long molecular dynamics coupled with enhanced sampling simulations of multiple Abl model systems, in the presence or absence of the SH2 domain and with the DFG motif flipped in two ways (in or out conformation). Through comparative analysis, our simulations augment the interpretation of the existing Abl experimental data, revealing a dynamical network of interactions that interconnect SH2 domain binding with A-loop plasticity and Y412 autophosphorylation in Abl. This signaling network engages the DFG motif and, importantly, other conserved structural elements of the kinase domain, namely, the EPK-ELK H-bond network and the HRD motif. Our results show that the signal propagation for modulating the A-loop spatial localization is highly dependent on the HRD motif conformation, which thus acts as the central hub of this (allosteric) signaling network controlling Abl activation and function.

Dosimetric Comparison of Intensity-Modulated Stereotactic Radiotherapy With Other Stereotactic Techniques for Locally Recurrent Nasopharyngeal Carcinoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kung, Shiris Wai Sum; Wu, Vincent Wing Cheung; Kam, Michael Koon Ming, E-mail: kamkm@yahoo.co

2011-01-01

Purpose: Locally recurrent nasopharyngeal carcinoma (NPC) patients can be salvaged by reirradiation with a substantial degree of radiation-related complications. Stereotactic radiotherapy (SRT) is widely used in this regard because of its rapid dose falloff and high geometric precision. The aim of this study was to examine whether the newly developed intensity-modulated stereotactic radiotherapy (IMSRT) has any dosimetric advantages over three other stereotactic techniques, including circular arc (CARC), static conformal beam (SmMLC), and dynamic conformal arc (mARC), in treating locally recurrent NPC. Methods and Materials: Computed tomography images of 32 patients with locally recurrent NPC, previously treated with SRT, were retrievedmore » from the stereotactic planning system for contouring and computing treatment plans. Treatment planning of each patient was performed for the four treatment techniques: CARC, SmMLC, mARC, and IMSRT. The conformity index (CI) and homogeneity index (HI) of the planning target volume (PTV) and doses to the organs at risk (OARs) and normal tissue were compared. Results: All four techniques delivered adequate doses to the PTV. IMSRT, SmMLC, and mARC delivered reasonably conformal and homogenous dose to the PTV (CI <1.47, HI <0.53), but not for CARC (p < 0.05). IMSRT presented with the smallest CI (1.37) and HI (0.40). Among the four techniques, IMSRT spared the greatest number of OARs, namely brainstem, temporal lobes, optic chiasm, and optic nerve, and had the smallest normal tissue volume in the low-dose region. Conclusion: Based on the dosimetric comparison, IMSRT was optimal for locally recurrent NPC by delivering a conformal and homogenous dose to the PTV while sparing OARs.« less

On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases.

PubMed

Faraldo-Gómez, José D; Roux, Benoît

2007-08-21

Regulation of signaling pathways in the cell often involves multidomain allosteric enzymes that are able to adopt alternate active or inactive conformations in response to specific stimuli. It is therefore of great interest to elucidate the energetic and structural determinants that govern the conformational plasticity of these proteins. In this study, free-energy computations have been used to address this fundamental question, focusing on one important family of signaling enzymes, the Src tyrosine kinases. Inactivation of these enzymes depends on the formation of an assembly comprising a tandem of SH3 and SH2 modules alongside a catalytic domain. Activation results from the release of the SH3 and SH2 domains, which are then believed to be structurally uncoupled by virtue of a flexible peptide link. In contrast to this view, this analysis shows that inactivation depends critically on the intrinsic propensity of the SH3-SH2 tandem to adopt conformations that are conducive to the assembled inactive state, even when no interactions with the rest of the kinase are possible. This funneling of the available conformational space is encoded within the SH3-SH2 connector, which appears to have evolved to modulate the flexibility of the tandem in solution. To further substantiate this notion, we show how constitutively activating mutations in the SH3-SH2 connector shift the assembly equilibrium toward the disassembled, active state. Based on a similar analysis of several constructs of the kinase complex, we propose that assembly is characterized by the progressive optimization of the protein's conformational energy, with little or no energetic frustration.

Phosphorylation of α3 Glycine Receptors Induces a Conformational Change in the Glycine-Binding Site

PubMed Central

2013-01-01

Inflammatory pain sensitization is initiated by prostaglandin-induced phosphorylation of α3 glycine receptors (GlyRs) that are specifically located in inhibitory synapses on spinal pain sensory neurons. Phosphorylation reduces the magnitude of glycinergic synaptic currents, thereby disinhibiting nociceptive neurons. Although α1 and α3 subunits are both expressed on spinal nociceptive neurons, α3 is a more promising therapeutic target as its sparse expression elsewhere implies a reduced risk of side-effects. Here we compared glycine-mediated conformational changes in α1 and α3 GlyRs to identify structural differences that might be exploited in designing α3-specific analgesics. Using voltage-clamp fluorometry, we show that glycine-mediated conformational changes in the extracellular M2-M3 domain were significantly different between the two GlyR isoforms. Using a chimeric approach, we found that structural variations in the intracellular M3-M4 domain were responsible for this difference. This prompted us to test the hypothesis that phosphorylation of S346 in α3 GlyR might also induce extracellular conformation changes. We show using both voltage-clamp fluorometry and pharmacology that Ser346 phosphorylation elicits structural changes in the α3 glycine-binding site. These results provide the first direct evidence for phosphorylation-mediated extracellular conformational changes in pentameric ligand-gated ion channels, and thus suggest new loci for investigating how phosphorylation modulates structure and function in this receptor family. More importantly, by demonstrating that phosphorylation alters α3 GlyR glycine-binding site structure, they raise the possibility of developing analgesics that selectively target inflammation-modulated GlyRs. PMID:23834509

Dosimetric study and in-vivo dose verification for conformal avoidance treatment of anal adenocarcinoma using helical tomotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han Chunhui; Chen Yijen; Liu An

2007-04-01

This study evaluated the efficacy of using helical tomotherapy for conformal avoidance treatment of anal adenocarcinoma. We retrospectively generated step-and-shoot intensity-modulated radiotherapy (sIMRT) plans and helical tomotherapy plans for two anal cancer patients, one male and one female, who were treated by the sIMRT technique. Dose parameters for the planning target volume (PTV) and the organs-at-risk (OARs) were compared between the sIMRT and the helical tomotherapy plans. The helical tomotherapy plans showed better dose homogeneity in the PTV, better dose conformity around the PTV, and, therefore, better sparing of nearby OARs compared with the sIMRT plans. In-vivo skin dose measurementsmore » were performed during conformal avoidance helical tomotherapy treatment of an anal cancer patient to verify adequate delivery of skin dose and sparing of OARs.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Utschig, L. M.; Dalosto, S. D.; Thurnauer, M. C.

Metal ion binding to a surface site on photosynthetic reaction centers (RCs) modulates light-induced electron and proton transfer events in the RC. Whereas many studies have elucidated aspects of metal ion modulation events in Rhodobacter sphaeroides RCs, much less is understood about the surface site in Blastochloris viridis (Blc. viridis) RCs. Interestingly, electron paramagnetic resonance studies revealed two spectroscopically distinct Cu{sup 2+} surface site environments in Blc. viridis RCs. Herein, Cu{sup 2+} has been used to spectroscopically probe the structure of these Cu{sup 2+} site(s) in response to freezing conditions, temperature, and charge separation. One Cu{sup 2+} environment in Blc.more » viridis RCs, termed CuA, exhibits temperature-dependent conformational flexibility. Different conformation states of the CuA{sup 2+} site are trapped when the RC is frozen in the dark either by fast-freeze or slow-freeze procedure. The second Cu{sup 2+} environment, termed CuB, is structurally invariant to different freezing conditions and shows resolved hyperfine coupling to three nitrogen atoms. Cu{sup 2+} is most likely binding at the same location on the RC, but in different coordination environments which may reflect two distinct conformational states of the isolated Blc. viridis RC protein.« less

An imaging genetics approach to understanding social influence

PubMed Central

Falk, Emily B.; Way, Baldwin M.; Jasinska, Agnes J.

2012-01-01

Normative social influences shape nearly every aspect of our lives, yet the biological processes mediating the impact of these social influences on behavior remain incompletely understood. In this Hypothesis, we outline a theoretical framework and an integrative research approach to the study of social influences on the brain and genetic moderators of such effects. First, we review neuroimaging evidence linking social influence and conformity to the brain's reward system. We next review neuroimaging evidence linking social punishment (exclusion) to brain systems involved in the experience of pain, as well as evidence linking exclusion to conformity. We suggest that genetic variants that increase sensitivity to social cues may predispose individuals to be more sensitive to either social rewards or punishments (or potentially both), which in turn increases conformity and susceptibility to normative social influences more broadly. To this end, we review evidence for genetic moderators of neurochemical responses in the brain, and suggest ways in which genes and pharmacology may modulate sensitivity to social influences. We conclude by proposing an integrative imaging genetics approach to the study of brain mediators and genetic modulators of a variety of social influences on human attitudes, beliefs, and actions. PMID:22701416

Dosimetric effect of beam arrangement for intensity-modulated radiation therapy in the treatment of upper thoracic esophageal carcinoma.

PubMed

Fu, Yuchuan; Deng, Min; Zhou, Xiaojuan; Lin, Qiang; Du, Bin; Tian, Xue; Xu, Yong; Wang, Jin; Lu, You; Gong, Youling

2017-01-01

To evaluate the lung sparing in intensity-modulated radiation therapy (IMRT) for patients with upper thoracic esophageal tumors extending inferiorly to the thorax by different beam arrangement. Overall, 15 patient cases with cancer of upper thoracic esophagus were selected for a retrospective treatment-planning study. Intensity-modulated radiation therapy plans using 4, 5, and 7 beams (4B, 5B, and 7B) were developed for each patient by direct machine parameter optimization (DMPO). All plans were evaluated with respect to dose volumes to irradiated targets and normal structures, with statistical comparisons made between 4B with 5B and 7B intensity-modulated radiation therapy plans. Differences among plans were evaluated using a two-tailed Friedman test at a statistical significance of p < 0.05. The maximum dose, average dose, and the conformity index (CI) of planning target volume 1 (PTV1) were similar for 3 plans for each case. No significant difference of coverage for planning target volume 1 and maximum dose for spinal cords were observed among 3 plans in present study (p > 0.05). The average V 5 , V 13 , V 20 , mean lung dose, and generalized equivalent uniform dose (gEUD) for the total lung were significantly lower in 4B-plans than those data in 5B-plans and 7B-plans (p < 0.01). Although the average V 30 for the total lung were significantly higher in 4B-plans than those in 5B-plans and 7B-plans (p < 0.05). In addition, when comparing with the 4B-plans, the conformity/heterogeneity index of the 5B- and 7B-plans were significantly superior (p < 0.05). The 4B-intensity-modulated radiation therapy plan has advantage to address the specialized problem of lung sparing to low- and intermediate-dose exposure in the thorax when dealing with relative long tumors extended inferiorly to the thoracic esophagus for upper esophageal carcinoma with the cost for less conformity. Studies are needed to compare the superiority of volumetric modulated arc therapy with intensity-modulated radiation therapy technique. Copyright © 2017 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.

System on chip module configured for event-driven architecture

DOEpatents

Robbins, Kevin; Brady, Charles E.; Ashlock, Tad A.

2017-10-17

A system on chip (SoC) module is described herein, wherein the SoC modules comprise a processor subsystem and a hardware logic subsystem. The processor subsystem and hardware logic subsystem are in communication with one another, and transmit event messages between one another. The processor subsystem executes software actors, while the hardware logic subsystem includes hardware actors, the software actors and hardware actors conform to an event-driven architecture, such that the software actors receive and generate event messages and the hardware actors receive and generate event messages.

SU-E-T-214: Intensity Modulated Proton Therapy (IMPT) Based On Passively Scattered Protons and Multi-Leaf Collimation: Prototype TPS and Dosimetry Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanchez-Parcerisa, D; Carabe-Fernandez, A

2014-06-01

Purpose. Intensity-modulated proton therapy is usually implemented with multi-field optimization of pencil-beam scanning (PBS) proton fields. However, at the view of the experience with photon-IMRT, proton facilities equipped with double-scattering (DS) delivery and multi-leaf collimation (MLC) could produce highly conformal dose distributions (and possibly eliminate the need for patient-specific compensators) with a clever use of their MLC field shaping, provided that an optimal inverse TPS is developed. Methods. A prototype TPS was developed in MATLAB. The dose calculation process was based on a fluence-dose algorithm on an adaptive divergent grid. A database of dose kernels was precalculated in order tomore » allow for fast variations of the field range and modulation during optimization. The inverse planning process was based on the adaptive simulated annealing approach, with direct aperture optimization of the MLC leaves. A dosimetry study was performed on a phantom formed by three concentrical semicylinders separated by 5 mm, of which the inner-most and outer-most were regarded as organs at risk (OARs), and the middle one as the PTV. We chose a concave target (which is not treatable with conventional DS fields) to show the potential of our technique. The optimizer was configured to minimize the mean dose to the OARs while keeping a good coverage of the target. Results. The plan produced by the prototype TPS achieved a conformity index of 1.34, with the mean doses to the OARs below 78% of the prescribed dose. This Result is hardly achievable with traditional conformal DS technique with compensators, and it compares to what can be obtained with PBS. Conclusion. It is certainly feasible to produce IMPT fields with MLC passive scattering fields. With a fully developed treatment planning system, the produced plans can be superior to traditional DS plans in terms of plan conformity and dose to organs at risk.« less

Applicator-guided volumetric-modulated arc therapy for low-risk endometrial cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cilla, Savino, E-mail: savinocilla@gmail.com; Macchia, Gabriella; Sabatino, Domenico

2013-04-01

The aim of this study was to report the feasibility of volumetric-modulated arc therapy (VMAT) in the postoperative irradiation of the vaginal vault. Moreover, the VMAT technique was compared with 3D conformal radiotherapy (3D-CRT) and fixed-field intensity-modulated radiotherapy (IMRT), in terms of target coverage and organs at risk sparing. The number of monitor units and the delivery time were analyzed to score the treatment efficiency. All plans were verified in a dedicated solid water phantom using a 2D array of ionization chambers. Twelve patients with endometrial carcinoma who underwent radical hystero-adenexectomy and fixed-field IMRT treatments were retrospectively included in thismore » analysis; for each patient, plans were compared in terms of dose-volume histograms, homogeneity index, and conformity indexes. All techniques met the prescription goal for planning target volume coverage, with VMAT showing the highest level of conformity at all dose levels. VMAT resulted in significant reduction of rectal and bladder volumes irradiated at all dose levels compared with 3D-CRT. No significant differences were found with respect to IMRT. Moreover, a significant improvement of the dose conformity was reached by VMAT technique not only at the 95% dose level (0.74 vs. 0.67 and 0.62) but also at 50% and 75% levels of dose prescription. In addition, VMAT plans showed a significant reduction of monitor units by nearly 28% with respect to IMRT, and reduced treatment time from 11 to <3 minutes for a single 6-Gy fraction. In conclusion, VMAT plans can be planned and carried out with high quality and efficiency for the irradiation of vaginal vault alone, providing similar or better sparing of organs at risk to fixed-field IMRT and resulting in the most efficient treatment option. VMAT is currently our standard approach for radiotherapy of low-risk endometrial cancer.« less

Memory, metamemory, and social cues: Between conformity and resistance.

PubMed

Zawadzka, Katarzyna; Krogulska, Aleksandra; Button, Roberta; Higham, Philip A; Hanczakowski, Maciej

2016-02-01

When presented with responses of another person, people incorporate these responses into memory reports: a finding termed memory conformity. Research on memory conformity in recognition reveals that people rely on external social cues to guide their memory responses when their own ability to respond is at chance. In this way, conforming to a reliable source boosts recognition performance but conforming to a random source does not impair it. In the present study we assessed whether people would conform indiscriminately to reliable and unreliable (random) sources when they are given the opportunity to exercise metamemory control over their responding by withholding answers in a recognition test. In Experiments 1 and 2, we found the pattern of memory conformity to reliable and unreliable sources in 2 variants of a free-report recognition test, yet at the same time the provision of external cues did not affect the rate of response withholding. In Experiment 3, we provided participants with initial feedback on their recognition decisions, facilitating the discrimination between the reliable and unreliable source. This led to the reduction of memory conformity to the unreliable source, and at the same time modulated metamemory decisions concerning response withholding: participants displayed metamemory conformity to the reliable source, volunteering more responses in their memory report, and metamemory resistance to the random source, withholding more responses from the memory report. Together, the results show how metamemory decisions dissociate various types of memory conformity and that memory and metamemory decisions can be independent of each other. PsycINFO Database Record (c) 2016 APA, all rights reserved.

Radiation therapy planning with photons and protons for early and advanced breast cancer: an overview

PubMed Central

Weber, Damien C; Ares, Carmen; Lomax, Antony J; Kurtz, John M

2006-01-01

Postoperative radiation therapy substantially decreases local relapse and moderately reduces breast cancer mortality, but can be associated with increased late mortality due to cardiovascular morbidity and secondary malignancies. Sophistication of breast irradiation techniques, including conformal radiotherapy and intensity modulated radiation therapy, has been shown to markedly reduce cardiac and lung irradiation. The delivery of more conformal treatment can also be achieved with particle beam therapy using protons. Protons have superior dose distributional qualities compared to photons, as dose deposition occurs in a modulated narrow zone, called the Bragg peak. As a result, further dose optimization in breast cancer treatment can be reasonably expected with protons. In this review, we outline the potential indications and benefits of breast cancer radiotherapy with protons. Comparative planning studies and preliminary clinical data are detailed and future developments are considered. PMID:16857055

Conformational Switching of a Foldamer in a Multicomponent System by pH-Filtered Selection between Competing Noncovalent Interactions

PubMed Central

2015-01-01

Biomolecular systems are able to respond to their chemical environment through reversible, selective, noncovalent intermolecular interactions. Typically, these interactions induce conformational changes that initiate a signaling cascade, allowing the regulation of biochemical pathways. In this work, we describe an artificial molecular system that mimics this ability to translate selective noncovalent interactions into reversible conformational changes. An achiral but helical foldamer carrying a basic binding site interacts selectively with the most acidic member of a suite of chiral ligands. As a consequence of this noncovalent interaction, a global absolute screw sense preference, detectable by 13C NMR, is induced in the foldamer. Addition of base, or acid, to the mixture of ligands competitively modulates their interaction with the binding site, and reversibly switches the foldamer chain between its left and right-handed conformations. As a result, the foldamer–ligand mixture behaves as a biomimetic chemical system with emergent properties, functioning as a “proton-counting” molecular device capable of providing a tunable, pH-dependent conformational response to its environment. PMID:25915163

Designing dual inhibitors of Mdm2/MdmX: Unexpected coupling of water with gatekeeper Y100/99.

PubMed

Lee, Xiong An; Verma, Chandra; Sim, Adelene Y L

2017-08-01

Mdm2 and MdmX share high structural similarity in their N-terminal domains, yet dual inhibitors are challenging to design due to differences in the conformations of the binding pockets, and notably of the proposed gatekeeper residue, Y100/99. Analysis of crystal structures and molecular dynamics (MD) simulations of complexes of Mdm2 and MdmX resulted in the identification of a water molecule with a long residence time that appears to be modulated by the conformation of Y100/99. These observations lead us to speculate that dual inhibitors either (i) stabilize both Mdm2 and MdmX with Y100/99 in the open conformation typically seen in complexes of Mdm2 with p53, or (ii) the dual inhibitors are agnostic to the conformation of Y100/99. The recently developed potent dual inhibitory stapled peptide Atsp7041 appears to be agnostic to the conformation of the gatekeeper residue. Proteins 2017; 85:1493-1506. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Fluctuations Magnetiques des Gaz D'electrons Bidimensionnels: Application AU Compose Supraconducteur LANTHANE(2-X) Strontium(x) Cuivre OXYGENE(4)

NASA Astrophysics Data System (ADS)

Benard, Pierre

Nous presentons une etude des fluctuations magnetiques de la phase normale de l'oxyde de cuivre supraconducteur La_{2-x}Sr _{x}CuO_4 . Le compose est modelise par le Hamiltonien de Hubbard bidimensionnel avec un terme de saut vers les deuxiemes voisins (modele tt'U). Le modele est etudie en utilisant l'approximation de la GRPA (Generalized Random Phase Approximation) et en incluant les effets de la renormalisation de l'interaction de Hubbard par les diagrammes de Brueckner-Kanamori. Dans l'approche presentee dans ce travail, les maximums du facteur de structure magnetique observes par les experiences de diffusion de neutrons sont associes aux anomalies 2k _{F} de reseau du facteur de structure des gaz d'electrons bidimensionnels sans interaction. Ces anomalies proviennent de la diffusion entre particules situees a des points de la surface de Fermi ou les vitesses de Fermi sont tangentes, et conduisent a des divergences dont la nature depend de la geometrie de la surface de Fermi au voisinage de ces points. Ces resultats sont ensuite appliques au modele tt'U, dont le modele de Hubbard usuel tU est un cas particulier. Dans la majorite des cas, les interactions ne determinent pas la position des maximums du facteur de structure. Le role de l'interaction est d'augmenter l'intensite des structures du facteur de structure magnetique associees a l'instabilite magnetique du systeme. Ces structures sont souvent deja presentes dans la partie imaginaire de la susceptibilite sans interaction. Le rapport d'intensite entre les maximums absolus et les autres structures du facteur de structure magnetique permet de determiner le rapport U_ {rn}/U_{c} qui mesure la proximite d'une instabilite magnetique. Le diagramme de phase est ensuite etudie afin de delimiter la plage de validite de l'approximation. Apres avoir discute des modes collectifs et de l'effet d'une partie imaginaire non-nulle de la self-energie, l'origine de l'echelle d'energie des fluctuations magnetiques est examinee. Il est ensuite demontre que le modele a trois bandes predit les memes resultats pour la position des structures du facteur de structure magnetique que le modele a une bande, dans la limite ou l'hybridation des orbitales des atomes d'oxygene des plans Cu-O_2 et l'amplitude de sauts vers les seconds voisins sont nulles. Il est de plus constate que l'effet de l'hybridation des orbitales des atomes d'oxygene est bien modelise par le terme de saut vers les seconds voisins. Meme si ils decrivent correctement le comportement qualitatif des maximums du facteur de structure magnetique, les modeles a trois bandes et a une bande ne permettent pas d'obtenir une position de ces structures conforme avec les mesures experimentales, si on suppose que la bande est rigide, c'est-a-dire que les parametres du Hamiltonien sont independants de la concentration de strontium. Ceci peut etre cause par la dependance des parametres du Hamiltonien sur la concentration de strontium. Finalement, les resultats sont compares avec les experiences de diffusion de neutrons et les autres theories, en particulier celles de Littlewood et al. (1993) et de Q. Si et al. (1993). La comparaison avec les resultats experimentaux pour le compose de lanthane suggere que le liquide de Fermi possede une surface de Fermi disjointe, et qu'il est situe pres d'une instabilite magnetique incommensurable.

Interactive Computer Graphics for Analysis and Design of Control Systems.

DTIC Science & Technology

1985-12-01

Post-multiplies AMAT by BMAT and stores the 4 result in CMAT. If AMAT and BMAT do not conform, the routine aborts. CALLS: none B-23 -.. v...27 .-. . . . . . . . . . . . . . . . . . -. L- ’. *. .*. .. - MODULE NAME: MADD .SL DESCRIPTION: Adds or subtracts matrices, 0MAT = AMAT + BMAT or 0MAT...AMAT - BMAT . If AMAT and BMAT do not have the same dimensions, the routine aborts. CALLS: none MODULE NAME: MAGLABEL FILE NAME: FRPLT.FOR AUTHOR

Orders and dimensions for sl(2) or sl(3) module categories and boundary conformal field theories on a torus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coquereaux, R.; Schieber, G.; Centro Brasileiro de Pesquisas Fisicas

2007-04-15

After giving a short description, in terms of action of categories, of some of the structures associated with sl(2) and sl(3) boundary conformal field theories on a torus, we provide tables of dimensions describing the semisimple and cosemisimple blocks of the corresponding weak bialgebras (quantum groupoids), tables of quantum dimensions and orders, and tables describing induction-restriction. For reasons of size, the sl(3) tables of induction are only given for theories with self-fusion (existence of a monoidal structure)

Characterizing China's energy consumption with selective economic factors and energy-resource endowment: a spatial econometric approach

NASA Astrophysics Data System (ADS)

Jiang, Lei; Ji, Minhe; Bai, Ling

2015-06-01

Coupled with intricate regional interactions, the provincial disparity of energy-resource endowment and other economic conditions in China have created spatially complex energy consumption patterns that require analyses beyond the traditional ones. To distill the spatial effect out of the resource and economic factors on China's energy consumption, this study recast the traditional econometric model in a spatial context. Several analytic steps were taken to reveal different aspects of the issue. Per capita energy consumption (AVEC) at the provincial level was first mapped to reveal spatial clusters of high energy consumption being located in either well developed or energy resourceful regions. This visual spatial autocorrelation pattern of AVEC was quantitatively tested to confirm its existence among Chinese provinces. A Moran scatterplot was employed to further display a relatively centralized trend occurring in those provinces that had parallel AVEC, revealing a spatial structure with attraction among high-high or low-low regions and repellency among high-low or low-high regions. By a comparison between the ordinary least square (OLS) model and its spatial econometric counterparts, a spatial error model (SEM) was selected to analyze the impact of major economic determinants on AVEC. While the analytic results revealed a significant positive correlation between AVEC and economic development, other determinants showed some intricate influential patterns. The provinces endowed with rich energy reserves were inclined to consume much more energy than those otherwise, whereas changing the economic structure by increasing the proportion of secondary and tertiary industries also tended to consume more energy. Both situations seem to underpin the fact that these provinces were largely trapped in the economies that were supported by technologies of low energy efficiency during the period, while other parts of the country were rapidly modernized by adopting advanced technologies and more efficient industries. On the other hand, institutional change (i.e., marketization) and innovation (i.e., technological progress) exerted positive impacts on AVEC improvement, as always expected in this and other studies. Finally, the model comparison indicated that SEM was capable of separating spatial effect from the error term of OLS, so as to improve goodness-of-fit and the significance level of individual determinants.

Anoplastie périnéale simple pour le traitement des malformations anorectales basses chez l'adulte, à propos de deux cas

PubMed Central

Echchaoui, Abdelmoughit; Benyachou, Malika; Hafidi, Jawad; Fathi, Nahed; Mohammadine, Elhamid; ELmazouz, Samir; Gharib, Nour-eddine; Abbassi, Abdellah

2014-01-01

Les malformations anorectales chez l'adulte sont des anomalies congénitales rares du tube digestif qui prédominent chez le sexe féminin. Notre étude porte sur deux observations de malformation anorectale basses vues et traitées au stade adulte par les 2 équipes (plasticiens et viscéralistes) à l'Hôpital Avicenne à Rabat. Il s'agit d'un homme de 24 ans avec une dyschésie anale l'autre cas est une femme de 18 ans avec une malformation anovulvaire Les caractéristiques cliniques combinées avec les imageries radiologiques (lavement baryté, et la manométrie anorectale) ont confirmé qu'il s'agit d'une malfomation anorectale basse. Les deux cas sont corrigés par une reconstruction sphinctérienne, réimplantation anale avec anoplastie périnéale. Les suites opératoires étaient simples, pas de souffrance cutanée ou nécrose, avec changement de pansement gras chaque jour. Le résultat fonctionnel (la continence) était favorable pour les 2 patients. La présentation des MAR à l’âge adulte est rare, d’étiologie mal connu, elles apparaissent selon le mode sporadique. Les caractéristiques cliniques, couplées à l'imagerie (lavement baryté, IRM pelvienne), l'endoscopie et la manométrie anorectale, permettent de confirmer le diagnostic et classer ces anomalies en 3 types: basses, intermédiaires, et hautes. Les formes basses sont traités d'emblée par une réimplantation anale et anoplastie périnéale simple tels nos deux cas, elles peuvent être traités dans certains cas par un abaissement anorectale associé à une plastie V-Y permettant ainsi un emplacement anatomique correct de l'anus; alors que les formes hautes ou intermédiaires relèvent d'une chirurgie complexe avec souvent une dérivation digestive transitoire. Contrairement aux autres formes, Les formes basses ont un pronostic fonctionnel favorable. PMID:25667689

Energy modulated electron therapy using a few leaf electron collimator in combination with IMRT and 3D-CRT: Monte Carlo-based planning and dosimetric evaluation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Al-Yahya, Khalid; Schwartz, Matthew; Shenouda, George

2005-09-15

Energy modulated electron therapy (EMET) based on Monte Carlo dose calculation is a promising technique that enhances the treatment planning and delivery of superficially located tumors. This study investigated the application of EMET using a novel few-leaf electron collimator (FLEC) in head and neck and breast sites in comparison with three-dimensional conventional radiation therapy (3D-CRT) and intensity modulated radiation therapy (IMRT) techniques. Treatment planning was performed for two parotid cases and one breast case. Four plans were compared for each case: 3D-CRT, IMRT, 3D-CRT in conjunction with EMET (EMET-CRT), and IMRT in conjunction with EMET (EMET-IMRT), all of which weremore » performed and calculated with Monte Carlo techniques. For all patients, dose volume histograms (DVHs) were obtained for all organs of interest and the DVHs were used as a means of comparing the plans. Homogeneity and conformity of dose distributions were calculated, as well as a sparing index that compares the effect of the low isodose lines. In addition, the whole-body dose equivalent (WBDE) was estimated for each plan. Adding EMET delivered with the FLEC to 3D-CRT improves sparing of normal tissues. For the two head and neck cases, the mean dose to the contralateral parotid and brain stem was reduced relative to IMRT by 43% and 84%, and by 57% and 71%, respectively. Improved normal tissue sparing was quantified as an increase in sparing index of 47% and 30% for the head and neck and the breast cases, respectively. Adding EMET to either 3D-CRT or IMRT results in preservation of target conformity and dose homogeneity. When adding EMET to the treatment plan, the WBDE was reduced by between 6% and 19% for 3D-CRT and by between 21% and 33% for IMRT, while WBDE for EMET-CRT was reduced by up to 72% when compared with IMRT. FLEC offers a practical means of delivering modulated electron therapy. Although adding EMET delivered using the FLEC results in perturbation of target conformity when compared to IMRT, it significantly improves normal tissue sparing while offering enhanced target conformity to the 3D-CRT planning. The addition of EMET systematically leads to a reduction in WBDE especially when compared with IMRT.« less

Méningiome en plaque sphéno-orbitaire: à propos d'un cas avec revue de la littérature

PubMed Central

Abdellaoui, Meriem; Andaloussi, Idriss Benatiya; Tahri, Hicham

2015-01-01

Le méningiome intra osseux est une variété des méningiomes ectopiques dans lequel les cellules méningothéliales envahissent la paroi osseuse et entraînent une hyperostose. Le méningiome en plaque, variante macroscopique des méningiomes intra osseux, est une tumeur rare et survient fréquemment au niveau de la région sphéno-orbitaire ce qui le confond avec les tumeurs osseuses primitives. Nous rapportons le cas d'une patiente de 50 ans qui présente une exophtalmie avec cécité unilatérale gauche d'installation progressive depuis un an. L'examen trouve une exophtalmie axile, indolore et non réductible ainsi qu'une limitation de la motilité oculaire dans tous les sens du regard. La palpation montre une masse temporale gauche dure et adhérente à l'os. L'examen du fond d’œil trouve un œdème papillaire gauche. Le scanner montre une lésion ostéocondensante temporo-sphéno-orbitaire gauche avec envahissement locorégional. Le diagnostic préopératoire fut une tumeur osseuse essentiellement maligne primitive ou secondaire. L’étude histologique a révélée un méningiome meningothélial de type en plaque. La patiente a bénéficié d'une exérèse avec reconstruction chirurgicale. Aucune récidive n'a été notée après 1 an de recul. PMID:26327996

Colobome maculaire unilatérale: à propos d’un cas

PubMed Central

El Bahloul, Meriem; Chraïbi, Fouad; Mohammed, Marrakchi; Abdellaoui, Meriem; Benatiya, Idriss

2017-01-01

Le colobome maculaire est une affection congénitale en rapport avec une anomalie de fermeture de la fissure fœtale, pouvant être intégré dans un cadre héréditaire. Il se caractérise cliniquement par une acuité visuelle basse avec une lésion excavée maculaire où le tissu rétinien normal est absent ou rudimentaire et la sclère est ectasique. La tomographie en cohérence optique maculaire est fortement évocatrice du diagnostic et le bilan électrophysiologique s'il est demandé est altéré. Le diagnostic différentiel se pose avec les pathologies entrainant une lésion atrophique et excavée de la macula, particulièrement la toxoplasmose congénitale. PMID:29184607

Intensity-modulated radiation therapy and volumetric-modulated arc therapy for adult craniospinal irradiation—A comparison with traditional techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Studenski, Matthew T., E-mail: matthew.studenski@jeffersonhospital.org; Shen, Xinglei; Yu, Yan

2013-04-01

Craniospinal irradiation (CSI) poses a challenging planning process because of the complex target volume. Traditional 3D conformal CSI does not spare any critical organs, resulting in toxicity in patients. Here the dosimetric advantages of intensity-modulated radiation therapy (IMRT) and volumetric-modulated arc therapy (VMAT) are compared with classic conformal planning in adults for both cranial and spine fields to develop a clinically feasible technique that is both effective and efficient. Ten adult patients treated with CSI were retrospectively identified. For the cranial fields, 5-field IMRT and dual 356° VMAT arcs were compared with opposed lateral 3D conformal radiotherapy (3D-CRT) fields. Formore » the spine fields, traditional posterior-anterior (PA) PA fields were compared with isocentric 5-field IMRT plans and single 200° VMAT arcs. Two adult patients have been treated using this IMRT technique to date and extensive quality assurance, especially for the junction regions, was performed. For the cranial fields, the IMRT technique had the highest planned target volume (PTV) maximum and was the least efficient, whereas the VMAT technique provided the greatest parotid sparing with better efficiency. 3D-CRT provided the most efficient delivery but with the highest parotid dose. For the spine fields, VMAT provided the best PTV coverage but had the highest mean dose to all organs at risk (OAR). 3D-CRT had the highest PTV and OAR maximum doses but was the most efficient. IMRT provides the greatest OAR sparing but the longest delivery time. For those patients with unresectable disease that can benefit from a higher, definitive dose, 3D-CRT–opposed laterals are the most clinically feasible technique for cranial fields and for spine fields. Although inefficient, the IMRT technique is the most clinically feasible because of the increased mean OAR dose with the VMAT technique. Quality assurance of the beams, especially the junction regions, is essential.« less

Single-arc volumetric-modulated arc therapy (sVMAT) as adjuvant treatment for gastric cancer: Dosimetric comparisons with three-dimensional conformal radiotherapy (3D-CRT) and intensity-modulated radiotherapy (IMRT)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xin; Li, Guangjun; Zhang, Yingjie

2013-01-01

To compare the dosimetric differences between the single-arc volumetric-modulated arc therapy (sVMAT), 3-dimensional conformal radiotherapy (3D-CRT), and intensity-modulated radiotherapy (IMRT) techniques in treatment planning for gastric cancer as adjuvant radiotherapy. Twelve patients were retrospectively analyzed. In each patient's case, the parameters were compared based on the dose-volume histogram (DVH) of the sVMAT, 3D-CRT, and IMRT plans, respectively. Three techniques showed similar target dose coverage. The maximum and mean doses of the target were significantly higher in the sVMAT plans than that in 3D-CRT plans and in the 3D-CRT/IMRT plans, respectively, but these differences were clinically acceptable. The IMRT and sVMATmore » plans successfully achieved better target dose conformity, reduced the V{sub 20/30}, and mean dose of the left kidney, as well as the V{sub 20/30} of the liver, compared with the 3D-CRT plans. And the sVMAT technique reduced the V{sub 20} of the liver much significantly. Although the maximum dose of the spinal cord were much higher in the IMRT and sVMAT plans, respectively (mean 36.4 vs 39.5 and 40.6 Gy), these data were still under the constraints. Not much difference was found in the analysis of the parameters of the right kidney, intestine, and heart. The IMRT and sVMAT plans achieved similar dose distribution to the target, but superior to the 3D-CRT plans, in adjuvant radiotherapy for gastric cancer. The sVMAT technique improved the dose sparings of the left kidney and liver, compared with the 3D-CRT technique, but showed few dosimetric advantages over the IMRT technique. Studies are warranted to evaluate the clinical benefits of the VMAT treatment for patients with gastric cancer after surgery in the future.« less

Rapid roll inflation with conformal coupling

NASA Astrophysics Data System (ADS)

Kofman, Lev; Mukohyama, Shinji

2008-02-01

Usual inflation is realized with a slow rolling scalar field minimally coupled to gravity. In contrast, we consider dynamics of a scalar with a flat effective potential, conformally coupled to gravity. Surprisingly, it contains an attractor inflationary solution with the rapidly rolling inflaton field. We discuss models with the conformal inflaton with a flat potential (including hybrid inflation). There is no generation of cosmological fluctuations from the conformally coupled inflaton. We consider realizations of modulated (inhomogeneous reheating) or curvaton cosmological fluctuations in these models. We also implement these unusual features for the popular string-theoretic warped inflationary scenario, based on the interacting D3-D¯3 branes. The original warped brane inflation suffers a large inflaton mass due to conformal coupling to 4-dimensional gravity. Instead of considering this as a problem and trying to cure it with extra engineering, we show that warped inflation with the conformally coupled, rapidly rolling inflaton is yet possible with N=37 efoldings, which requires low-energy scales 1 100 TeV of inflation. Coincidentally, the same warping numerology can be responsible for the hierarchy. It is shown that the scalars associated with angular isometries of the warped geometry of compact manifold (e.g. S3 of Klebanov-Strassler (KS) geometry) have solutions identical to conformally coupled modes and also cannot be responsible for cosmological fluctuations. We discuss other possibilities.

Improving a scissor-action couch for conformal arc radiotherapy and radiosurgery.

PubMed

Li, Kaile; Yu, Cedric X; Ma, Lijun

2004-01-01

We have developed a method to improve the setup accuracy of a Varian Clinac 6/100 couch for delivering conformal arc therapy using a tertiary micro multileaf collimator (MLC) system. Several immobilization devices have been developed to improve the mechanical stability and isocenter alignment of the couch: turn-knob harnesses, double-track alignment plates, and a drop-in rod that attaches the couch to the concrete floor. These add-on components minimize the intercomponent motion of the couch's scissor elevator, which allows consistent treatment setup. The accuracy of our isocenter couch alignment is an improvement over the above devices, within 1 mm of their accuracy. The couch has been used with over 15 patients and with over 50 modulated conformal arc treatment deliveries at our institution.

Simulations of absorption spectra of conjugated oligomers: role of planar conformation and aggregation in condensed phase

NASA Astrophysics Data System (ADS)

Yuan, Xiang-Ai; Wen, Jin; Zheng, Dong; Ma, Jing

2018-04-01

This Review highlights the structure/property relationship underlying the morphology modulation through various factors towards the exploration of light-absorbing materials for efficient utilisation of solar power. Theoretical study using a combination of molecular dynamics imulations and the time-dependent density functional theory demonstrated that the planarity plays an important role in tuning spectral properties of oligomer aggregates. The aggregation-induced blue-shift in absorption spectra of oligothiophenes and the red-shift for oligofluorenols were rationalised in a unified way from the reduced (and increased) content of planar conformations in molecular aggregates. The planarity versus non-planarity of oligomers can be modulated by introduction of alkyl side chain or steric bulky substituents. The substitution with various groups in the ortho-position of azobenzene leads to the distorted backbone, breaking symmetry, and hence the red-shift in spectra, expanding the application in biological systems with visible light absorption. The donor-acceptor substituent groups in conjugated oligomers can increase the degree of planarity, electron delocalisation and polarisation, and charge separation, giving rise to the red-shift in spectra and enhancement in polarisability and charge mobility for device applications. The solvent dependent and pH-sensitive properties and intramolecular hydrogen bonds also caused the shift of absorption spectra with the appearance of planar conformers.

Conformational Flexibility and Subunit Arrangement of the Modular Yeast Spt-Ada-Gcn5 Acetyltransferase Complex*

PubMed Central

Setiaputra, Dheva; Ross, James D.; Lu, Shan; Cheng, Derrick T.; Dong, Meng-Qiu; Yip, Calvin K.

2015-01-01

The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex is a highly conserved, 19-subunit histone acetyltransferase complex that activates transcription through acetylation and deubiquitination of nucleosomal histones in Saccharomyces cerevisiae. Because SAGA has been shown to display conformational variability, we applied gradient fixation to stabilize purified SAGA and systematically analyzed this flexibility using single-particle EM. Our two- and three-dimensional studies show that SAGA adopts three major conformations, and mutations of specific subunits affect the distribution among these. We also located the four functional modules of SAGA using electron microscopy-based labeling and transcriptional activator binding analyses and show that the acetyltransferase module is localized in the most mobile region of the complex. We further comprehensively mapped the subunit interconnectivity of SAGA using cross-linking mass spectrometry, revealing that the Spt and Taf subunits form the structural core of the complex. These results provide the necessary restraints for us to generate a model of the spatial arrangement of all SAGA subunits. According to this model, the chromatin-binding domains of SAGA are all clustered in one face of the complex that is highly flexible. Our results relate information of overall SAGA structure with detailed subunit level interactions, improving our understanding of its architecture and flexibility. PMID:25713136

Quality assurance of intensity-modulated radiation therapy.

PubMed

Palta, Jatinder R; Liu, Chihray; Li, Jonathan G

2008-01-01

The current paradigm for the quality assurance (QA) program for intensity-modulated radiation therapy (IMRT) includes QA of the treatment planning system, QA of the delivery system, and patient-specific QA. Although the IMRT treatment planning and delivery system is the same as for conventional three-dimensional conformal radiation therapy, it has more parameters to coordinate and verify. Because of complex beam intensity modulation, each IMRT field often includes many small irregular off-axis fields, resulting in isodose distributions for each IMRT plan that are more conformal than those from conventional treatment plans. Therefore, these features impose a new and more stringent set of QA requirements for IMRT planning and delivery. The generic test procedures to validate dose calculation and delivery accuracy for both treatment planning and IMRT delivery have to be customized for each type of IMRT planning and delivery strategy. The rationale for such an approach is that the overall accuracy of IMRT delivery is incumbent on the piecewise uncertainties in both the planning and delivery processes. The end user must have well-defined evaluation criteria for each element of the planning and delivery process. Such information can potentially be used to determine a priori the accuracy of IMRT planning and delivery.

Protein–Protein Interactions Modulate the Docking-Dependent E3-Ubiquitin Ligase Activity of Carboxy-Terminus of Hsc70-Interacting Protein (CHIP)*

PubMed Central

Narayan, Vikram; Landré, Vivien; Ning, Jia; Hernychova, Lenka; Muller, Petr; Verma, Chandra; Walkinshaw, Malcolm D.; Blackburn, Elizabeth A.; Ball, Kathryn L.

2015-01-01

CHIP is a tetratricopeptide repeat (TPR) domain protein that functions as an E3-ubiquitin ligase. As well as linking the molecular chaperones to the ubiquitin proteasome system, CHIP also has a docking-dependent mode where it ubiquitinates native substrates, thereby regulating their steady state levels and/or function. Here we explore the effect of Hsp70 on the docking-dependent E3-ligase activity of CHIP. The TPR-domain is revealed as a binding site for allosteric modulators involved in determining CHIP's dynamic conformation and activity. Biochemical, biophysical and modeling evidence demonstrate that Hsp70-binding to the TPR, or Hsp70-mimetic mutations, regulate CHIP-mediated ubiquitination of p53 and IRF-1 through effects on U-box activity and substrate binding. HDX-MS was used to establish that conformational-inhibition-signals extended from the TPR-domain to the U-box. This underscores inter-domain allosteric regulation of CHIP by the core molecular chaperones. Defining the chaperone-associated TPR-domain of CHIP as a manager of inter-domain communication highlights the potential for scaffolding modules to regulate, as well as assemble, complexes that are fundamental to protein homeostatic control. PMID:26330542

Estimation of the genetic correlations between twisted legs and growth or conformation traits in broiler chickens.

PubMed

Bihan-Duval, E L; Beaumont, C; Colleau, J J

1997-01-12

Genetic correlations between two types of leg deformities, valgus and varus angulations, and some growth or conformation traits were estimated in two commercial broiler strains. 14 264 chickens of both sexes in line A were measured for leg defects at 6 weeks and body weight at 3 (BW3) or 6 (BW6) weeks. The same measures were taken in line B on 8 164 chickens, as well as breast angle (BRA) and breast meat yield (BRM) at 6 weeks on 70% of the male birds. The multinomial logit model previously developed for the genetic analysis of valgus and varus deformities was extended to deal with the joint analysis of one unordered categorical trait and one continuous variable. The model assumed a competition between latent susceptibility variates related to the various deformities and linearly dependent on the continuous performances. Location parameters for latent susceptibilities and continuous trait were estimated by the 'Maximum A Posteriori' approach and dispersion parameters by the 'Maximum Marginal Likelihood' using a tilda-hat approximation. The genetic model took into account the effects of the sire, maternal grandsire and dam within maternal grandsire. As described in a previous study, leg deformities showed moderate heritabilities. Mean heritability estimate for both lines, based on the sire/maternal-grandsire (S/MGS) component, was equal to 0.22 for valgus and varus; when based on the dam component, mean estimates were equal to 0.37 and 0.29 for the two deformities respectively. Except for BRA, heritability of growth and conformation traits appeared to be smaller when based on S/MGS component (from 0.18 to 0.47) than on dam component (from 0.41 to 0.63). Very low genetic correlations were found between susceptibilities to leg deformities and growth performances: average estimates for both lines of the genetic correlation with BW3 were -0.03 and -0.05 for valgus and varus respectively. Respective genetic correlations with BW6 were estimated to be +0.05 and +0.01. According to a simulation study these small estimates were unlikely to be due to the negative back effects of severe disorders on growth performances. According to these results, including leg defects in breeding schemes would not delay improvement on growth through unfavourable genetic correlations. Susceptibility to valgus deformity appeared to be genetically independent of conformation traits (genetic correlation was estimated to be -0.06 and -0.08 with BRA and BRM respectively), whereas moderate unfavourable genetic correlations were found for varus (+0.16 and +0.19 with BRA and BRM respectively). Care must be taken when considering the impact of the actual intensive selection for greater conformation on the incidence of varus deformity. RÉSUMÉ: Les corrélations génétiques entre deux types de déformations osseuses, le valgus et le varus, et des caractères de croissance et de conformation ont été estimées dans deux lignées commerciales de poulet de type chair. Dans la lignée "A", 14 264 poulets des deux sexes ont été mesurés pour les problèmes de pattes à 6 semaines, ainsi que pour le poids vif aux âges de 3 et 6 semaines. Ces mêmes mesures ont été faites dans la lignée "B"sur 8 164 poulets; on disposait en plus pour un échantillon des animaux de cette lignée de la mesure de l'angle de poitrine et du rendement en filet à 6 semaines. Des développements du modèle logistique multinomial déjà utilisé pour l'analyse génétique des valgus et varus ont été réalisés pour permettre l'analyse conjointe de plusieurs caractères discrets non ordonnés et d'une variable continue. Le modèle d'analyse fait l'hypothèse d'une compétition entre plusieurs variables sous-jacentes de sensibilité aux déformations, dépendant linéairement de la performance continue. Les paramètres de position pour les sensibilités sous-jacentes et le caractère continu ont été estimés par l'approche bayésienne du "Maximum A Posteriori"et les paramètres de dispersion par une approximation de type tilde-hat du "Maximum de Vraisemblance Marginale". Le modèle génétique d'analyse comprenait les effets des père, grand-père maternel et mère intra grand-père. Comme démontré dans une étude précédente, la sensibilité aux problèmes de patte présente une héritabilité modérée. En moyenne sur les deux lignées, l'estimation obtenue par la voie père/grand-père maternel (P-GPM) est de 0.22 pour les deux déformations et celle pour la voie mère de 0.37 pour le valgus et de 0.29 pour le varus. A l'exception de l'angle de poitrine, l'héritabilité des caractères de croissance et de conformation apparaît largement supérieure par la voie mère (de 0.41 à 0.63) que par la voie P-GPM (de 0.18 à 0.47). Les corrélations génétiques entre les sensibilités aux déformations osseuses et les performances de croissance apparaissent très faibles: la moyenne des estimations de la corrélation avec le poids vif à 3 semaines est de -0.03 pour le valgus et -0.05 pour le varus. Les corrélations avec le poids à 6 semaines sont du même ordre, estimées à respectivement +0.05 et +0.01 pour les valgus et varus. Une étude par simulation a permis de vérifier que ces faibles corrélations n'étaient pas dues à des biais éventuels liés aux effets secondaires négatifs des pathologies sévères sur les performances de croissance. D'après ces rèsultats, la prise en compte en sélection de la sensibilité aux problèmes de pattes n'introdurait pas, par une corrélation génétique défavorable, de réponse indirecte négative sur le poids. Si la sensibilité au valgus apparaît génétiquement indépendante des caractères de conformation (avec des corrélations génétiques avec l'angle de poitrine et le pourcentage de filet estimées à -0.06 et -0.8 respectivement), la liaison génétique apparaît plutôt défavorable pour le varus: +0.16 et +0.19 respectivement avec l'angle et le pourcentage de filet. Ces résultats doivent inciter à surveiller l'impact sur l'incidence des varus des fortes pressions de sélection appliquées actuellement sur les caractères de conformation. ZUSAMMENFASSUNG: Genetische Korrelationen zwischen verbogenen Füßen und Wachstums- und Formmerkmalen in Broilern Genetische Korrelationen zwischen 2 Arten von Beindeformationen, Valgus und Varus Angulationen, und einigen Wachtums- und Formmerkmalen wurden bei zwei kommerziellen Broiler Herkünften geschätzt, 14 264 Hühner beiderlei Geschlechter wurden in Linie A auf Beinfehler bei 6 Wochen Alter und Körpergewicht bei 3 (BW3) und 6 Wochen (BW6) untersucht, in Linie B 8 164 Tiere, wo aber auch Brustwinkel (BRA) und Brustfleisch (BRM) von ca. 70% der Hähne erhoben worden ist. Das für die genetische Analyse von Valgus und Varus Deformationen entwickelte multinomiale logit Modell wurde für die gemeinsame Analyse eines ungeordneten kategorischen Merkmals und einer kontinuierlichen Variablen erweitert. Dieses unterstellt Kompetition zwischen latenter Anfälligkeiten für verschiedene Deformationen und lineare Beziehung zu kontinuierlich verteilter Leistung. Lokationsparameter wurden mittels "Maximum A Posteriori" Ansatz und Dispersionsparameter mittels "Maximum Marginaler Likelihood" unter Verwendung von 'tilde-hat' Approximation geschätzt. Das genetische Modell berücksichtigte Vater-, maternale Großvater- und Muttertier-innerhalb der letzteren-Wirkungen. Beindeformationen zeigen mittlere Heritabilitätswerte, 0.22 für Valgus and Varus aus Vater/maternalem Großvater Komponenten, 0.37 bez. 0.29 aus der Muttertierkomponente. Mit Ausnahme von BRA waren Heritabilitätswerte für Wachstum- und Formmerkmale aus S/MGS-Komponenten (0.18-0.47) kleiner als die aus Muttertierkomponenten (0.41-0.63). Genetische Korrelationen zwischen letzeren und Anfällikeiten waren sehr niedrig: zwischen BW3 und Valgus und Varus -0.03 bzw. -0.05, BW6 +0.05 und 0.01. Simulation zeigte, daß die niedrigen Werte kaum auf negative Rückwirkung der Defekte auf Leistung zurückzuführen sind, sodaß deren Berücksichtigung in der Selektion den Zuchtfortschritt nicht beeinträchtigen sollte. Valgusdeformation scheint genetisch unabhängig von Formmerkmalen zu sein (r(G) -0.06, -0.08 mit BRA und BRM), während Varus mäßig ungünstige Korrelationen zeigt (+0.16, -0.19 mit BRA und BRM), sodaß Selektion auf Bemuskelung dies zu beachten hat. 1997 Blackwell Verlag GmbH.

Non-degradative Ubiquitination of Protein Kinases

PubMed Central

Ball, K. Aurelia; Johnson, Jeffrey R.; Lewinski, Mary K.; Guatelli, John; Verschueren, Erik; Krogan, Nevan J.; Jacobson, Matthew P.

2016-01-01

Growing evidence supports other regulatory roles for protein ubiquitination in addition to serving as a tag for proteasomal degradation. In contrast to other common post-translational modifications, such as phosphorylation, little is known about how non-degradative ubiquitination modulates protein structure, dynamics, and function. Due to the wealth of knowledge concerning protein kinase structure and regulation, we examined kinase ubiquitination using ubiquitin remnant immunoaffinity enrichment and quantitative mass spectrometry to identify ubiquitinated kinases and the sites of ubiquitination in Jurkat and HEK293 cells. We find that, unlike phosphorylation, ubiquitination most commonly occurs in structured domains, and on the kinase domain, ubiquitination is concentrated in regions known to be important for regulating activity. We hypothesized that ubiquitination, like other post-translational modifications, may alter the conformational equilibrium of the modified protein. We chose one human kinase, ZAP-70, to simulate using molecular dynamics with and without a monoubiquitin modification. In Jurkat cells, ZAP-70 is ubiquitinated at several sites that are not sensitive to proteasome inhibition and thus may have other regulatory roles. Our simulations show that ubiquitination influences the conformational ensemble of ZAP-70 in a site-dependent manner. When monoubiquitinated at K377, near the C-helix, the active conformation of the ZAP-70 C-helix is disrupted. In contrast, when monoubiquitinated at K476, near the kinase hinge region, an active-like ZAP-70 C-helix conformation is stabilized. These results lead to testable hypotheses that ubiquitination directly modulates kinase activity, and that ubiquitination is likely to alter structure, dynamics, and function in other protein classes as well. PMID:27253329

Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

PubMed Central

Papaleo, Elena; Renzetti, Giulia; Tiberti, Matteo

2012-01-01

Protein dynamics and the underlying networks of intramolecular interactions and communicating residues within the three-dimensional (3D) structure are known to influence protein function and stability, as well as to modulate conformational changes and allostery. Acylaminoacyl peptidase (AAP) subfamily of enzymes belongs to a unique class of serine proteases, the prolyl oligopeptidase (POP) family, which has not been thoroughly investigated yet. POPs have a characteristic multidomain three-dimensional architecture with the active site at the interface of the C-terminal catalytic domain and a β-propeller domain, whose N-terminal region acts as a bridge to the hydrolase domain. In the present contribution, protein dynamics signatures of a hyperthermophilic acylaminoacyl peptidase (AAP) of the prolyl oligopeptidase (POP) family, as well as of a deletion variant and alanine mutants (I12A, V13A, V16A, L19A, I20A) are reported. In particular, we aimed at identifying crucial residues for long range communications to the catalytic site or promoting the conformational changes to switch from closed to open ApAAP conformations. Our investigation shows that the N-terminal α1-helix mediates structural intramolecular communication to the catalytic site, concurring to the maintenance of a proper functional architecture of the catalytic triad. Main determinants of the effects induced by α1-helix are a subset of hydrophobic residues (V16, L19 and I20). Moreover, a subset of residues characterized by relevant interaction networks or coupled motions have been identified, which are likely to modulate the conformational properties at the interdomain interface. PMID:22558199

A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors

NASA Astrophysics Data System (ADS)

Ortega, Davi R.; Yang, Chen; Ames, Peter; Baudry, Jerome; Parkinson, John S.; Zhulin, Igor B.

2013-12-01

Bacterial chemoreceptors are widely used as a model system for elucidating the molecular mechanisms of transmembrane signalling and have provided a detailed understanding of how ligand binding by the receptor modulates the activity of its associated kinase CheA. However, the mechanisms by which conformational signals move between signalling elements within a receptor dimer and how they control kinase activity remain unknown. Here, using long molecular dynamics simulations, we show that the kinase-activating cytoplasmic tip of the chemoreceptor fluctuates between two stable conformations in a signal-dependent manner. A highly conserved residue, Phe396, appears to serve as the conformational switch, because flipping of the stacked aromatic rings of an interacting F396-F396‧ pair in the receptor homodimer takes place concomitantly with the signal-related conformational changes. We suggest that interacting aromatic residues, which are common stabilizers of protein tertiary structure, might serve as rotameric molecular switches in other biological processes as well.

Dehydrated DNA in B-form: ionic liquids in rescue

PubMed Central

Ghoshdastidar, Debostuti; Senapati, Sanjib

2018-01-01

Abstract The functional B-conformation of DNA succumbs to the A-form at low water activity. Methods for room temperature DNA storage that rely upon ‘anhydrobiosis’, thus, often encounter the loss of DNA activity due to the B→A-DNA transition. Here, we show that ionic liquids, an emerging class of green solvents, can induce conformational transitions in DNA and even rescue the dehydrated DNA in the functional B-form. CD spectroscopic analyses not only reveal rapid transition of A-DNA in 78% ethanol medium to B-conformation in presence of ILs, but also the high resistance of IL-bound B-form to transit to A-DNA under dehydration. Molecular dynamics simulations show the unique ability of ILs to disrupt Na+ ion condensation and form ‘IL spine’ in DNA minor groove to drive the A→B transition. Implications of these findings range from the plausible use of ILs as novel anhydrobiotic DNA storage medium to a switch for modulating DNA conformational transitions. PMID:29669113

Evidence of conformational exchange averaging in the thermal rotational spectrum of ethyl cyanoformate.

PubMed

True, Nancy S

2006-06-15

The Stark modulated low resolution microwave spectrum of ethyl cyanoformate between 21.5 and 24.0 GHz at 210, 300, and 358 K, which shows the J + 1 <-- J = 8 <-- 7 bands of three species, is compared to simulations based on electronic structure calculations at the MP2/6-311++G theory level. Calculations at this theory level reproduce the relative energies of the syn-anti and syn-gauche conformers, obtained in a previous study, and indicate that the barrier to conformer exchange is approximately 360 cm(-1) higher in energy than the syn-anti minimum. Simulated spectra of the eigenstates of the calculated O-ethyl torsional potential function reproduce the relative intensities and shapes of the lower and higher frequency bands which correspond to transitions of the syn-anti and syn-gauche conformers, respectively, but fail to reproduce the intense center band in the experimental spectra. A model incorporating exchange averaging reproduces the intensity of the center band and its temperature dependence. These simulations indicate that a large fraction of the thermal population at all three temperatures undergoes conformational exchange with an average energy specific rate constant, , of approximately 25 GHz. This model can explain anomalies present in rotational spectra of many other compounds composed of mixtures of conformers.

Potential for Improved Intelligence Quotient Using Volumetric Modulated Arc Therapy Compared With Conventional 3-Dimensional Conformal Radiation for Whole-Ventricular Radiation in Children

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qi, X. Sharon, E-mail: xqi@mednet.ucla.edu; Department of Radiation Oncology, University of Colorado Denver, Aurora, Colorado; Stinauer, Michelle

Purpose: To compare volumetric modulated arc therapy (VMAT) with 3-dimensional conformal radiation therapy (3D-CRT) in the treatment of localized intracranial germinoma. We modeled the effect of the dosimetric differences on intelligence quotient (IQ). Method and Materials: Ten children with intracranial germinomas were used for planning. The prescription doses were 23.4 Gy to the ventricles followed by 21.6 Gy to the tumor located in the pineal region. For each child, a 3D-CRT and full arc VMAT was generated. Coverage of the target was assessed by computing a conformity index and heterogeneity index. We also generated VMAT plans with explicit temporal lobemore » sparing and with smaller ventricular margin expansions. Mean dose to the temporal lobe was used to estimate IQ 5 years after completion of radiation, using a patient age of 10 years. Results: Compared with the 3D-CRT plan, VMAT improved conformality (conformity index 1.10 vs 1.85), with slightly higher heterogeneity (heterogeneity index 1.09 vs 1.06). The averaged mean doses for left and right temporal lobes were 31.3 and 31.7 Gy, respectively, for VMAT plans and 37.7 and 37.6 Gy for 3D-CRT plans. This difference in mean temporal lobe dose resulted in an estimated IQ difference of 3.1 points at 5 years after radiation therapy. When the temporal lobes were explicitly included in the VMAT optimization, the mean temporal lobe dose was reduced 5.6-5.7 Gy, resulting in an estimated IQ difference of an additional 3 points. Reducing the ventricular margin from 1.5 cm to 0.5 cm decreased mean temporal lobe dose 11.4-13.1 Gy, corresponding to an estimated increase in IQ of 7 points. Conclusion: For treatment of children with intracranial pure germinomas, VMAT compared with 3D-CRT provides increased conformality and reduces doses to normal tissue. This may result in improvements in IQ in these children.« less

Dosimetric comparison between proton beam therapy and photon radiation therapy for locally advanced non-small cell lung cancer.

PubMed

Wu, Chen-Ta; Motegi, Atsushi; Motegi, Kana; Hotta, Kenji; Kohno, Ryosuke; Tachibana, Hidenobu; Kumagai, Motoki; Nakamura, Naoki; Hojo, Hidehiro; Niho, Seiji; Goto, Koichi; Akimoto, Tetsuo

2016-08-10

To assess the feasibility of proton beam therapy for the patients with locally advanced non-small lung cancer. The dosimetry was analyzed retrospectively to calculate the doses to organs at risk, such as the lung, heart, esophagus and spinal cord. A dosimetric comparison between proton beam therapy and dummy photon radiotherapy (three-dimensional conformal radiotherapy) plans was performed. Dummy intensity-modulated radiotherapy plans were also generated for the patients for whom curative three-dimensional conformal radiotherapy plans could not be generated. Overall, 33 patients with stage III non-small cell lung cancer were treated with proton beam therapy between December 2011 and August 2014. The median age of the eligible patients was 67 years (range: 44-87 years). All the patients were treated with chemotherapy consisting of cisplatin/vinorelbine or carboplatin. The median prescribed dose was 60 GyE (range: 60-66 GyE). The mean normal lung V20 GyE was 23.6% (range: 14.9-32%), and the mean normal lung dose was 11.9 GyE (range: 6.0-19 GyE). The mean esophageal V50 GyE was 25.5% (range: 0.01-63.6%), the mean heart V40 GyE was 13.4% (range: 1.4-29.3%) and the mean maximum spinal cord dose was 40.7 GyE (range: 22.9-48 GyE). Based on dummy three-dimensional conformal radiotherapy planning, 12 patients were regarded as not being suitable for radical thoracic three-dimensional conformal radiotherapy. All the dose parameters of proton beam therapy, except for the esophageal dose, were lower than those for the dummy three-dimensional conformal radiotherapy plans. In comparison to the intensity-modulated radiotherapy plan, proton beam therapy also achieved dose reduction in the normal lung. None of the patients experienced grade 4 or worse non-hematological toxicities. Proton beam therapy for patients with stage III non-small cell lung cancer was feasible and was superior to three-dimensional conformal radiotherapy for several dosimetric parameters. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A Multi-institutional Clinical Trial of Rectal Dose Reduction via Injected Polyethylene-Glycol Hydrogel During Intensity Modulated Radiation Therapy for Prostate Cancer: Analysis of Dosimetric Outcomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Danny Y., E-mail: dsong2@jhmi.edu; Herfarth, Klaus K.; Uhl, Matthias

2013-09-01

Purpose: To characterize the effect of a prostate-rectum spacer on dose to rectum during external beam radiation therapy for prostate cancer and to assess for factors correlated with rectal dose reduction. Methods and Materials: Fifty-two patients at 4 institutions were enrolled into a prospective pilot clinical trial. Patients underwent baseline scans and then were injected with perirectal spacing hydrogel and rescanned. Intensity modulated radiation therapy plans were created on both scans for comparison. The objectives were to establish rates of creation of ≥7.5 mm of prostate-rectal separation, and decrease in rectal V70 of ≥25%. Multiple regression analysis was performed tomore » evaluate the associations between preinjection and postinjection changes in rectal V70 and changes in plan conformity, rectal volume, bladder volume, bladder V70, planning target volume (PTV), and postinjection midgland separation, gel volume, gel thickness, length of PTV/gel contact, and gel left-to-right symmetry. Results: Hydrogel resulted in ≥7.5-mm prostate-rectal separation in 95.8% of patients; 95.7% had decreased rectal V70 of ≥25%, with a mean reduction of 8.0 Gy. There were no significant differences in preinjection and postinjection prostate, PTV, rectal, and bladder volumes. Plan conformities were significantly different before versus after injection (P=.02); plans with worse conformity indexes after injection compared with before injection (n=13) still had improvements in rectal V70. In multiple regression analysis, greater postinjection reduction in V70 was associated with decreased relative postinjection plan conformity (P=.01). Reductions in V70 did not significantly vary by institution, despite significant interinstitutional variations in plan conformity. There were no significant relationships between reduction in V70 and the other characteristics analyzed. Conclusions: Injection of hydrogel into the prostate-rectal interface resulted in dose reductions to rectum for >90% of patients treated. Rectal sparing was statistically significant across a range of 10 to 75 Gy and was demonstrated within the presence of significant interinstitutional variability in plan conformity, target definitions, and injection results.« less

Computational Study on the Different Ligands Induced Conformation Change of β2 Adrenergic Receptor-Gs Protein Complex

PubMed Central

Bai, Qifeng; Zhang, Yang; Ban, Yihe; Liu, Huanxiang; Yao, Xiaojun

2013-01-01

β2 adrenergic receptor (β2AR) regulated many key physiological processes by activation of a heterotrimeric GTP binding protein (Gs protein). This process could be modulated by different types of ligands. But the details about this modulation process were still not depicted. Here, we performed molecular dynamics (MD) simulations on the structures of β2AR-Gs protein in complex with different types of ligands. The simulation results demonstrated that the agonist BI-167107 could form hydrogen bonds with Ser2035.42, Ser2075.46 and Asn2936.55 more than the inverse agonist ICI 118,551. The different binding modes of ligands further affected the conformation of β2AR. The energy landscape profiled the energy contour map of the stable and dissociated conformation of Gαs and Gβγ when different types of ligands bound to β2AR. It also showed the minimum energy pathway about the conformational change of Gαs and Gβγ along the reaction coordinates. By using interactive essential dynamics analysis, we found that Gαs and Gβγ domain of Gs protein had the tendency to separate when the inverse agonist ICI 118,551 bound to β2AR. The α5-helix had a relatively quick movement with respect to transmembrane segments of β2AR when the inverse agonist ICI 118,551 bound to β2AR. Besides, the analysis of the centroid distance of Gαs and Gβγ showed that the Gαs was separated from Gβγ during the MD simulations. Our results not only could provide details about the different types of ligands that induced conformational change of β2AR and Gs protein, but also supplied more information for different efficacies of drug design of β2AR. PMID:23922653

Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li+, Na+, K+ and Rb+ via Water-Mediated Hydrogen Bonding

PubMed Central

Savelyev, Alexey; MacKerell, Alexander D.

2015-01-01

Recently, we reported the differential impact of the monovalent cations Li+, Na+, K+ and Rb+ on DNA conformational properties. These were identified from variations in the calculated solution-state X-ray DNA spectra as a function of the ion type in the solvation buffer in MD simulations using our recently developed polarizable force field based on the classical Drude oscillator. Changes in the DNA structure were found to mainly involve variations in the minor groove width. Because minor groove dimensions vary significantly in protein-DNA complexes and have been shown to play a critical role in both specific and nonspecific DNA readout, understanding the origins of the observed differential DNA modulation by the first-group monovalent ions is of great biological importance. In the present study we show that the primary microscopic mechanism for the phenomenon is the formation of the water-mediated hydrogen bonds between solvated cations located inside the minor groove and simultaneously to two DNA strands, a process whose intensity and impact on DNA structure depends on both the type of the ion and DNA sequence. Additionally, it is shown that formation of such ion-DNA hydrogen bond complexes appreciably modulates the conformation of the backbone by increasing the population of the BII substate. Notably, the differential impact of the ions on DNA conformational behavior is only predicted by the Drude polarizable model for DNA, with virtually no effect observed from MD simulations utilizing the additive CHARMM36 model. Analysis of dipole moments of the water shows the Drude SWM4 model to possess high sensitivity to changes in the local environment, which indicates the important role of electronic polarization in the salt-dependent conformational properties. This also suggests that inclusion of polarization effects is required to model even relatively simple biological systems such as DNA in various ionic solutions. PMID:26575937

Allostery Mediates Ligand Binding to WWOX Tumor Suppressor via a Conformational Switch

PubMed Central

Schuchardt, Brett J.; Mikles, David C.; Bhat, Vikas; McDonald, Caleb B.; Sudol, Marius; Farooq, Amjad

2014-01-01

While being devoid of the ability to recognize ligands itself, the WW2 domain is believed to aid ligand binding to WW1 domain in the context of WW1-WW2 tandem module of WWOX tumor suppressor. In an effort to test the generality of this hypothesis, we have undertaken here a detailed biophysical analysis of the binding of WW domains of WWOX alone and in the context of WW1-WW2 tandem module to an array of putative PPXY ligands. Our data show that while the WW1 domain of WWOX binds to all ligands in a physiologically-relevant manner, the WW2 domain does not. Moreover, ligand binding to WW1 domain in the context of WW1-WW2 tandem module is two-to-three-fold stronger than when treated alone. We also provide evidence that the WW domains within the WW1-WW2 tandem module physically associate so as to adopt a fixed spatial orientation relative to each other. Of particular note is the observation that the physical association of WW2 domain with WW1 blocks access to ligand. Consequently, ligand binding to WW1 domain not only results in the displacement of WW2 lid but also disrupts the physical association of WW domains in the liganded conformation. Taken together, our study underscores a key role of allosteric communication in the ability of WW2 orphan domain to chaperone physiological action of WW1 domain within the context of the WW1-WW2 tandem module of WWOX. PMID:25703206

Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels*♦

PubMed Central

VanSchouwen, Bryan; Akimoto, Madoka; Sayadi, Maryam; Fogolari, Federico; Melacini, Giuseppe

2015-01-01

The hyperpolarization-activated cyclic nucleotide-modulated (HCN) ion channels control rhythmicity in neurons and cardiomyocytes. Cyclic AMP allosterically modulates HCN through the cAMP-dependent formation of a tetrameric gating ring spanning the intracellular region (IR) of HCN, to which cAMP binds. Although the apo versus holo conformational changes of the cAMP-binding domain (CBD) have been previously mapped, only limited information is currently available on the HCN IR dynamics, which have been hypothesized to play a critical role in the cAMP-dependent gating of HCN. Here, using molecular dynamics simulations validated and complemented by experimental NMR and CD data, we comparatively analyze HCN IR dynamics in the four states of the thermodynamic cycle arising from the coupling between cAMP binding and tetramerization equilibria. This extensive set of molecular dynamics trajectories captures the active-to-inactive transition that had remained elusive for other CBDs, and it provides unprecedented insight on the role of IR dynamics in HCN autoinhibition and its release by cAMP. Specifically, the IR tetramerization domain becomes more flexible in the monomeric states, removing steric clashes that the apo-CDB structure would otherwise impose. Furthermore, the simulations reveal that the active/inactive structural transition for the apo-monomeric CBD occurs through a manifold of pathways that are more divergent than previously anticipated. Upon cAMP binding, these pathways become disallowed, pre-confining the CBD conformational ensemble to a tetramer-compatible state. This conformational confinement primes the IR for tetramerization and thus provides a model of how cAMP controls HCN channel gating. PMID:25944904

Advances in radiotherapy techniques and delivery for non-small cell lung cancer: benefits of intensity-modulated radiation therapy, proton therapy, and stereotactic body radiation therapy

PubMed Central

Diwanji, Tejan P.; Mohindra, Pranshu; Vyfhuis, Melissa; Snider, James W.; Kalavagunta, Chaitanya; Mossahebi, Sina; Yu, Jen; Feigenberg, Steven

2017-01-01

The 21st century has seen several paradigm shifts in the treatment of non-small cell lung cancer (NSCLC) in early-stage inoperable disease, definitive locally advanced disease, and the postoperative setting. A key driver in improvement of local disease control has been the significant evolution of radiation therapy techniques in the last three decades, allowing for delivery of definitive radiation doses while limiting exposure of normal tissues. For patients with locally-advanced NSCLC, the advent of volumetric imaging techniques has allowed a shift from 2-dimensional approaches to 3-dimensional conformal radiation therapy (3DCRT). The next generation of 3DCRT, intensity-modulated radiation therapy and volumetric-modulated arc therapy (VMAT), have enabled even more conformal radiation delivery. Clinical evidence has shown that this can improve the quality of life for patients undergoing definitive management of lung cancer. In the early-stage setting, conventional fractionation led to poor outcomes. Evaluation of altered dose fractionation with the previously noted technology advances led to advent of stereotactic body radiation therapy (SBRT). This technique has dramatically improved local control and expanded treatment options for inoperable, early-stage patients. The recent development of proton therapy has opened new avenues for improving conformity and the therapeutic ratio. Evolution of newer proton therapy techniques, such as pencil-beam scanning (PBS), could improve tolerability and possibly allow reexamination of dose escalation. These new progresses, along with significant advances in systemic therapies, have improved survival for lung cancer patients across the spectrum of non-metastatic disease. They have also brought to light new challenges and avenues for further research and improvement. PMID:28529896

Effects of proline cis-trans isomerization on TB domain secondary structure.

PubMed Central

Yuan, X.; Werner, J. M.; Knott, V.; Handford, P. A.; Campbell, I. D.; Downing, K.

1998-01-01

The transforming growth factor beta (TGF-beta) binding protein-like (TB) domain is found principally in proteins localized to extracellular matrix fibrils, including human fibrillin-1, the defective protein in the Marfan syndrome. Analysis of the nuclear magnetic resonance (NMR) data for the sixth TB module from human fibrillin-1 has revealed the existence of two stable conformers that differ in the isomerization states of two proline residues. Unusually, the two isoforms do not readily interconvert and are stable on the time scale of milliseconds. We have computed independent structures of the major and minor conformers of TB6 to assess how the domain fold adjusts to incorporate alternatively cis- or trans-prolines. Based on previous observations, it has been suggested that multiple conformers can only be accommodated in flexible regions of protein structure. In contrast, P22, which exists in trans in the major form and cis in the minor form of TB6, is in a rigid region of the domain, which is confirmed by backbone dynamics measurements. Overall, the structures of the major and minor conformers are similar. However, the secondary structure topologies of the two forms differ as a direct consequence of the changes in proline conformation. PMID:9792099

[Compounds modulating parathyroid hormone (PTH) secretion].

PubMed

Nagano, N; Iijima, H

2001-08-01

The control of parathyroid hormone (PTH) secretion is strictly regulated by the parathyroid Ca receptor (CaR). Calcimimetics and calcilytics selectively act on the parathyroid CaR to inhibit and enhance PTH secretion, respectively. According to the recent pharmacological two-state model, calcimimetics act on the CaR as allosteric agonists to stabilize an active conformation of CaR. Conversely, calcilytics act on the CaR as allosteric inverse agonists to stabilize an inactive conformation of CaR. These compounds that can alter circulating levels of PTH and bone turnover might provide novel treatments for adynamic bone disease in patients with chronic renal failure.

Detection de la fin de la compaction des anodes par le son

NASA Astrophysics Data System (ADS)

Sanogo, Bazoumana

L'objectif de ce projet etait de developper un outil de controle en temps reel du temps de compaction en se servant du son genere par le vibrocompacteur pendant le formage des anodes crues. Ainsi, une application a ete developpee pour l'analyse des sons enregistres. Des essais ont ete realises avec differents microphones pour une meilleure qualite des mesures et un a ete choisi pour la suite du projet. De meme, differents tests ont ete realises sur des anodes de laboratoire ainsi que des anodes a l'echelle industrielle afin de mettre en place une methode pour la detection du temps optimal necessaire au formage des anodes. Les travaux au laboratoire de carbone a l'Universite du Quebec a Chicoutimi (UQAC) ont consiste a l'enregistrement de son des anodes fabriquees sur place avec differentes configurations; et a la caracterisation de certaines anodes de l'usine. Les anodes fabriquees au laboratoire sont reparties en deux groupes. Le premier regroupe les anodes pour la validation de notre methode. Ce sont des anodes produites avec des temps de compaction differents. Le laboratoire de carbone a l'UQAC est unique et il est possible de produire des anodes avec les memes proprietes que celles des anodes industrielles. Par consequent, la validation initialement prevue a l'usine a ete effectuee avec les anodes de laboratoire. Le deuxieme groupe a servi a etudier les effets des matieres premieres sur le temps de compaction. Le type de coke et le type de brai ont constitue les differentes variations dans ce deuxieme groupe. Quant aux tests et mesures a l'usine, ils ont ete realises en trois campagnes de mesure. La premiere campagne en juin 2014 a servi a standardiser et a trouver le meilleur positionnement des appareils pour les mesures, a regler le logiciel et a faire les premieres mesures. Une deuxieme campagne en mai 2015 a fait l'objet d'enregistrement de son en classant les anodes selon differents temps de compaction. La troisieme et derniere campagne en decembre 2015 a ete le lieu de tests finaux a l'usine en fabriquant des anodes avec differents criteres (variation du temps de compaction, taux de brai, arret manuel du compacteur, variation de la pression des ballons du haut du compacteur). Ces anodes ont ete ensuite analysees au laboratoire a l'UQAC. En parallele a ces travaux precites, l'amelioration de l'application d'analyse du son a ete faite avec le choix des parametres d'analyse et leur standardisation. Les resultats des premiers tests au laboratoire et ceux de la campagne de juin 2014 ont montre que la formation des anodes se fait suivant trois etapes : rearrangement des particules et du brai, compaction et consolidation et enfin la finition. Ces travaux ont montre en outre que le temps de compaction joue un role tres important dans la definition des proprietes finales des anodes. Ainsi, en plus du type de brai, du taux de brai et du type de coke, il faut tenir compte du temps de sur-compaction et de sous-compaction. En effet, ceci a ete demontre a travers les deux validations qui ont ete realisees. Les resultats de la caracterisation des echantillons (venant des anodes de la campagne de decembre 2015) ont montre qu'une anode compactee a un temps optimal acquiert une bonne resistance a la compression et sa resistivite electrique baisse. En outre, on note que le temps de compaction dans notre cas a baisse legerement avec l'augmentation de la pression des ballons de haut du vibrocompacteur. Ce qui a eu pour effet d'augmenter la densite crue de l'anode. Toutefois, il faut s'abstenir de generaliser ce constat car le nombre d'anodes testees est faible dans notre cas. Par ailleurs, cette etude montre que le temps necessaire pour le formage d'une anode croit avec l'augmentation du taux de brai et baisse legerement avec l'augmentation de la pression des ballons. (Abstract shortened by ProQuest.).

Investigation of proposed process sequence for the array automated assembly task, phases 1 and 2

NASA Technical Reports Server (NTRS)

Mardesich, N.; Garcia, A.; Eskenas, K.

1980-01-01

Progress was made on the process sequence for module fabrication. A shift from bonding with a conformal coating to laminating with ethylene vinyl acetate and a glass superstrate is recommended for further module fabrication. The processes that were retained for the selected process sequence, spin-on diffusion, print and fire aluminum p+ back, clean, print and fire silver front contact and apply tin pad to aluminum back, were evaluated for their cost contribution.

Katanin spiral and ring structures shed light on power stroke for microtubule severing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zehr, Elena; Szyk, Agnieszka; Piszczek, Grzegorz

Microtubule-severing enzymes katanin, spastin and fidgetin are AAA ATPases critical for the biogenesis and maintenance of complex microtubule arrays in axons, spindles and cilia. Because of a lack of 3D structures, their mechanism has remained poorly understood. We report the first X-ray structure of the monomeric AAA katanin module and cryo-EM reconstructions of the hexamer in two conformations. These reveal an unexpected asymmetric arrangement of the AAA domains mediated by structural elements unique to severing enzymes and critical for their function. Our reconstructions show that katanin cycles between open spiral and closed ring conformations, depending on the ATP occupancy ofmore » a gating protomer that tenses or relaxes inter-protomer interfaces. Cycling of the hexamer between these conformations would provide the power stroke for microtubule severing.« less

A key agonist-induced conformational change in the cannabinoid receptor CB1 is blocked by the allosteric ligand Org 27569.

PubMed

Fay, Jonathan F; Farrens, David L

2012-09-28

Allosteric ligands that modulate how G protein-coupled receptors respond to traditional orthosteric drugs are an exciting and rapidly expanding field of pharmacology. An allosteric ligand for the cannabinoid receptor CB1, Org 27569, exhibits an intriguing effect; it increases agonist binding, yet blocks agonist-induced CB1 signaling. Here we explored the mechanism behind this behavior, using a site-directed fluorescence labeling approach. Our results show that Org 27569 blocks conformational changes in CB1 that accompany G protein binding and/or activation, and thus inhibit formation of a fully active CB1 structure. The underlying mechanism behind this behavior is that simultaneous binding of Org 27569 produces a unique agonist-bound conformation, one that may resemble an intermediate structure formed on the pathway to full receptor activation.

The Microwave Spectroscopy Study of 1,2-DIMETHOXYETHANE

NASA Astrophysics Data System (ADS)

Li, Weixing; Vigorito, Annalisa; Calabrese, Camilla; Evangelisti, Luca; Favero, Laura B.; Maris, Assimo; Melandri, Sonia

2017-06-01

With Pulsed-Jet Fourier Transform MicroWave (PJ-FTMW) spectroscopy and Stark modulated Free Jet Millimeter-Wave absorption (FJ-AMMW) spectroscopy, the rotational spectra of two conformers of 1,2-Dimethoxyethane were identified and characterized. Besides the normal species, the spectra of all the mono-substituted ^{13}C isotopologues in natural abundance were also measured. By fitting the rotational transitions split by the methyl internal rotations using both XIAM and ERHAM programs, the spectroscopic parameters were obtained and compared. The rotational constants indicated the conformers to be TGT and TGG', respectively. With the rotational constants of the normal and ^{13}C species, the coordinates of the substituted carbon atoms could be calculated with Kraitchmann's equations. The carbon-frameworks further confirmed the assignment of the two conformations. The V_{3} barriers of the two methyl groups' internal rotations were also experimentally determined.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kole, Thomas P.; Aghayere, Osarhieme; Kwah, Jason

Purpose: To compare heart and coronary artery radiation exposure using intensity-modulated radiotherapy (IMRT) vs. four-field three-dimensional conformal radiotherapy (3D-CRT) treatment plans for patients with distal esophageal cancer undergoing chemoradiation. Methods and Materials: Nineteen patients with distal esophageal cancers treated with IMRT from March 2007 to May 2008 were identified. All patients were treated to 50.4 Gy with five-field IMRT plans. Theoretical 3D-CRT plans with four-field beam arrangements were generated. Dose-volume histograms of the planning target volume, heart, right coronary artery, left coronary artery, and other critical normal tissues were compared between the IMRT and 3D-CRT plans, and selected parameters weremore » statistically evaluated using the Wilcoxon rank-sum test. Results: Intensity-modulated radiotherapy treatment planning showed significant reduction (p < 0.05) in heart dose over 3D-CRT as assessed by average mean dose (22.9 vs. 28.2 Gy) and V30 (24.8% vs. 61.0%). There was also significant sparing of the right coronary artery (average mean dose, 23.8 Gy vs. 35.5 Gy), whereas the left coronary artery showed no significant improvement (mean dose, 11.2 Gy vs. 9.2 Gy), p = 0.11. There was no significant difference in percentage of total lung volume receiving at least 10, 15, or 20 Gy or in the mean lung dose between the planning methods. There were also no significant differences observed for the kidneys, liver, stomach, or spinal cord. Intensity-modulated radiotherapy achieved a significant improvement in target conformity as measured by the conformality index (ratio of total volume receiving 95% of prescription dose to planning target volume receiving 95% of prescription dose), with the mean conformality index reduced from 1.56 to 1.30 using IMRT. Conclusions: Treatment of patients with distal esophageal cancer using IMRT significantly decreases the exposure of the heart and right coronary artery when compared with 3D-CRT. Long-term studies are necessary to determine how this will impact on development of coronary artery disease and other cardiac complications.« less

Amyloid fibril formation of peptides derived from the C-terminus of CETP modulated by lipids

DOE Office of Scientific and Technical Information (OSTI.GOV)

García-González, Victor; Mas-Oliva, Jaime, E-mail: jmas@ifc.unam.mx; División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 México, DF

2013-04-26

Highlights: •The secondary structure of a C-terminal peptide derived from CETP was studied. •Lipids modulate secondary structure changes of a C-terminal peptide derived from CETP. •Lysophosphatidic acid maintains a functional α-helix and prevents fibril formation. •Transfer of lipids by CETP is related to the presence of an α-helix at its C-end. -- Abstract: Cholesteryl-ester transfer protein (CETP) is a plasmatic protein involved in neutral lipid transfer between lipoproteins. Focusing on the last 12 C-terminus residues we have previously shown that mutation D{sub 470}N promotes a conformational change towards a β-secondary structure. In turn, this modification leads to the formation ofmore » oligomers and fibrillar structures, which cause cytotoxic effects similar to the ones provoked by amyloid peptides. In this study, we evaluated the role of specific lipid arrangements on the structure of peptide helix-Z (D{sub 470}N) through the use of thioflavin T fluorescence, peptide bond absorbance, circular dichroism and electron microscopy. The results indicate that the use of micelles formed with lysophosphatidylcholine and lysophosphatidic acid (LPA) under neutral pH induce a conformational transition of peptide helix-Z containing a β-sheet conformation to a native α-helix structure, therefore avoiding the formation of amyloid fibrils. In contrast, incubation with phosphatidic acid does not change the profile for the β-sheet conformation. When the electrostatic charge at the surface of micelles or vesicles is regulated through the use of lipids such as phospholipid and LPA, minimal changes and the presence of β-structures were recorded. Mixtures with a positive net charge diminished the percentage of β-structure and the amount of amyloid fibrils. Our results suggest that the degree of solvation determined by the presence of a free hydroxyl group on lipids such as LPA is a key condition that can modulate the secondary structure and the consequent formation of amyloid fibrils in the highly flexible C-terminus domain of CETP.« less

Proline N-oxides: modulators of the 3D conformation of linear peptides through "NO-turns".

PubMed

Farahani, Majid D; Honarparvar, Bahareh; Albericio, Fernando; Maguire, Glenn E M; Govender, Thavendran; Arvidsson, Per I; Kruger, Hendrik G

2014-07-07

Small peptides are essential mediators of numerous physiological processes. Consequently, there is huge interest in the de novo design of peptides with a predictable folding and related biological activity. In this study, we investigate the possibility of modulating the secondary structure of tetrapeptides through proline N-oxide moieties and N-methylation of the peptide backbone. A series of tetrapeptides were synthesised to investigate the combined effect of Pro N-oxide and N-methylation of the amide bond on the (n + 1) residue in terms of cis- and trans-isomerization, as well as how these modifications direct potential intramolecular hydrogen bonding interactions. The right combination of both these parameters led to a trans to cis-conformational interconversion and a change in the nature of the hydrogen bonding interactions, as demonstrated by NMR spectroscopic, molecular modeling analysis and thermal coefficient studies. Proline N-oxide residues were proposed to induce turns we named as NO-γ-turns and NO-β-turns based on their similarity to traditional γ- and β-turns.

Selective Modulators of PPAR-γ Activity: Molecular Aspects Related to Obesity and Side-Effects

PubMed Central

Zhang, Fang; Lavan, Brian E.; Gregoire, Francine M.

2007-01-01

Peroxisome proliferator-activated receptor γ (PPAR-γ) is a key regulator of lipid metabolism and energy balance implicated in the development of insulin resistance and obesity. The identification of putative natural and synthetic ligands and activators of PPAR-γ has helped to unravel the molecular basis of its function, including molecular details regarding ligand binding, conformational changes of the receptor, and cofactor binding, leading to the emergence of the concept of selective PPAR-γ modulators (SPPARγMs). SPPARγMs bind in distinct manners to the ligand-binding pocket of PPAR-γ, leading to alternative receptor conformations, differential cofactor recruitment/displacement, differential gene expression, and ultimately differential biological responses. Based on this concept, new and improved antidiabetic agents for the treatment of diabetes are in development. This review summarizes the current knowledge on the mechanism of action and biological effects of recently characterized SPPARγMs, including metaglidasen/halofenate, PA-082, and the angiotensin receptor antagonists, recently characterized as a new class of SPPARγMs. PMID:17389769

Posttranslational Modifications and Plant-Environment Interaction.

PubMed

Hashiguchi, A; Komatsu, S

2017-01-01

Posttranslational modifications (PTMs) of proteins such as phosphorylation and ubiquitination are crucial for controlling protein stability, localization, and conformation. Genetic information encoded in DNA is transcribed, translated, and increases its complexity by multiple PTMs. Conformational change introduced by PTMs affects interacting partners of each proteins and their downstream signaling; therefore, PTMs are the major level of modulations of total outcome of living cells. Plants are living in harsh environment that requires unremitting physiological modulation to survive, and the plant response to various environment stresses is regulated by PTMs of proteins. This review deals with the novel knowledge of PTM-focused proteomic studies on various life conditions. PTMs are focused that mediate plant-environment interaction such as stress perception, protein homeostasis, control of energy shift, and defense by immune system. Integration of diverse signals on a protein via multiple PTMs is discussed as well, considering current situation where signal integration became an emerging area approached by systems biology into account. © 2017 Elsevier Inc. All rights reserved.

Structure and symmetry inform gating principles of ionotropic glutamate receptors.

PubMed

Zhu, Shujia; Gouaux, Eric

2017-01-01

Ionotropic glutamate receptors (iGluRs) transduce signals derived from release of the excitatory neurotransmitter glutamate from pre-synaptic neurons into excitation of post-synaptic neurons on a millisecond time-scale. In recent years, the elucidation of full-length iGluR structures of NMDA, AMPA and kainate receptors by X-ray crystallography and single particle cryo-electron microscopy has greatly enhanced our understanding of the interrelationships between receptor architecture and gating mechanism. Here we briefly review full-length iGluR structures and discuss the similarities and differences between NMDA receptors and non-NMDA iGluRs. We focus on distinct conformations, including ligand-free, agonist-bound active, agonist-bound desensitized and antagonist-bound conformations as well as modulator and auxiliary protein-bound states. These findings provide insights into structure-based mechanisms of iGluR gating and modulation which together shape the amplitude and time course of the excitatory postsynaptic potential. This article is part of the Special Issue entitled 'Ionotropic glutamate receptors'. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural Basis for Modulation of Quality Control Fate in a Marginally Stable Protein.

PubMed

Brock, Kelly P; Abraham, Ayelet-chen; Amen, Triana; Kaganovich, Daniel; England, Jeremy L

2015-07-07

The human von Hippel-Lindau (VHL) tumor suppressor is a marginally stable protein previously used as a model substrate of eukaryotic refolding and degradation pathways. When expressed in the absence of its cofactors, VHL cannot fold and is quickly degraded by the quality control machinery of the cell. We combined computational methods with in vivo experiments to examine the basis of the misfolding propensity of VHL. By expressing a set of randomly mutated VHL sequences in yeast, we discovered a more stable mutant form. Subsequent modeling suggested the mutation had caused a conformational change affecting cofactor and chaperone interaction, and this hypothesis was then confirmed by additional knockout and overexpression experiments targeting a yeast cofactor homolog. These findings offer a detailed structural basis for the modulation of quality control fate in a model misfolded protein and highlight burial mode modeling as a rapid means to detect functionally important conformational changes in marginally stable globular domains. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery

PubMed Central

Bonomi, Massimiliano; Agard, David A.; Jacobson, Matthew P.

2014-01-01

αβ-tubulin dimers need to convert between a ‘bent’ conformation observed for free dimers in solution and a ‘straight’ conformation required for incorporation into the microtubule lattice. Here, we investigate the free energy landscape of αβ-tubulin using molecular dynamics simulations, emphasizing implications for models of assembly, and modulation of the conformational landscape by colchicine, a tubulin-binding drug that inhibits microtubule polymerization. Specifically, we performed molecular dynamics, potential-of-mean force simulations to obtain the free energy profile for unpolymerized GDP-bound tubulin as a function of the ∼12° intradimer rotation differentiating the straight and bent conformers. Our results predict that the unassembled GDP-tubulin heterodimer exists in a continuum of conformations ranging between straight and bent, but, in agreement with existing structural data, suggests that an intermediate bent state has a lower free energy (by ∼1 kcal/mol) and thus dominates in solution. In agreement with predictions of the lattice model of microtubule assembly, lateral binding of two αβ-tubulins strongly shifts the conformational equilibrium towards the straight state, which is then ∼1 kcal/mol lower in free energy than the bent state. Finally, calculations of colchicine binding to a single αβ-tubulin dimer strongly shifts the equilibrium toward the bent states, and disfavors the straight state to the extent that it is no longer thermodynamically populated. PMID:24516374

Conformational and stereoelectronic investigation of tryptamine. An AIM/NBO study.

PubMed

Lobayan, Rosana M; Pérez Schmit, María C; Jubert, Alicia H; Vitale, Arturo

2012-06-01

Due to the free radical scavenger properties of Tryptamine (TRA), as well as of others indole derivatives, it is in our interest to explore deeply the stereoelectronic aspects that would be relevant in their stabilization and antioxidant activity. In this work the conformational space of TRA was scanned using molecular dynamics complemented with functional density calculations at B3LYP/6-31 + G** level. Twenty one conformers of lowest energy were obtained, their electronic distributions were analyzed at a higher calculation level, thus improving the basis set (B3LYP/6-311++G**). A topological study based on Bader's theory ( atoms in molecules) and natural bond orbital (NBO) framework was performed. The study was enriched by a deep analysis of maps of molecular electrostatic potential (MEP) through a coordinated NBO/AIM analysis. The conformational preferences were explained by hyperconjugative interactions, which were revealed by NBO data. Because radical scavenging by indolic compounds is strongly modulated by their functional residues our study was related to similar analysis done previously on Indole and 1H-indole-3-acetic acid (IAA). Therefore, the conformational space of TRA was studied from a new perspective focusing on a deep analysis of the geometric and electronic properties of TRA conformers. The changes of the electronic distribution introduced by the substituent and the conformational flexibility of the side chain were addressed. The results reported contribute to the understanding of the structure, stability and reactivity of TRA and others indole derivatives.

Binding ability of impromidine, a potent H2 agonist of histamine

NASA Astrophysics Data System (ADS)

Anouar, A.; Lhadi, E.; Decock, P.; Kozlowskyinst4, H.

1999-09-01

Impromidine (fig.1) is a potent and selective histamine H2 receptor agonist and its structure comprises a strongly basic guanidine group containing two different imidazole-containing side chains. The present work deals with the study of coordination equilibria between impromidine and Cu(II) and Ni(II) in aqueous solution at 25 circC. Potentiometric, UV-Visible and EPR studies on Cu(II) complexes with impromidine have shown that this anti-ulcerogenic drug is a very potent chelating agent. This drug is found to be a very effective ligand for Ni(II) ions also. The effective coordination of impromidine to metal ions may have significant biological implications. L'impromidine est un agoniste H2 de l'histamine, sa structure possède un groupement guanidinique de forte basicité et dont l'environne ment des deux groupements imidazoliques est différent. Le présent travail consiste en l'étude de la coordination de l'impromidine avec le Cu(II) et le Ni(II) en milieu aqueux à 25 circC. La potentiométrie, LíUV-Visible et la RPE montrent que le cuivre se coordine très fortement avec l'impromidine. Nous avons trouvé que ce médicament se coordine aussi fortement avec le nickel(II). La coordination de l'impromidine avec les métaux pourrait avoir des applications importantes en médecine.

[Not Available].

PubMed

El Ketani, A; Amir, F; Ali, T B; Hamdani, M; Zaghloul, K

2006-12-31

Les enfants célèbrent la fête de Achoura au Maroc par des jeux de feu, ce qui occasionne des blessures oculaires plus au moins graves. Nous rapportons 15 observations de malades traités au Service d'Ophtalmologie Pédiatrique de l'Hôpital 20 Août 1953 de Casablanca. L'âge moyen des patients était de 12 ans et demi, avec des extrêmes de 3 et 25 ans. Les pétards, la première cause des accidents (50%), ont occasionné des contusions oculaires avec parfois un oedème de Berlin (deux cas). L'atteinte oculaire par fusée a occasionné un éclatement de globe et une plaie de paupière. Les bombes de carbone ont été responsables de brûlures de deuxième degré palpébrales et conjonctivo-cornéennes avec de multiples corps étrangers cornéens profonds. Les «étoiles» et la limaille de fer ont provoqué des brûlures cornéennes moins graves avec des corps étrangers superficiels. Les pistolets à bille ont été responsables de contusions oculaires. La réglementation de vente des jeux de feu et la sensibilisation du grand public par les moyens audiovisuels permettraient de prévenir ces blessures oculaires.

Lupus systémique et atteinte rénale: apport des anticorps anti-SSA

PubMed Central

Baline, Kenza; Zaher, Karim; Fellah, Hassan; Benchikhi, Hakima

2015-01-01

Le but de notre travail est de déterminer le profil des auto-anticorps chez 30 patients ayant un lupus systémique avec ou sans atteinte rénale afin d’établir une corrélation clinico-immunologique entre la néphropathie lupique et ces auto-anticorps. Il s'agit d'une étude transversale de 30 patients atteints de lupus érythémateux systémique diagnostiqués au service de dermatologie durant la période de Décembre 2010 à Décembre 2012 et réalisée conjointement avec le laboratoire d'immunologie. Les anticorps anti-ADN étaient retrouvés chez 17 patients (56.7%) suivis des anti-SSA dans 12 cas (40%). Cinq patients (62.5%) ayant une atteinte rénale avaient des anticorps anti DNA négatifs. Parmi ces patients avec atteinte rénale, 37.5% avaient des anticorps anti SSA sans anticorps anti DNA. La moitié des patients ayant une atteinte rénale (50%) avaient des anticorps anti SSA positifs. Notre série montre l'importance des anticorps anti-SSA surtout chez des patients avec des anticorps anti-DNA négatifs non seulement pour le diagnostic du lupus systémique mais aussi pour déceler certaines manifestations systémiques comme l'atteinte rénale. PMID:26029328

Management of three-dimensional intrafraction motion through real-time DMLC tracking.

PubMed

Sawant, Amit; Venkat, Raghu; Srivastava, Vikram; Carlson, David; Povzner, Sergey; Cattell, Herb; Keall, Paul

2008-05-01

Tumor tracking using a dynamic multileaf collimator (DMLC) represents a promising approach for intrafraction motion management in thoracic and abdominal cancer radiotherapy. In this work, we develop, empirically demonstrate, and characterize a novel 3D tracking algorithm for real-time, conformal, intensity modulated radiotherapy (IMRT) and volumetric modulated arc therapy (VMAT)-based radiation delivery to targets moving in three dimensions. The algorithm obtains real-time information of target location from an independent position monitoring system and dynamically calculates MLC leaf positions to account for changes in target position. Initial studies were performed to evaluate the geometric accuracy of DMLC tracking of 3D target motion. In addition, dosimetric studies were performed on a clinical linac to evaluate the impact of real-time DMLC tracking for conformal, step-and-shoot (S-IMRT), dynamic (D-IMRT), and VMAT deliveries to a moving target. The efficiency of conformal and IMRT delivery in the presence of tracking was determined. Results show that submillimeter geometric accuracy in all three dimensions is achievable with DMLC tracking. Significant dosimetric improvements were observed in the presence of tracking for conformal and IMRT deliveries to moving targets. A gamma index evaluation with a 3%-3 mm criterion showed that deliveries without DMLC tracking exhibit between 1.7 (S-IMRT) and 4.8 (D-IMRT) times more dose points that fail the evaluation compared to corresponding deliveries with tracking. The efficiency of IMRT delivery, as measured in the lab, was observed to be significantly lower in case of tracking target motion perpendicular to MLC leaf travel compared to motion parallel to leaf travel. Nevertheless, these early results indicate that accurate, real-time DMLC tracking of 3D tumor motion is feasible and can potentially result in significant geometric and dosimetric advantages leading to more effective management of intrafraction motion.

Unique structural features of the AIPL1–FKBP domain that support prenyl lipid binding and underlie protein malfunction in blindness

PubMed Central

Yadav, Ravi P.; Gakhar, Lokesh; Yu, Liping

2017-01-01

FKBP-domain proteins (FKBPs) are pivotal modulators of cellular signaling, protein folding, and gene transcription. Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) is a distinctive member of the FKBP superfamily in terms of its biochemical properties, and it plays an important biological role as a chaperone of phosphodiesterase 6 (PDE6), an effector enzyme of the visual transduction cascade. Malfunction of mutant AIPL1 proteins triggers a severe form of Leber congenital amaurosis and leads to blindness. The mechanism underlying the chaperone activity of AIPL1 is largely unknown, but involves the binding of isoprenyl groups on PDE6 to the FKBP domain of AIPL1. We solved the crystal structures of the AIPL1–FKBP domain and its pathogenic mutant V71F, both in the apo form and in complex with isoprenyl moieties. These structures reveal a module for lipid binding that is unparalleled within the FKBP superfamily. The prenyl binding is enabled by a unique “loop-out” conformation of the β4-α1 loop and a conformational “flip-out” switch of the key W72 residue. A second major conformation of apo AIPL1–FKBP was identified by NMR studies. This conformation, wherein W72 flips into the ligand-binding pocket and renders the protein incapable of prenyl binding, is supported by molecular dynamics simulations and appears to underlie the pathogenicity of the V71F mutant. Our findings offer critical insights into the mechanisms that underlie AIPL1 function in health and disease, and highlight the structural and functional diversity of the FKBPs. PMID:28739921

DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio

The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequencesmore » in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.« less

DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

DOE PAGES

Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio; ...

2016-03-09

The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequencesmore » in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.« less

On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brokaw, Jason B.; Chu, Jhih-wei

2010-11-17

We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier worksmore » of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.« less

Validity of Basic Electronic 1 Module Integrated Character Value Based on Conceptual Change Teaching Model to Increase Students Physics Competency in STKIP PGRI West Sumatera

NASA Astrophysics Data System (ADS)

Hidayati, A.; Rahmi, A.; Yohandri; Ratnawulan

2018-04-01

The importance of teaching materials in accordance with the characteristics of students became the main reason for the development of basic electronics I module integrated character values based on conceptual change teaching model. The module development in this research follows the development procedure of Plomp which includes preliminary research, prototyping phase and assessment phase. In the first year of this research, the module is validated. Content validity is seen from the conformity of the module with the development theory in accordance with the demands of learning model characteristics. The validity of the construct is seen from the linkage and consistency of each module component developed with the characteristic of the integrated learning model of character values obtained through validator assessment. The average validation value assessed by the validator belongs to a very valid category. Based on the validator assessment then revised the basic electronics I module integrated character values based on conceptual change teaching model.

Active Site Gate Dynamics Modulate the Catalytic Activity of the Ubiquitination Enzyme E2-25K.

PubMed

Rout, Manoj K; Lee, Brian L; Lin, Aiyang; Xiao, Wei; Spyracopoulos, Leo

2018-05-03

The ubiquitin proteasome system (UPS) signals for degradation of proteins through attachment of K48-linked polyubiquitin chains, or alterations in protein-protein recognition through attachment of K63-linked chains. Target proteins are ubiquitinated in three sequential chemical steps by a three-component enzyme system. Ubiquitination, or E2 enzymes, catalyze the central step by facilitating reaction of a target protein lysine with the C-terminus of Ub that is attached to the active site cysteine of the E2 through a thioester bond. E2 reactivity is modulated by dynamics of an active site gate, whose central residue packs against the active site cysteine in a closed conformation. Interestingly, for the E2 Ubc13, which specifically catalyzes K63-linked ubiquitination, the central gate residue adopts an open conformation. We set out to determine if active site gate dynamics play a role in catalysis for E2-25K, which adopts the canonical, closed gate conformation, and which selectively synthesizes K48-linked ubiquitin chains. Gate dynamics were characterized using mutagenesis of key residues, combined with enzyme kinetics measurements, and main chain NMR relaxation. The experimental data were interpreted with all atom MD simulations. The data indicate that active site gate opening and closing rates for E2-25K are precisely balanced.

Gas-Phase Dopant-Induced Conformational Changes Monitored with Transversal Modulation Ion Mobility Spectrometry.

PubMed

Meyer, Nicole Andrea; Root, Katharina; Zenobi, Renato; Vidal-de-Miguel, Guillermo

2016-02-16

The potential of a Transversal Modulation Ion Mobility Spectrometry (TMIMS) instrument for protein analysis applications has been evaluated. The Collision Cross Section (CCS) of cytochrome c measured with the TMIMS is in agreement with values reported in the literature. Additionally, it enables tandem IMS-IMS prefiltration in dry gas and in vapor doped gas. The chemical specificity of the different dopants enables interesting studies on the structure of proteins as CCS changed strongly depending on the specific dopant. Hexane produced an unexpectedly high CCS shift, which can be utilized to evaluate the exposure of hydrophobic parts of the protein. Alcohols produced higher shifts with a dual behavior: an increase in CCS due to vapor uptake at specific absorption sites, followed by a linear shift typical for unspecific and unstable vapor uptake. The molten globule +8 shows a very specific transition. Initially, its CCS follows the trend of the compact folded states, and then it rapidly increases to the levels of the unfolded states. This strong variation suggests that the +8 charge state undergoes a dopant-induced conformational change. Interestingly, more sterically demanding alcohols seem to unfold the protein more effectively also in the gas phase. This study shows the capabilities of the TMIMS device for protein analysis and how tandem IMS-IMS with dopants could provide better understanding of the conformational changes of proteins.

Volumetric modulated arc therapy versus step-and-shoot intensity modulated radiation therapy in the treatment of large nerve perineural spread to the skull base: a comparative dosimetric planning study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorayski, Peter; Fitzgerald, Rhys; Barry, Tamara

Cutaneous squamous cell carcinoma with large nerve perineural (LNPN) infiltration of the base of skull is a radiotherapeutic challenge given the complex target volumes to nearby organs at risk (OAR). A comparative planning study was undertaken to evaluate dosimetric differences between volumetric modulated arc therapy (VMAT) versus intensity modulated radiation therapy (IMRT) in the treatment of LNPN. Five consecutive patients previously treated with IMRT for LNPN were selected. VMAT plans were generated for each case using the same planning target volumes (PTV), dose prescriptions and OAR constraints as IMRT. Comparative parameters used to assess target volume coverage, conformity and homogeneitymore » included V95 of the PTV (volume encompassed by the 95% isodose), conformity index (CI) and homogeneity index (HI). In addition, OAR maximum point doses, V20, V30, non-target tissue (NTT) point max doses, NTT volume above reference dose, monitor units (MU) were compared. IMRT and VMAT plans generated were comparable for CI (P = 0.12) and HI (P = 0.89). VMAT plans achieved better V95 (P = < 0.001) and reduced V20 and V30 by 652 cubic centimetres (cc) (28.5%) and 425.7 cc (29.1%), respectively. VMAT increased MU delivered by 18% without a corresponding increase in NTT dose. Compared with IMRT plans for LNPN, VMAT achieved comparable HI and CI.« less

Dosimetric comparison of helical tomotherapy, intensity-modulated radiation therapy, volumetric-modulated arc therapy, and 3-dimensional conformal therapy for the treatment of T1N0 glottic cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ekici, Kemal, E-mail: drkemal06@hotmail.com; Pepele, Eda K.; Yaprak, Bahaddin

2016-01-01

Various radiotherapy planning methods for T1N0 laryngeal cancer have been proposed to decrease normal tissue toxicity. We compare helical tomotherapy (HT), linac-based intensity-modulated radiation therapy (IMRT), volumetric-modulated arc therapy (VMAT), and 3-D conformal radiotherapy (3D-CRT) techniques for T1N0 laryngeal cancer. Overall, 10 patients with T1N0 laryngeal cancer were selected and evaluated. Furthermore, 10 radiotherapy treatment plans have been created for all 10 patients, including HT, IMRT, VMAT, and 3D-CRT. IMRT, VMAT, and HT plans vs 3D-CRT plans consistently provided superior planning target volume (PTV) coverage. Similar target coverage was observed between the 3 IMRT modalities. Compared with 3D-CRT, IMRT, HT,more » and VMAT significantly reduced the mean dose to the carotid arteries. VMAT resulted in the lowest mean dose to the submandibular and thyroid glands. Compared with 3D-CRT, IMRT, HT, and VMAT significantly increased the maximum dose to the spinal cord It was observed that the 3 IMRT modalities studied showed superior target coverage with less variation between each plan in comparison with 3D-CRT. The 3D-CRT plans performed better at the D{sub max} of the spinal cord. Clinical investigation is warranted to determine if these treatment approaches would translate into a reduction in radiation therapy–induced toxicities.« less

Clinical utility of RapidArc™ radiotherapy technology

PubMed Central

Infusino, Erminia

2015-01-01

RapidArc™ is a radiation technique that delivers highly conformal dose distributions through the complete rotation (360°) and speed variation of the linear accelerator gantry. This technique, called volumetric modulated arc therapy (VMAT), compared with conventional radiotherapy techniques, can achieve high-target volume coverage and sparing damage to normal tissues. RapidArc delivers precise dose distribution and conformity similar to or greater than intensity-modulated radiation therapy in a short time, generally a few minutes, to which image-guided radiation therapy is added. RapidArc has become a currently used technology in many centers, which use RapidArc technology to treat a large number of patients. Large and small hospitals use it to treat the most challenging cases, but more and more frequently for the most common cancers. The clinical use of RapidArc and VMAT technology is constantly growing. At present, a limited number of clinical data are published, mostly concerning planning and feasibility studies. Clinical outcome data are increasing for a few tumor sites, even if only a little. The purpose of this work is to discuss the current status of VMAT techniques in clinical use through a review of the published data of planning systems and clinical outcomes in several tumor sites. The study consisted of a systematic review based on analysis of manuscripts retrieved from the PubMed, BioMed Central, and Scopus databases by searching for the keywords “RapidArc”, “Volumetric modulated arc radiotherapy”, and “Intensity-modulated radiotherapy”. PMID:26648755

Structural Basis of Tonic Inhibition by Dimers of Dimers in Hyperpolarization-Activated Cyclic-Nucleotide-Modulated (HCN) Ion Channels.

PubMed

VanSchouwen, Bryan; Melacini, Giuseppe

2016-10-03

The hyperpolarization-activated cyclic-nucleotide-modulated (HCN) ion channels control rhythmicity in neurons and cardiomyocytes. Cyclic AMP (cAMP) modulates HCN activity through cAMP-dependent formation of a tetrameric gating ring spanning the intracellular region (IR) of HCN. In the absence of cAMP, the IR cAMP-binding domain (CBD) mainly samples its inactive conformation, resulting in steric clashes that destabilize the IR tetramer. Although these clashes with the inactive CBD are released through tetramer dissociation into monomers, functional mutagenesis suggests that the apo IR is not fully monomeric. To investigate the inhibitory non-monomeric IR species, we performed molecular dynamics simulations starting from "hybrid" structures that are tetrameric, but contain inactive apo-state CBD conformations. The ensemble of simulated trajectories reveals that full dissociation of the tetramer into monomers is not necessary to release the steric hindrance with the inactive CBD. Specifically, we found that partial dissociation of the tetramer into dimers is sufficient to accommodate four inactive CBDs, while reduction of the quaternary symmetry of the non-dissociated tetramer from four- to two-fold permits accommodation of two inactive CBDs. Our findings not only rationalize available electrophysiological, fluorometry and sedimentation equilibrium data, but they also provide unprecedented structural insight into previously elusive non-monomeric auto-inhibitory HCN species.

Analytical Solutions for Predicting Underwater Explosion Gas Bubble Behaviour

DTIC Science & Technology

2010-11-01

donne les meilleures prévisions comparativement aux ajustements avec les données expérimentales. Le modèle à fluide incompressible exige d’utiliser une...couplage des mouvements radial et migratoire. L’étude montre que, comparativement aux résultats d’expérience, la réduction du rayon de la bulle... comparativement aux ajustements avec les données expérimentales. Le modèle à fluide incompressible exige d’utiliser une fonction empirique de perte d’énergie

Leadership and Innovation-Listening to and Learning From Young People in Burundi.

PubMed

Nininahazwe, Cédric; Alesi, Jacquelyne; Caswell, Georgina; Lumumba, Musah; Mellin, Julie; Ndayizeye, Nicholas-Monalisa; Orza, Luisa; Rahimi, Michaela; Westerhof, Nienke

2017-02-01

This commentary describes young people's leadership from the perspective of a youth-led organization in the Link Up project in Burundi, Réseau National des Jeunes vivant avec le VIH. It describes processes that enable young people to guide, influence, deliver, and improve health service provision; the challenges faced by Réseau National des Jeunes vivant avec le VIH and how they are addressing these challenges. Copyright © 2016 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Conformational Sampling and Binding Site Assessment of Suppression of Tumorigenicity 2 Ectodomain

PubMed Central

Yang, Chao-Yie; Delproposto, James; Chinnaswamy, Krishnapriya; Brown, William Clay; Wang, Shuying; Stuckey, Jeanne A.; Wang, Xinquan

2016-01-01

Suppression of Tumorigenicity 2 (ST2), a member of the interleukin-1 receptor (IL-1R) family, activates type 2 immune responses to pathogens and tissue damage via binding to IL-33. Dysregulated responses contribute to asthma, graft-versus-host and autoinflammatory diseases and disorders. To study ST2 structure for inhibitor development, we performed the principal component (PC) analysis on the crystal structures of IL1-1R1, IL1-1R2, ST2 and the refined ST2 ectodomain (ST2ECD) models, constructed from previously reported small-angle X-ray scattering data. The analysis facilitates mapping of the ST2ECD conformations to PC subspace for characterizing structural changes. Extensive coverage of ST2ECD conformations was then obtained using the accelerated molecular dynamics simulations started with the IL-33 bound ST2ECD structure as instructed by their projected locations on the PC subspace. Cluster analysis of all conformations further determined representative conformations of ST2ECD ensemble in solution. Alignment of the representative conformations with the ST2/IL-33 structure showed that the D3 domain of ST2ECD (containing D1-D3 domains) in most conformations exhibits no clashes with IL-33 in the crystal structure. Our experimental binding data informed that the D1-D2 domain of ST2ECD contributes predominantly to the interaction between ST2ECD and IL-33 underscoring the importance of the D1-D2 domain in binding. Computational binding site assessment revealed one third of the total detected binding sites in the representative conformations may be suitable for binding to potent small molecules. Locations of these sites include the D1-D2 domain ST2ECD and modulation sites conformed to ST2ECD conformations. Our study provides structural models and analyses of ST2ECD that could be useful for inhibitor discovery. PMID:26735493

The Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed by Single-Molecule FRET.

PubMed

Yang, Mengyi; Peng, Sijia; Sun, Ruirui; Lin, Jingdi; Wang, Nan; Chen, Chunlai

2018-01-09

Off-target binding and cleavage by Cas9 pose major challenges in its application. How the conformational dynamics of Cas9 govern its nuclease activity under on- and off-target conditions remains largely unknown. Here, using intra-molecular single-molecule fluorescence resonance energy transfer measurements, we revealed that Cas9 in apo, sgRNA-bound, and dsDNA/sgRNA-bound forms spontaneously transits among three major conformational states, mainly reflecting significant conformational mobility of the catalytic HNH domain. We also uncovered surprising long-range allosteric communication between the HNH domain and the RNA/DNA heteroduplex at the PAM-distal end to ensure correct positioning of the catalytic site, which demonstrated that a unique proofreading mechanism served as the last checkpoint before DNA cleavage. Several Cas9 residues were likely to mediate the allosteric communication and proofreading step. Modulating interactions between Cas9 and heteroduplex at the PAM-distal end by introducing mutations on these sites provides an alternative route to improve and optimize the CRISPR/Cas9 toolbox. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Strand swapping regulates the iron-sulfur cluster in the diabetes drug target mitoNEET

PubMed Central

Baxter, Elizabeth Leigh; Jennings, Patricia A.; Onuchic, José N.

2012-01-01

MitoNEET is a recently identified diabetes drug target that coordinates a transferable 2Fe-2S cluster, and additionally contains an unusual strand swap. In this manuscript, we use a dual basin structure-based model to predict and characterize the folding and functionality of strand swapping in mitoNEET. We demonstrate that a strand unswapped conformation is kinetically accessible and that multiple levels of control are employed to regulate the conformational dynamics of the system. Environmental factors such as temperature can shift route preference toward the unswapped pathway. Additionally we see that a region recently identified as contributing to frustration in folding acts as a regulatory hinge loop that modulates conformational balance. Interestingly, strand unswapping transfers strain specifically to cluster-coordinating residues, opening the cluster-coordinating pocket. Strengthening contacts within the cluster-coordinating pocket opens a new pathway between the swapped and unswapped conformation that utilizes cracking to bypass the unfolded basin. These results suggest that local control within distinct regions affect motions important in regulating mitoNEET’s 2Fe-2S clusters. PMID:22308404

Fluoxetine (Prozac) Binding to Serotonin Transporter Is Modulated by Chloride and Conformational Changes

PubMed Central

Tavoulari, Sotiria; Forrest, Lucy R.; Rudnick, Gary

2010-01-01

Serotonin transporter (SERT) is the main target for widely used antidepressant agents. Several of these drugs, including imipramine, citalopram, sertraline, and fluoxetine (Prozac), bound more avidly to SERT in the presence of Cl–. In contrast, Cl– did not enhance cocaine or paroxetine binding. A Cl– binding site recently identified in SERT, and shown to be important for Cl– dependent transport, was also critical for the Cl– dependence of antidepressant affinity. Mutation of the residues contributing to this site eliminated the Cl–-mediated affinity increase for imipramine and fluoxetine. Analysis of ligand docking to a single state of SERT indicated only small differences in the energy of interaction between bound ligands and Cl–. These differences in interaction energy cannot account for the affinity differences observed for Cl– dependence. However, fluoxetine binding led to a conformational change, detected by cysteine accessibility experiments, that was qualitatively different from that induced by cocaine or other ligands. Given the known Cl– requirement for serotonin-induced conformational changes, we propose that Cl– binding facilitates conformational changes required for optimal binding of fluoxetine and other antidepressant drugs. PMID:19641126

Temporal switching of an amphiphilic self-assembly by a chemical fuel-driven conformational response† †Electronic supplementary information (ESI) available: Experimental section, synthetic procedures and supporting figures. See DOI: 10.1039/c7sc01730h Click here for additional data file.

PubMed Central

Jalani, Krishnendu; Dhiman, Shikha

2017-01-01

The spatial and temporal control of self-assemblies is the latest scientific hurdle in supramolecular chemistry which is inspired by the functioning of biological systems fueled by chemical signals. In this study, we work towards alleviating this scenario by employing a unique amphiphilic foldamer that operates under the effect of a chemical fuel. The conformational changes in the foldamer amplify into observable morphological changes in its amphiphilic assembly that are controlled by external molecular cues (fuel). We take advantage of this redox responsive foldamer to affect its conformation in a temporal manner by an enzymatic pathway. The temporal characteristics of the transient conformation/assembly can be modulated by varying the concentrations of the fuel and enzyme. We believe that such a design strategy can have positive consequences in designing molecular and supramolecular systems for future active, adaptive and autonomous materials. PMID:28989632

Temperature-Dependent Conformations of a Membrane Supported ‘Zinc Porphyrin Tweezer’ by 2D Fluorescence Spectroscopy

PubMed Central

Widom, Julia R.; Lee, Wonbae; Perdomo-Ortiz, Alejandro; Rappoport, Dmitrij; Molinski, Tadeusz F.; Aspuru-Guzik, Alán; Marcus, Andrew H.

2013-01-01

We studied the equilibrium conformations of a ‘zinc porphyrin tweezer’ composed of two carboxylphenyl-functionalized zinc tetraphenyl porphyrin subunits connected by a 1,4 butyndiol spacer, which was suspended inside the amphiphilic regions of 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) liposomes. By combining phase-modulation two-dimensional fluorescence spectroscopy (2D FS) with linear absorbance and fluorimetry, we determined that the zinc porphyrin tweezer adopts a mixture of ‘folded’ and ‘extended’ conformations in the membrane. By fitting an exciton-coupling model to a series of data sets recorded over a range of temperatures (17 – 85 °C) and at different laser center wavelengths, we determined that the folded form of the tweezer is stabilized by a favorable change in the entropy of the local membrane environment. Our results provide insights toward understanding the balance of thermodynamic factors that govern molecular assembly in membranes. PMID:23480874

Ethane-Bridged Bisporphyrin Conformational Changes As an Effective Analytical Tool for Nonenzymatic Detection of Urea in the Physiological Range.

PubMed

Buccolieri, Alessandro; Hasan, Mohammed; Bettini, Simona; Bonfrate, Valentina; Salvatore, Luca; Santino, Angelo; Borovkov, Victor; Giancane, Gabriele

2018-06-05

Conformational switching induced in ethane-bridged bisporphyrins was used as a sensitive transduction method for revealing the presence of urea dissolved in water via nonenzymatic approach. Bisporphyrins were deposited on solid quartz slides by means of the spin-coating method. Molecular conformations of Zn and Ni monometalated bis-porphyrins were influenced by water solvated urea molecules and their fluorescence emission was modulated by the urea concentration. Absorption, fluorescence and Raman spectroscopies allowed the identification of supramolecular processes, which are responsible for host-guest interaction between the active layers and urea molecules. A high selectivity of the sensing mechanism was highlighted upon testing the spectroscopic responses of bis-porphyrin films to citrulline and glutamine used as interfering agents. Additionally, potential applicability was demonstrated by quantifying the urea concentration in real physiological samples proposing this new approach as a valuable alternative analytical procedure to the traditionally used enzymatic methods.

Chain registry and load-dependent conformational dynamics of collagen.

PubMed

Teng, Xiaojing; Hwang, Wonmuk

2014-08-11

Degradation of fibrillar collagen is critical for tissue maintenance. Yet, understanding collagen catabolism has been challenging partly due to a lack of atomistic picture for its load-dependent conformational dynamics, as both mechanical load and local unfolding of collagen affect its cleavage by matrix metalloproteinase (MMP). We use molecular dynamics simulation to find the most cleavage-prone arrangement of α chains in a collagen triple helix and find amino acids that modulate stability of the MMP cleavage domain depending on the chain registry within the molecule. The native-like state is mechanically inhomogeneous, where the cleavage site interfaces a stiff region and a locally unfolded and flexible region along the molecule. In contrast, a triple helix made of the stable glycine-proline-hydroxyproline motif is uniformly flexible and is dynamically stabilized by short-lived, low-occupancy hydrogen bonds. These results provide an atomistic basis for the mechanics, conformation, and stability of collagen that affect catabolism.

Modulation of activation-loop phosphorylation by JAK inhibitors is binding mode dependent

PubMed Central

Bonenfant, Débora; Rubert, Joëlle; Vangrevelinghe, Eric; Scheufler, Clemens; Marque, Fanny; Régnier, Catherine H.; De Pover, Alain; Ryckelynck, Hugues; Bhagwat, Neha; Koppikar, Priya; Goel, Aviva; Wyder, Lorenza; Tavares, Gisele; Baffert, Fabienne; Pissot-Soldermann, Carole; Manley, Paul W.; Gaul, Christoph; Voshol, Hans; Levine, Ross L.; Sellers, William R.; Hofmann, Francesco; Radimerski, Thomas

2016-01-01

JAK inhibitors are being developed for the treatment of rheumatoid arthritis, psoriasis, myeloproliferative neoplasms and leukemias. Most of these drugs target the ATP-binding pocket and stabilize the active conformation of the JAK kinases. This type-I binding mode leads to an increase in JAK activation-loop phosphorylation, despite blockade of kinase function. Here we report that stabilizing the inactive state via type-II inhibition acts in the opposite manner, leading to a loss of activation-loop phosphorylation. We used X-ray crystallography to corroborate the binding mode and report for the first time the crystal structure of the JAK2 kinase domain in an inactive conformation. Importantly, JAK inhibitor-induced activation-loop phosphorylation requires receptor interaction, as well as intact kinase and pseudokinase domains. Hence, depending on the respective conformation stabilized by a JAK inhibitor, hyperphosphorylation of the activation-loop may or may not be elicited. PMID:22684457

47 CFR 73.691 - Visual modulation monitoring.

Code of Federal Regulations, 2010 CFR

2010-10-01

... must have measuring equipment for determining that the transmitted visual signal conforms to the... a period of not more than 30 days without specific authority from the FCC: provided that, the date... operation at variance will exceed 10 consecutive days, a notification must be sent to the FCC in Washington...

Allostery mediates ligand binding to WWOX tumor suppressor via a conformational switch.

PubMed

Schuchardt, Brett J; Mikles, David C; Bhat, Vikas; McDonald, Caleb B; Sudol, Marius; Farooq, Amjad

2015-04-01

While being devoid of the ability to recognize ligands itself, the WW2 domain is believed to aid ligand binding to the WW1 domain in the context of a WW1-WW2 tandem module of WW domain-containing oxidoreductase (WWOX) tumor suppressor. In an effort to test the generality of this hypothesis, we have undertaken here a detailed biophysical analysis of the binding of WW domains of WWOX alone and in the context of the WW1-WW2 tandem module to an array of putative proline-proline-x-tyrosine (PPXY) ligands. Our data show that while the WW1 domain of WWOX binds to all ligands in a physiologically relevant manner, the WW2 domain does not. Moreover, ligand binding to the WW1 domain in the context of the WW1-WW2 tandem module is two-to-three-fold stronger than when treated alone. We also provide evidence that the WW domains within the WW1-WW2 tandem module physically associate so as to adopt a fixed spatial orientation relative to each other. Of particular note is the observation that the physical association of the WW2 domain with WW1 blocks access to ligands. Consequently, ligand binding to the WW1 domain not only results in the displacement of the WW2 lid but also disrupts the physical association of WW domains in the liganded conformation. Taken together, our study underscores a key role of allosteric communication in the ability of the WW2 orphan domain to chaperone physiological action of the WW1 domain within the context of the WW1-WW2 tandem module of WWOX. Copyright © 2015 John Wiley & Sons, Ltd.

Catalytic thermometric titrations in non-aqueous solvents by coulometrically generated titrant.

PubMed

Vajgand, V J; Gaál, F F; Brusin, S S

1970-05-01

Catalytic thermometric titrations have been developed for tertiary amines and salts of organic acids in acetic and propionic anhydride with titrant coulometrically generated at a mercury and/or platinum anode, hydroquinone being added to the solution titrated if the platinum anode is used. The results obtained are compared with those obtained by coulometric titration with the end-point detected either photometrically or potentiometrically. On a élaboré des titrages thermométriques catalytiques pour les amines tertiaires et les sels d'acides organiques en anhydrides aétique et propionique avec l'agent de titrage engendré coulométriquement sur une anode de mercure et/ou platine, de l'hydroquinone étant ajoutée à la solution titrée si l'on emploie l'anode de platine. Les résultats obtenus sont comparés avec ceux obtenus par titrage coulométrique avec le point de fin de réaction détecté soit photométriquement soit potentioétriquement.

SU-E-T-62: Cardiac Toxicity in Dynamic Conformal Arc Therapy, Intensity-Modulated Radiation Therapy and Volumetric Modulated Arc Therapy of Lung Cancers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ming, X; Zhang, Y; Yale University, New Haven, CT, US

2014-06-01

Purpose: The cardiac toxicity for lung cancer patients, each treated with dynamic conformal arc therapy (DAT), intensity-modulated radiation therapy (IMRT), or volumetric modulated arc therapy (VMAT) is investigated. Methods: 120 lung patients were selected for this study: 25 treated with DAT, 50 with IMRT and 45 with VMAT. For comparison, all plans were generated in the same treatment planning system, normalized such that the 100% isodose lines encompassed 95% of planning target volume. The plan quality was evaluated in terms of homogeneity index (HI) and 95% conformity index (%95 CI) for target dose coverage and mean dose, maximum dose, V{submore » 30} Gy as well as V{sub 5} Gy for cardiac toxicity analysis. Results: When all the plans were analyzed, the VMAT plans offered the best target coverage with 95% CI = 0.992 and HI = 1.23. The DAT plans provided the best heart sparing with mean heart dose = 2.3Gy and maximum dose = 11.6Gy, as compared to 5.7 Gy and 31.1 Gy by IMRT as well as 4.6 Gy and 30.9 Gy by VMAT. The mean V30Gy and V5Gy of the heart in the DAT plans were up to 11.7% lower in comparison to the IMRT and VMAT plans. When the tumor volume was considered, the VMAT plans spared up to 70.9% more doses to the heart when the equivalent diameter of the tumor was larger than 4cm. Yet the maximum dose to the heart was reduced the most in the DAT plans with up to 139.8% less than that of the other two plans. Conclusion: Overall, the VMAT plans achieved the best target coverage among the three treatment modalities, and would spare the heart the most for the larger tumors. The DAT plans appeared advantageous in delivering the least maximum dose to the heart as compared to the IMRT and VMAT plans.« less

Entropy in molecular recognition by proteins

PubMed Central

Caro, José A.; Harpole, Kyle W.; Kasinath, Vignesh; Lim, Jackwee; Granja, Jeffrey; Valentine, Kathleen G.; Sharp, Kim A.

2017-01-01

Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein–ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein–ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy. We find that the contribution of conformational entropy can range from favorable to unfavorable, which demonstrates the potential of this thermodynamic variable to modulate protein–ligand interactions. For about one-quarter of these complexes, the absence of conformational entropy would render the resulting affinity biologically meaningless. The dynamical proxy for conformational entropy or “entropy meter” also allows for refinement of the contributions of solvent entropy and the loss in rotational-translational entropy accompanying formation of high-affinity complexes. Furthermore, structure-based application of the approach can also provide insight into long-lived specific water–protein interactions that escape the generic treatments of solvent entropy based simply on changes in accessible surface area. These results provide a comprehensive and unified view of the general role of entropy in high-affinity molecular recognition by proteins. PMID:28584100

Entropy in molecular recognition by proteins.

PubMed

Caro, José A; Harpole, Kyle W; Kasinath, Vignesh; Lim, Jackwee; Granja, Jeffrey; Valentine, Kathleen G; Sharp, Kim A; Wand, A Joshua

2017-06-20

Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein-ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein-ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy. We find that the contribution of conformational entropy can range from favorable to unfavorable, which demonstrates the potential of this thermodynamic variable to modulate protein-ligand interactions. For about one-quarter of these complexes, the absence of conformational entropy would render the resulting affinity biologically meaningless. The dynamical proxy for conformational entropy or "entropy meter" also allows for refinement of the contributions of solvent entropy and the loss in rotational-translational entropy accompanying formation of high-affinity complexes. Furthermore, structure-based application of the approach can also provide insight into long-lived specific water-protein interactions that escape the generic treatments of solvent entropy based simply on changes in accessible surface area. These results provide a comprehensive and unified view of the general role of entropy in high-affinity molecular recognition by proteins.

Substantial conformational change mediated by charge-triad residues of the death effector domain in protein-protein interactions.

PubMed

Twomey, Edward C; Cordasco, Dana F; Kozuch, Stephen D; Wei, Yufeng

2013-01-01

Protein conformational changes are commonly associated with the formation of protein complexes. The non-catalytic death effector domains (DEDs) mediate protein-protein interactions in a variety of cellular processes, including apoptosis, proliferation and migration, and glucose metabolism. Here, using NMR residual dipolar coupling (RDC) data, we report a conformational change in the DED of the phosphoprotein enriched in astrocytes, 15 kDa (PEA-15) protein in the complex with a mitogen-activated protein (MAP) kinase, extracellular regulated kinase 2 (ERK2), which is essential in regulating ERK2 cellular distribution and function in cell proliferation and migration. The most significant conformational change in PEA-15 happens at helices α2, α3, and α4, which also possess the highest flexibility among the six-helix bundle of the DED. This crucial conformational change is modulated by the D/E-RxDL charge-triad motif, one of the prominent structural features of DEDs, together with a number of other electrostatic and hydrogen bonding interactions on the protein surface. Charge-triad motif promotes the optimal orientation of key residues and expands the binding interface to accommodate protein-protein interactions. However, the charge-triad residues are not directly involved in the binding interface between PEA-15 and ERK2.

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

PubMed Central

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-01-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health. PMID:26213417

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

NASA Astrophysics Data System (ADS)

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-10-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Tq Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health.

Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures

PubMed Central

Genshaft, Alexander; Moser, Joe-Ann S.; D'Antonio, Edward L.; Bowman, Christine M.; Christianson, David W.

2013-01-01

The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular “switch” for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly-accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations. PMID:23401043

Two-dimensional RCFT's without Kac-Moody symmetry

NASA Astrophysics Data System (ADS)

Hampapura, Harsha R.; Mukhi, Sunil

2016-07-01

Using the method of modular-invariant differential equations, we classify a family of Rational Conformal Field Theories with two and three characters having no Kac-Moody algebra. In addition to unitary and non-unitary minimal models, we find "dual" theories whose characters obey bilinear relations with those of the minimal models to give the Moonshine Module. In some ways this relation is analogous to cosets of meromorphic CFT's. The theory dual in this sense to the Ising model has central charge 47/2 and is related to the Baby Monster Module.

Moya moya: étiologie rare d’accident vasculaire cérébral ischémique chez l’enfant: à propos d’un cas

PubMed Central

Chibli, Radia; Omor, Youssef; Sebbouba, Nadir Slimani; Hassani, Moulay Rachid El; Jiddane, Mohamed; Fikri, Meriem

2017-01-01

La maladie de Moya Moya est une maladie angiogénique, caractérisée par un rétrécissement de l'artère carotide interne distale qui s'étend aux segments proximaux des artères cérébrales moyennes et antérieures, induisant la formation de vaisseaux de suppléance. Ces derniers proviennent des collatérales parenchymateuses, perforantes, leptoméningées et autres anastomoses transdurales. Ces vaisseaux collatéraux ont un aspect caractéristique à l'angiographie formant un nuage de fumée : réseau Moya Moya. Son étiologie reste encore mal élucidée et représente 10 à 15% des causes d'accidents vasculaires cérébraux (AVC), avec 2 pics d'âge où l'atteinte est plus fréquente: les enfants autour de 5 ans et les adultes autour de 40 ans. Son évolution peut être lente avec des symptômes intermittents ou être fulminante avec un déclin neurologique rapide. Les données actuelles montrent l'importance du traitement chirurgical comme méthode de référence pour la prise en charge du syndrome de Moya en particulier chez les patients avec des symptômes progressifs et récidivants. PMID:29599890

Etude de faisabilite d'un systeme eolien diesel avec stockage d'air comprime

NASA Astrophysics Data System (ADS)

Benchaabane, Youssef

Le Systeme Hybride Eolien-Diesel avec Stockage d'Air Comprime (SHEDAC) utilise l'hybridation pneumatique pour remplacer la consommation des combustibles fossiles par de l'energie renouvelable, plus particulierement de l'energie eolienne. Le surplus de l'energie eolienne est utilise pour comprimer et stocker de l'air qui est utilise ensuite pour suralimenter le moteur diesel. Le memoire de maitrise est constitue de deux articles scientifiques. Le premier article presente le developpement d'un logiciel dedie a l'etude de faisabilite d'un systeme eolien-diesel avec stockage d'air comprime. Cette etude est basee sur l'analyse des couts et des revenus, des couts des equipements (eolienne, moteur diesel, systeme de stockage d'air). Elle est completee par une analyse de sensibilite aux differents parametres, une analyse des risques et des emissions des gaz a effet de serre (GES). Le deuxieme article est une application de ce logiciel pour l'installation d'un systeme SHEDAC au camp minier Esker au Quebec en remplacement des sources actuelles de production d'energie. L'utilisation du stockage d'air comprime a l'aide d'un systeme SHEDAC est le plus rentable par rapport a l'utilisation de l'energie eolienne seule ou d'une centrale thermique au diesel seule ou des deux combinees. Avec une valeur actuelle nette et un taux de rendement interne plus eleves, cette solution permet d'obtenir le plus bas cout de l'energie pour cette region eloignee. None None None

Optimisation de l'émission du continuum femtoseconde de lumière blanche entre 600 nm et 800 nm

NASA Astrophysics Data System (ADS)

Ramstein, S.; Mottin, S.

2005-06-01

Un dispositif de spectroscopie avec résolution du temps de vol des photons en milieu diffus a été développé. Celui-ci repose sur l'utilisation d'un continuum de lumière blanche généré par focalisation d'un laser amplifié (830 nm, 1 kHz, 0.5 W, 170 fs) dans de l'eau déminéralisée. Afin d'optimiser spectralement et en puissance la source blanche sur la fenêtre spectrale 600 800 nm, une étude de la mise en forme spatio-temporelle avant autofocalisation de l'impulsion laser par le milieu a été menée. Cette mise en forme est effectuée de manière spatiale en changeant la focale de la lentille de focalisation et de manière temporelle en changeant le taux de compression de l'impulsion. L'étude montre que le cône de lumière émise possède plus de puissance dans la fenêtre spectrale d'intérêt pour des focales longues. Sur la fenêtre 600-800 nm, le rendement énergétique intégré varie de 5%, avec une focalef=6cm, à 15%, avec une focale f = 30 cm. La mise en forme temporelle montre des effets similaires avec les mêmes ordres de grandeur.

Extended Generation Profile - E.B.I.C. Model

NASA Astrophysics Data System (ADS)

Guermazi, S.; Toureille, A.; Grill, C.; El Jani, B.; Lakhoua, N.

1996-04-01

We have developed a model for the calculation of the induced current due to an electron beam with an extended profile. As well as the number of absorbed and diffuse electrons as a function of the depth, the generation profile takes into account the lateral diffusion and the effect of defects, dislocations and recombination surfaces. The expression from the Electron Beam Induced Current (EBIC) is obtained by solving the continuity equation in permanent regime by the Green function method. In the case of a Schottky diode Au/InP, obtained by ionic scattering followed by a quick thermal treatment, the induced current profile is compared to the theoretical profiles whose analytical expressions are given by Van Roosbroeck and Bresse. The experimental current profile, measured by S.E.M provided us with the calculation of the diffusion length of the minority carriers, L_n=1 μm. The theoretical curve obtained from the proposed model is in good agreement with the experimental one for a surface recombination velocity of 104 cm s^{-1}. Our results are found to be consistent with those obtained by other experimental techniques on the same samples. Nous avons développé un modèle de calcul du courant induit par un faisceau d'électrons avec un profil de génération élargi. Le profil de génération tient compte, en plus du nombre d'électrons absorbés et du nombre d'électrons diffusés en fonction de la profondeur, de la diffusion latérale (en prenant en considération la diffusion angulaire), de l'effet des défauts, des dislocations et de la recombinaison à la surface. L'expression analytique du courant induit E.B.I.C est déterminée par résolution de l'équation de continuité en régime permanent par la méthode des fonctions de Green. Le profil de courant induit obtenu dans le cas d'une diode Schottky Au/InP dopé p et fabriqué par implantation suivit d'un recuit, est comparé au profil de courant théorique dont l'expression analytique est explicité par Van Roosbroeck et Bresse. Le profil de courant expérimental, mesuré par un microscope électronique à balayage, nous a permis de calculer la longueur de diffusion des porteurs minoritaires L_n=1 μm. La courbe théorique, tracée à partir du modèle proposé, est en bon accord avec la courbe expérimental pour une vitesse de recombinaison à la surface de 104 cm s^{-1}. Ces résultats sont conformes avec ceux obtenus par d'autres techniques expérimentales sur les mêmes échantillons.

Nocardiose pulmonaire sur un terrain immunocompétent: à propos de 2 cas

PubMed Central

Rhofir, Yasmina; Zahraoui, Rachida; Tiress, Nabil; Naji-Amrani, Hicham; Soualhi, Mouna; Bourkadi, Jamal Eddine

2017-01-01

La nocardiose est une infection rare, mais sévère, causée par des bactéries du genre nocardia, qui appartiennent à l'ordre des actinomycétales. Si elles peuvent toucher l'adulte immunocompétent, les nocardioses restent des pathologies de l'individu fragilisé sur le plan immunitaire. L'atteinte pulmonaire reste la plus fréquente, sa prise en charge correcte est liée au diagnostic qui est souvent retardé par des présentations non spécifiques et des prélèvements non concluants. Nous rapportons ici deux cas de nocardiose chez des patients immunocompétents. Le premier cas est celui d'un homme de 24 ans, avec notion de tabagisme et d'éthylisme, hospitalisé pour des douleurs thoraciques et des hémoptysies de faible abondance, évoluant depuis deux mois, avec apparition d'abcès sous cutanés dorsaux fistulisés. L'exploration radiologique découvre une masse tissulaire médiastino-pulmonaire droite avec lyse costale adjacente et diffusion aux tissus para vertébraux droits. Les prélèvements bactériologiques restent négatifs motivant une biopsie scannoguidée de la lésion qui est revenue en faveur d'infection à nocardiose. Le second cas concerne un homme de 22 ans, aux antécédents de tuberculose pleurale traitée il y a 8 ans puis une rechute de tuberculose en 2011 (abcès médiastinal). Admis pour suspicion de rechute de tuberculose devant une toux chronique avec altération de l'état général et une hépatosplénomégalie. Le scanner thoracique montre des condensations alvéolaires avec pleurésie. Au cours de son hospitalisation, apparition de tuméfactions sous cutanées purulentes dont l'étude bactériologique du pus est revenue en faveur de nocardiose avec une souche résistante à tous les antibiotiques sauf colistine et bactrim. Les auteurs illustrent à travers ces deux observations, les aspects cliniques et radiologiques de nocardiose pulmonaire en mettant le point sur les difficultés diagnostiques et thérapeutiques surtout dans un pays à forte prévalence de tuberculose et très faible incidence de nocardiose. PMID:28904677

Synthese et Caracterisation de Nanocomposites d'Argile et de Graphene Formes a Partir de Precurseurs Organiques =

NASA Astrophysics Data System (ADS)

Boussaboun, Zakariae

Les mineraux d'argile sont des catalyseurs possibles pour la formation du graphene a partir de precurseurs organiques, comme le saccharose. Les argiles sont abondantes, securitaires et economiques pour la formation du graphene. L'objectif principal de ce memoire est de demontrer qu'il est possible de synthetiser un materiau hybride contenant de l'argile et du graphene. La preparation de ces materiaux carbones a base de l'argile (bentonite et cloisite) et le saccharose a ete realisee selon deux methodes. La premiere methode est faite en trois etapes : 1) periode de contact entre l'argile et la source de carbone dans un environnement humide, 2) infiltration de la matiere carbonee et transformation au four a micro-onde, 3) chauffage a 750°C sous azote pour obtenir des materiaux carbones. Par contre la deuxieme methode est faite en deux etapes, sans micro-onde, et avec une augmentation de la quantite de source de carbone (saccharose et alginate). La caracterisation du materiau a permis de suivre les reactions de transformation de la source de carbone vers le graphene. Cette caracterisation a ete faite par la spectroscopie IRTF et Raman, l'analyse thermogravimetrique (TGA), la surface specifique (methode BET) et le microscope electronique a balayage (MEB). La conductivite electrique a ete mesuree par un spectrometre dielectrique et en fonction de la pression appliquee avec un multimetre. Le materiau realise etait incorpore dans une matrice avec un polyethylene a basse densite pour avoir un polymere avec des caracteristiques specifiques. La conductivite thermique a ete ensuite mesuree suivant la norme ASTM E1530. L'echantillon realise avec la deuxieme methode avec une proportion de bentonite pour 5 proportions de saccharose (M2 B1 : S5) signale la possibilite de produire des materiaux de graphene a partir de ressources naturelles. La surface specifique a considerablement augmente de (75,88 m2/g) pour bentonite non traiter a (139,76 m2/g) pour l'echantillon (M2 B1 : S5). Une augmentation significative de la conductivite par pression (95,3 S/m sous une pression de 6,5 MPa par rapport a 1,45*10 -3 S/m pour la bentonite) et la conductivite thermique dans le polyethylene basse densite a une concentration de 10% d'additif (0,332 W/m.K a 0,279 W/m.K) ont ete observes pour le meme echantillon M2 B1 : S5 comparativement a la bentonite non traitee. Les applications possibles sont par exemple les senseurs et les actuateurs par pression.

Frustration-guided motion planning reveals conformational transitions in proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Budday, Dominik; Fonseca, Rasmus; Leyendecker, Sigrid

Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here in this paper, we present a new, robotics-inspired motion planning procedure called dCCRRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eightmore » proteins determined in two conformations separated by, on average, 7.5Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. Additionally, we then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions.Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/.« less

Target dose conformity in 3-dimensional conformal radiotherapy and intensity modulated radiotherapy.

PubMed

Wu, Vincent W C; Kwong, Dora L W; Sham, Jonathan S T

2004-05-01

Dose conformity to the planning target volume is an important criterion in radiotherapy treatment planning, for which the conformity index is a useful assessment tool. The purpose of this study is to compare the differences in CI for the treatment planning of four cancers including the nasopharynx, oesophagus, lung and prostate. Seventy patients with cancers of nasopharynx (30), oesophagus (15), lung (15) and prostate (10) were recruited. Each of these patients was planned with three sets of treatment plans using the FOCUS treatment planning system: the forward and inverse 3DCRT plans and the IMRT plan. The CI was generated for each treatment plan. The mean CI from each cancer patient group was calculated and compared with the other three cancer groups. The mean value of CI was also compared among the three planning methods. The oesophageal and lung cancers demonstrated relatively higher overall mean CI values (0.64 and 0.62, respectively), whereas that of the nasopharynx and prostate were lower (0.54 and 0.50, respectively). With regards to the planning method groups, the IMRT plans produced the highest overall mean CI (0.62), while those for the forward and inverse 3DCRT were similar (0.57 and 0.55, respectively). For the four selected cancers, oesophageal and lung cancers were easier to conform than the nasopharyngeal and prostate cancers. The IMRT plans were more effective in achieving better dose conformity than that of the 3DCRT.

Frustration-guided motion planning reveals conformational transitions in proteins.

PubMed

Budday, Dominik; Fonseca, Rasmus; Leyendecker, Sigrid; van den Bedem, Henry

2017-10-01

Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics-inspired motion planning procedure called dCC-RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5 Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. We then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25 Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions. Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/. © 2017 Wiley Periodicals, Inc.

Frustration-guided motion planning reveals conformational transitions in proteins

DOE PAGES

Budday, Dominik; Fonseca, Rasmus; Leyendecker, Sigrid; ...

2017-07-12

Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here in this paper, we present a new, robotics-inspired motion planning procedure called dCCRRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eightmore » proteins determined in two conformations separated by, on average, 7.5Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. Additionally, we then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions.Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/.« less

New parasite inhibitors encompassing novel conformationally-locked 5'-acyl sulfamoyl adenosines.

PubMed

Dixit, Shailesh S; Upadhayaya, Ram Shankar; Chattopadhyaya, Jyoti

2012-08-14

We describe the design, synthesis and biological evaluation of conformationally-locked 5'-acyl sulfamoyl adenosine derivatives as new parasitic inhibitors against Trypanosoma and Leishmania. The conformationally-locked (3'-endo, North-type) nucleosides have been synthesized by covalently attaching a 4'-CH(2)-O-2' bridge () across C2'-C4' of adenosine in order to reduce the conformational flexibility of the pentose ring. This is designed to decrease the entropic penalty for complex formation with the target protein, which may improve free-energy of stabilization of the complex leading to improved potency. Conformationally-locked 5'-acyl sulfamoyl adenosine derivatives (16-22) were tested against parasitic protozoans for the first time in this work, and showed potent inhibition of Trypanosoma cruzi, Trypanosoma brucei, Trypanosoma rhodesiense and Leishmania infantum with IC(50) = 0.25-0.51 μM. In particular, the potent 5'-pentanyl acyl sulfamoyl adenosine derivative 17 (IC(50) = 0.25 μM) against intracellular L. infantum amastigotes and Trypanosoma subspecies is interesting in view of its almost insignificant cytotoxicity in murine macrophage host cells (CC(50) >4 μM) and in diploid human fibroblasts MRC-5 cell lines (CC(50) 4 μM). This work also suggests that variable alkyl chain length of the acyl group on the acylsulfamoyl side chain at 5' can modulate the toxicity of 5'-O-sulfamoylnucleoside analogues. This conformationally-locked sulfamoyl adenosine scaffold presents some interesting possibilities for further drug design and lead optimization.

Ceremony 25th birthday Cern

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2006-05-08

Célébration du 25ème anniversaire du Cern (jour par jour) avec discours de L.Van Hove et J.B.Adams, des interludes musicals offerts par Mme Mey et ses collègues (au debut 1.mouvement du quatuor avec piano no 3 de L.van Beethoven) Les directeurs généraux procéderont à la remise du souvenir aux membres de personnel ayant 25 années de service dans l'organisation. Un témoignage de reconnaissance est auss fait à l'interprète Mme Zwerner

Filtrage Lineaire par Morceaux Avec Petit Bruit d’Observation (Piecewise Linear Filtering with Small Observation Noise)

DTIC Science & Technology

1990-11-19

stir divers exemple-s le comportement des filtres l)r0pose5 par ra.)pDort ceux du processus estliner et dti filtre optimal obtenu de fa~on approch6e...Piecewise monotone filtering with small observation noise, Siam J., Control Optim. 20, 261-285, 1989 . Vii [10 W.ll. Fleming and R.W. Rishel...Milbeiro, de Oliveira : Filtres approch~s pour un probl~me de filtrage non lin~aire discret avec petit bruit d’observation,rapport INVRIA, 1142. 1989

Opacités nodulaires diffuses et calcifiées

PubMed Central

Jabri, Hasna; Bopaka, Régis Gothard; Lakhdar, Nawal; Moubachir, Houda; Khattabi, Wiam El; Afif, Hicham

2016-01-01

L’adénocarcinome pulmonaire est difficile à évoquer d’emblée devant les données anamnestiques et même radiologiques. Nous rapportons une observation d’une femme présentant une dyspnée avec la radiographie une opacité micronodulaire disséminée, confluente dans les deux champs pulmonaires avec des calcifications par endroit. L’histologie à travers les biopsies transbronchiques a permis de poser le diagnostic. Le pronostic était sombre par le décès de la patiente. PMID:27795800

A method for determining the actual rate of orientation switching of DNA self-assembled monolayers using optical and electrochemical frequency response analysis.

PubMed

Casanova-Moreno, J; Bizzotto, D

2015-02-17

Electrostatic control of the orientation of fluorophore-labeled DNA strands immobilized on an electrode surface has been shown to be an effective bioanalytical tool. Modulation techniques and later time-resolved measurements were used to evaluate the kinetics of the switching between lying and standing DNA conformations. These measurements, however, are the result of a convolution between the DNA "switching" response time and the other frequency limited responses in the measurement. In this work, a method for analyzing the response of a potential driven DNA sensor is presented by calculating the potential effectively dropped across the electrode interface (using electrochemical impedance spectroscopy) as opposed to the potential applied to the electrochemical cell. This effectively deconvolutes the effect of the charging time on the observed frequency response. The corrected response shows that DNA is able to switch conformation faster than previously reported using modulation techniques. This approach will ensure accurate measurements independent of the electrochemical system, removing the uncertainty in the analysis of the switching response, enabling comparison between samples and measurement systems.

The First Extracellular Linker Is Important for Several Aspects of the Gating Mechanism of Human TRPA1 Channel

PubMed Central

Marsakova, Lenka; Barvik, Ivan; Zima, Vlastimil; Zimova, Lucie; Vlachova, Viktorie

2017-01-01

Transient receptor potential ankyrin 1 (TRPA1) is an excitatory ion channel involved in pain, inflammation and itching. This channel gates in response to many irritant and proalgesic agents, and can be modulated by calcium and depolarizing voltage. While the closed-state structure of TRPA1 has been recently resolved, also having its open state is essential for understanding how this channel works. Here we use molecular dynamics simulations combined with electrophysiological measurements and systematic mutagenesis to predict and explore the conformational changes coupled to the expansion of the presumptive channel's lower gate. We show that, upon opening, the upper part of the sensor module approaches the pore domain of an adjacent subunit and the conformational dynamics of the first extracellular flexible loop may govern the voltage-dependence of multimodal gating, thereby serving to stabilize the open state of the channel. These results are generally important in understanding the structure and function of TRPA1 and offer new insights into the gating mechanism of TRPA1 and related channels. PMID:28197074

Insights into Autoregulation of Notch3 from Structural and Functional Studies of Its Negative Regulatory Region.

PubMed

Xu, Xiang; Choi, Sung Hee; Hu, Tiancen; Tiyanont, Kittichoat; Habets, Roger; Groot, Arjan J; Vooijs, Marc; Aster, Jon C; Chopra, Rajiv; Fryer, Christy; Blacklow, Stephen C

2015-07-07

Notch receptors are transmembrane proteins that undergo activating proteolysis in response to ligand stimulation. A negative regulatory region (NRR) maintains receptor quiescence by preventing protease cleavage prior to ligand binding. We report here the X-ray structure of the NRR of autoinhibited human Notch3, and compare it with the Notch1 and Notch2 NRRs. The overall architecture of the autoinhibited conformation, in which three LIN12-Notch repeat (LNR) modules wrap around a heterodimerization domain, is preserved in Notch3, but the autoinhibited conformation of the Notch3 NRR is less stable. The Notch3 NRR uses a highly conserved surface on the third LNR module to form a dimer in the crystal. Similar homotypic interfaces exist in Notch1 and Notch2. Together, these studies reveal distinguishing structural features associated with increased basal activity of Notch3, demonstrate increased ligand-independent signaling for disease-associated mutations that map to the Notch3 NRR, and identify a conserved dimerization interface present in multiple Notch receptors. Copyright © 2015 Elsevier Ltd. All rights reserved.

Signal Transduction by BvgS Sensor Kinase

PubMed Central

Dupré, Elian; Lesne, Elodie; Guérin, Jérémy; Lensink, Marc F.; Verger, Alexis; de Ruyck, Jérôme; Brysbaert, Guillaume; Vezin, Hervé; Locht, Camille; Antoine, Rudy; Jacob-Dubuisson, Françoise

2015-01-01

The two-component sensory transduction system BvgAS controls the virulence regulon of the whooping-cough agent Bordetella pertussis. The periplasmic moiety of the homodimeric sensor kinase BvgS is composed of four bilobed Venus flytrap (VFT) perception domains followed by α helices that extend into the cytoplasmic membrane. In the virulent phase, the default state of B. pertussis, the cytoplasmic enzymatic moiety of BvgS acts as kinase by autophosphorylating and transferring the phosphoryl group to the response regulator BvgA. Under laboratory conditions, BvgS shifts to phosphatase activity in response to modulators, notably nicotinate ions. Here we characterized the effects of nicotinate and related modulators on the BvgS periplasmic moiety by using site-directed mutagenesis and in silico and biophysical approaches. Modulators bind with low affinity to BvgS in the VFT2 cavity. Electron paramagnetic resonance shows that their binding globally affects the conformation and dynamics of the periplasmic moiety. Specific amino acid substitutions designed to slacken interactions within and between the VFT lobes prevent BvgS from responding to nicotinate, showing that BvgS shifts from kinase to phosphatase activity in response to this modulator via a tense transition state that involves a large periplasmic structural block. We propose that this transition enables the transmembrane helices to adopt a distinct conformation that sets the cytoplasmic enzymatic moiety in the phosphatase mode. The bona fide, in vivo VFT ligands that remain to be identified are likely to trigger similar effects on the transmembrane and cytoplasmic moieties. This mechanism may be relevant to the other VFT-containing sensor kinases homologous to BvgS. PMID:26203186

Structural and molecular conformation of myosin in intact muscle fibers by second harmonic generation

NASA Astrophysics Data System (ADS)

Nucciotti, V.; Stringari, C.; Sacconi, L.; Vanzi, F.; Linari, M.; Piazzesi, G.; Lombardi, V.; Pavone, F. S.

2009-02-01

Recently, the use of Second Harmonic Generation (SHG) for imaging biological samples has been explored with regard to intrinsic SHG in highly ordered biological samples. As shown by fractional extraction of proteins, myosin is the source of SHG signal in skeletal muscle. SHG is highly dependent on symmetries and provides selective information on the structural order and orientation of the emitting proteins and the dynamics of myosin molecules responsible for the mechano-chemical transduction during contraction. We characterise the polarization-dependence of SHG intensity in three different physiological states: resting, rigor and isometric tetanic contraction in a sarcomere length range between 2.0 μm and 4.0 μm. The orientation of motor domains of the myosin molecules is dependent on their physiological states and modulate the SHG signal. We can discriminate the orientation of the emitting dipoles in four different molecular conformations of myosin heads in intact fibers during isometric contraction, in resting and rigor. We estimate the contribution of the myosin motor domain to the total second order bulk susceptibility from its molecular structure and its functional conformation. We demonstrate that SHG is sensitive to the fraction of ordered myosin heads by disrupting the order of myosin heads in rigor with an ATP analog. We estimate the fraction of myosin motors generating the isometric force in the active muscle fiber from the dependence of the SHG modulation on the degree of overlap between actin and myosin filaments during an isometric contraction.

Membrane Phospholipid Augments Cytochrome P4501a Enzymatic Activity by Modulating Structural Conformation during Detoxification of Xenobiotics

PubMed Central

Ghosh, Manik C.; Ray, Arun K.

2013-01-01

Cytochrome P450 is a superfamily of membrane-bound hemoprotein that gets involved with the degradation of xenobiotics and internal metabolites. Accumulated body of evidence indicates that phospholipids play a crucial role in determining the enzymatic activity of cytochrome P450 in the microenvironment by modulating its structure during detoxification; however, the structure-function relationship of cytochrome P4501A, a family of enzymes responsible for degrading lipophilic aromatic hydrocarbons, is still not well defined. Inducibility of cytochrome P4501A in cultured catfish hepatocytes in response to carbofuran, a widely used pesticide around the world, was studied earlier in our laboratory. In this present investigation, we observed that treating catfish with carbofuran augmented total phospholipid in the liver. We examined the role of phospholipid on the of cytochrome P4501A-marker enzyme which is known as ethoxyresorufin-O-deethylase (EROD) in the context of structure and function. We purified the carbofuran-induced cytochrome P4501A protein from catfish liver. Subsequently, we examined the enzymatic activity of purified P4501A protein in the presence of phospholipid, and studied how the structure of purified protein was influenced in the phospholipid environment. Membrane phospholipid appeared to accelerate the enzymatic activity of EROD by changing its structural conformation and thus controlling the detoxification of xenobiotics. Our study revealed the missing link of how the cytochrome P450 restores its enzymatic activity by changing its structural conformation in the phospholipid microenvironment. PMID:23469105

Toxicity and dosimetric analysis of non-small cell lung cancer patients undergoing radiotherapy with 4DCT and image-guided intensity modulated radiotherapy: a regional centre's experience.

PubMed

Livingston, Gareth C; Last, Andrew J; Shakespeare, Thomas P; Dwyer, Patrick M; Westhuyzen, Justin; McKay, Michael J; Connors, Lisa; Leader, Stephanie; Greenham, Stuart

2016-09-01

For patients receiving radiotherapy for locally advance non-small cell lung cancer (NSCLC), the probability of experiencing severe radiation pneumonitis (RP) appears to rise with an increase in radiation received by the lungs. Intensity modulated radiotherapy (IMRT) provides the ability to reduce planned doses to healthy organs at risk (OAR) and can potentially reduce treatment-related side effects. This study reports toxicity outcomes and provides a dosimetric comparison with three-dimensional conformal radiotherapy (3DCRT). Thirty curative NSCLC patients received radiotherapy using four-dimensional computed tomography and five-field IMRT. All were assessed for early and late toxicity using common terminology criteria for adverse events. All plans were subsequently re-planned using 3DCRT to the same standard as the clinical plans. Dosimetric parameters for lungs, oesophagus, heart and conformity were recorded for comparison between the two techniques. IMRT plans achieved improved high-dose conformity and reduced OAR doses including lung volumes irradiated to 5-20 Gy. One case each of oesophagitis and erythema (3%) were the only Grade 3 toxicities. Rates of Grade 2 oesophagitis were 40%. No cases of Grade 3 RP were recorded and Grade 2 RP rates were as low as 3%. IMRT provides a dosimetric benefit when compared to 3DCRT. While the clinical benefit appears to increase with increasing target size and increasing complexity, IMRT appears preferential to 3DCRT in the treatment of NSCLC.

Membrane phospholipid augments cytochrome P4501a enzymatic activity by modulating structural conformation during detoxification of xenobiotics.

PubMed

Ghosh, Manik C; Ray, Arun K

2013-01-01

Cytochrome P450 is a superfamily of membrane-bound hemoprotein that gets involved with the degradation of xenobiotics and internal metabolites. Accumulated body of evidence indicates that phospholipids play a crucial role in determining the enzymatic activity of cytochrome P450 in the microenvironment by modulating its structure during detoxification; however, the structure-function relationship of cytochrome P4501A, a family of enzymes responsible for degrading lipophilic aromatic hydrocarbons, is still not well defined. Inducibility of cytochrome P4501A in cultured catfish hepatocytes in response to carbofuran, a widely used pesticide around the world, was studied earlier in our laboratory. In this present investigation, we observed that treating catfish with carbofuran augmented total phospholipid in the liver. We examined the role of phospholipid on the of cytochrome P4501A-marker enzyme which is known as ethoxyresorufin-O-deethylase (EROD) in the context of structure and function. We purified the carbofuran-induced cytochrome P4501A protein from catfish liver. Subsequently, we examined the enzymatic activity of purified P4501A protein in the presence of phospholipid, and studied how the structure of purified protein was influenced in the phospholipid environment. Membrane phospholipid appeared to accelerate the enzymatic activity of EROD by changing its structural conformation and thus controlling the detoxification of xenobiotics. Our study revealed the missing link of how the cytochrome P450 restores its enzymatic activity by changing its structural conformation in the phospholipid microenvironment.

Clinical results of conformal versus intensity-modulated radiotherapy using a focal simultaneous boost for muscle-invasive bladder cancer in elderly or medically unfit patients.

PubMed

Lutkenhaus, Lotte J; van Os, Rob M; Bel, Arjan; Hulshof, Maarten C C M

2016-03-18

For elderly or medically unfit patients with muscle-invasive bladder cancer, cystectomy or chemotherapy are contraindicated. This leaves radical radiotherapy as the only treatment option. It was the aim of this study to retrospectively analyze the treatment outcome and associated toxicity of conformal versus intensity-modulated radiotherapy (IMRT) using a focal simultaneous tumor boost for muscle-invasive bladder cancer in patients not suitable for cystectomy. One hundred eighteen patients with T2-4 N0-1 M0 bladder cancer were analyzed retrospectively. Median age was 80 years. Treatment consisted of either a conformal box technique or IMRT and included a simultaneous boost to the tumor. To enable an accurate boost delivery, fiducial markers were placed around the tumor. Patients were treated with 40 Gy in 20 fractions to the elective treatment volumes, and a daily tumor boost up to 55-60 Gy. Clinical complete response was seen in 87 % of patients. Three-year overall survival was 44 %, with a locoregional control rate of 73 % at 3 years. Toxicity was low, with late urinary and intestinal toxicity rates grade ≥ 2 of 14 and 5 %, respectively. The use of IMRT reduced late intestinal toxicity, whereas fiducial markers reduced acute urinary toxicity. Radical radiotherapy using a focal boost is feasible and effective for elderly or unfit patients, with a 3-year locoregional control of 73 %. Toxicity rates were low, and were reduced by the use of IMRT and fiducial markers.

Proof of Principle of Ocular sparing in dogs with sinonasal tumors treated with intensity-modulated radiation therapy

PubMed Central

Lawrence, Jessica A.; Forrest, Lisa J.; Turek, Michelle M.; Miller, Paul E.; Mackie, T. Rockwell; Jaradat, Hazim A.; Vail, David M.; Dubielzig, Richard R.; Chappell, Richard; Mehta, Minesh P.

2010-01-01

Intensity modulated radiation therapy (IMRT) allows optimization of radiation dose delivery to complex tumor volumes with rapid dose drop-off to surrounding normal tissues. A prospective study was performed to evaluate the concept of conformal avoidance using IMRT in canine sinonasal cancer. The potential of IMRT to improve clinical outcome with respect to acute and late ocular toxicity was evaluated. Thirty-one dogs with sinonasal cancer were treated definitively with IMRT using helical tomotherapy and/or dynamic multileaf collimator (DMLC) delivery. Ocular toxicity was evaluated prospectively and compared to a comparable group of historical controls treated with conventional two-dimensional radiotherapy (2D-RT) techniques. Treatment plans were devised for each dog using helical tomotherapy and DMLC that achieved the target dose to the planning treatment volume and limited critical normal tissues to the prescribed dose-volume constraints. Overall acute and late toxicities were limited and minor, detectable by an experienced observer. This was in contrast to the profound ocular morbidity observed in the historical control group treated with 2D-RT. Overall median survival for IMRT treated and 2D treated dogs was 420 days and 411 days, respectively. Compared with conventional techniques, IMRT reduced dose delivered to eyes and resulted in bilateral ocular sparing in the dogs reported herein. These data provide proof-of-principle that conformal avoidance radiotherapy can be delivered through high conformity IMRT, resulting in decreased normal tissue toxicity as compared to historical controls treated with 2D-RT. PMID:20973393

[Comparison of SIB-IMRT treatment plans for upper esophageal carcinoma].

PubMed

Fu, Wei-hua; Wang, Lv-hua; Zhou, Zong-mei; Dai, Jian-rong; Hu, Yi-min

2003-06-01

To implement simultaneous integrated boost intensity-modulated radiotherapy(SIB-IMRT) plans for upper esophageal carcinoma and investigate the dose profiles of tumor and electively treated region and the dose to organs at risk (OARs). SIB-IMRT plans were designed for two patients with upper esophageal carcinoma. Two target volumes were predefined: PTV1, the target volume of the primary lesion, which was given to 67.2 Gy, and PTV2, the target volume of electively treated region, which was given to 50.4 Gy. With the same dose-volume constraints, but different beams arrangements (3, 5, 7, or 9 equispaced coplanar beams), four plans were generated. Indices, including dose distribution, dose volume histogram (DVH) and conformity index, were used for comparison of these plans. The plan with three intensity-modulated beams could produce good dose distribution for the two target volumes. The dose conformity to targets and the dose to OARs were improved as the beam number increased. The dose distributions in targets changed little when the beam number increased from 7 to 9. Five to seven intensity-modulated beams can produce desirable dose distributions for simultaneous integrated boost (SIB) treatment for upper esophageal carcinoma. The primary tumor can get higher equivalent dose by SIB treatments. It is easier and more efficient to design plans with equispaced coplanar beams. The efficacy of SIB-IMRT remains to be determined by the clinical outcome.

Resveratrol Interferes with an Early Step in the Fibrillization Pathway of Human Lysozyme and Modulates it towards Less-Toxic, Off-Pathway Aggregates.

PubMed

Kamal Zaidi, Fatima; Bhat, Rajiv

2018-01-18

The effect of resveratrol, a polyphenol in red wine, on the amyloid fibril formation of human lysozyme (HuL) was investigated, towards elucidating the mechanism of resveratrol action and probing its role as a possible modulator of lysozyme aggregation and toxicity. By using a number of biophysical tools, resveratrol was observed to alter the fibrillization kinetics of HuL and inhibit its fibrillization by binding with weak to moderate affinity to the conformations populated at the early stages of the pathway with concomitant stabilization of these initial conformations. The marginal decrease in the lifetime of HuL in the presence of resveratrol by time-resolved fluorescence measurements indicated the involvement of a static quenching mechanism in the interaction between HuL and resveratrol. Docking studies predicted the binding of resveratrol to aggregation-prone regions in HuL, and structure and activity analyses demonstrated the retention of much of the α-helical structure and activity of HuL in the presence of resveratrol. Resveratrol modulated the fibrillization pathway towards less-hydrophobic, less-toxic, off-pathway aggregates. These results demonstrate that binding of resveratrol to HuL could protect against the formation of pathogenic, cytotoxic aggregates formed in amyloidogenic disorders, such as systemic amyloidosis; thus suggesting its potential as a plausible therapeutic agent against lysozyme amyloidosis. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analyse des facteurs histo-pronostiques du cancer du rectum non métastatique dans une série ouest Algérienne de 58 cas au CHU-Tlemcen

PubMed Central

Mesli, Smain Nabil; Regagba, Derbali; Tidjane, Anisse; Benkalfat, Mokhtar; Abi-Ayad, Chakib

2016-01-01

Introduction L'objectif de notre travail est d'analyser les facteurs histo-pronostiques des cancers du rectum non métastatique opérés au service de chirurgie «A» de Tlemcen à ouest Algérien durant une période de six ans. Méthodes Etude rétrospective de 58 patients qui avait un adénocarcinome rectal. Le critère de jugement était la survie. Les paramètres étudiés, le sexe, l’âge, stade tumoral, et les récidives tumorales. Résultats L’âge moyen était de 58 ans. Avec 52% d'hommes contre 48% femmes avec sex-ratio (1,08). Le siège tumoral était: moyen rectum avec 41,37%, 34,48% au bas rectum et dans 24,13% au haut rectum. La classification TNM avec 17,65% au stade I, 18,61% au stade II, 53, 44% au stade III et 7,84% au stade IV. La survie médiane globale était de 40 mois ±2,937 mois. La survie en fonction du stade tumoral, le stade III et IV avait un faible taux de survie (19%) a 3 ans contre le stade I, II avait un taux de survie de (75%) (P = 0,000) (IC 95%). Les patients avec récidives tumorales avaient un taux de survie faible à 3 ans par rapport à ceux n'ayant pas eu de récidive (30,85% Vs 64,30% P = 0,043). Conclusion Dans cette série, l’étude uni varié des différents facteurs pronostiques conditionnant la survie n'a permis de retenir que trois facteurs influençant la survie, à savoir la taille tumorale, le stade, et les récidives tumorales. En analyse multi variée en utilisant le modèle Cox un seul facteur été retenu la récidive tumorale. PMID:27583069

Forme pseudotumorale de la tuberculose pulmonaire et les difficultés diagnostic: à propos d’un cas

PubMed Central

Ouarssani, Aziz; Atoini, Fouad; Reda, Rafik; Lhou, Fatima Ait; Rguibi, Mustapha Idrissi

2013-01-01

La tuberculose pulmonaire est un problème majeur de santé publique. Dans sa forme commune, le diagnostic est habituellement aisé, mais elle peut se présenter sous une forme trompeuse et entrainer un retard diagnostic et thérapeutique. Nous rapportons le cas d’un patient âgé de 25ans, étudiant, sans antécédents pathologiques particuliers, hospitalisé dans notre formation pour un syndrome bronchique trainant avec altération de l’état général. L’examen clinique pleuropulmonaire est normal, l’examen des aires ganglionnaires trouve une adénopathie sus claviculaire droite, la radiographie thoracique de face objective une opacité hilaire droite hétérogène à contours irréguliers, la TDM thoracique retrouve un processus lésionnel tissulaire du lobe supérieur droit qui s’étend vers le médiastin et englobe partiellement la veine cave supérieure avec une adénopathie latérotracheale droite nécrosée. La fibroscopie bronchique objective un élargissement des éperons intersegmentaires du lobe supérieur droit, les biopsies réalisées avec étude histologique sont non concluantes. Les recherches de BK dans les expectorations et dans le liquide d’aspiration bronchique sont negatives. L’IDR à la tuberculine est à 15mm. C’est la ponction transparietale scannoguidée avec étude anatomopathologique qui confirme le diagnostic de tuberculose caseofolliculaire. La sérologie VIH est négative. Le diagnostic de tuberculose pulmonaire pseudotumorale chez un immunocompétent a été retenu et le patient a été mis sous traitement antibacillaire (régime standard national Marocain) par rifampicine, isoniazide, pyrazinamide et éthambutol pendant 6 mois avec évolution clinique et radiologique favorable. La tuberculose pulmonaire ne cesse de tromper le clinicien par son polymorphisme clinique et radiologique, elle doit être évoquée devant toute atteinte pulmonaire d’allure tumorale pour permettre une prise en charge précoce de la maladie. PMID:23646217

Place du traitement chirurgical sous circulation extracorporelle à cœur battant dans les cancers du rein avec envahissement cave supra-diaphragmatique: à propos de sept cas

PubMed Central

Lahyani, Mounir; Karmouni, Tarik; Elkhader, Khalid; Koutani, Abdellatif; Andaloussi, Ahmed Ibn Attya

2014-01-01

Ce travail vise à analyser les résultats de la néphrectomie avec thrombectomie atrio-cave sous circulation extracorporelle (CEC) chez sept patients ayant un cancer du rein avec envahissement cave supra-diaphragmatique et de discuter les indications opératoires. Sept patients, six hommes et une femme dont l’âge varie entre 46ans et 65ans, ont été opérés d'un cancer du rein avec extension atrio-cave. L’écho-doppler a toujours permis la mise en évidence de l'extension veineuse mais la limite supérieure du thrombus était formellement identifiée par l'examen tomodensitométrique quatre fois, et par la résonance magnétique nucléaire dans tous les cas. Tous les patients ont été opérés sous CEC à cœur battant en normothermie. Un seul décès postopératoire est survenu. La durée du séjour en réanimation a été de 4,5 jours. Cinq patients ont eu à distance une dissémination métastatique. Cinq malades ont eu une médiane de survie de 11,5 mois (de 7 à16). Un malade a subi une métastasectomie pulmonaire 6 mois après la néphrectomie. L'exérèse des thrombi atrio-caves a été facilitée par la CEC avec une mortalité et une morbidité postopératoires acceptables mais les résultats à distance ont été décevants. Cette intervention ne peut être proposée qu'aux patients n'ayant aucune extension locorégionale et générale décelable, ce qui souligne l'importance des examens morphologiques préopératoires. PMID:25995777

Fréquence et caractéristiques des AVC impliquant les artères perforantes dans le Service de Neurologie de l’Hopital Bafelatanana, Antananarivo

PubMed Central

Rasaholiarison, Nomena Finiavana; Randrianasolo, Rahamefy Odilon; Rajaonarison, Lala Andriamasinavalona; Rakotomanana, Jenny Larissa; Razafimahefa, Julien; Tehindrazanarivelo, Alain Djacoba

2017-01-01

Introduction Les accidents vasculaires cérébraux des artères perforantes sont surtout des artériolopathies. Ils évoluent vers la démence et la récurrence. Pour mieux prévenir ces complications notre étude avait pour but d'évaluer la fréquence et les caractéristiques de ces AVC. Méthodes c'est une étude descriptive rétrospective du 01 Mars au 25 Septembre 2015 au service de Neurologie CHU-JRB. Ont été inclus les patients présentant un déficit neurologique brutal et un scanner cérébral avec atteinte du territoire profonde. Les caractéristiques des AVC des artères perforantes ont été recueillies. Les données étaient traitées par le logiciel SPSS 20. Résultats Quatre-vingt-trois (48,25%) patients avaient des AVC des artères perforantes sur 172 AVC. Pour les AVC des artères perforantes la population était jeune avec 65,06% moins de 65 ans et à prédominance masculine avec 61,44%. Les formes hémorragiques étaient à 67,46%. Trente et un patients (37,34%) ont connu des récurrences et parmi eux presque le quart avait 2 récurrences avec 38,70% en moins de un an. Tous les patients avec récurrence avaient un trouble dysexécutif (p < 0,0001) et une mauvaise observance thérapeutique d'antihypertenseur. La mortalité n'était qu'à 6,02% pour ces types d'AVC pendant l'hospitalisation. Conclusion Un suivi spécifique en neurologie est nécessaire dès le premier accident vasculaire cérébral d'artère perforante pour dépister un début de démence et prévenir les récurrences. PMID:29255546

Cancer du sein au Cameroun, profil histo-épidémiologique: à propos de 3044 cas

PubMed Central

Engbang, Jean Paul Ndamba; Essome, Henri; Koh, Valère Mve; Simo, Godefroy; Essam, Jean Daniel Sime; Mouelle, Albert Sone; Essame, Jean Louis Oyono

2015-01-01

Décrire les caractéristiques épidémiologiques et histo-pathologiques des tumeurs malignes du sein au Cameroun. Il s'agissait d'une étude rétrospective descriptive portant sur les tumeurs malignes du sein, colligées, dans les registres des différents laboratoires d'Anatomie Pathologique publiques et privés repartis dans cinq régions (centre, littoral, Ouest, Nord-ouest, Sud-ouest), pendant une période de 10 ans (2004-2013). Les paramètres étudiés étaient la fréquence, l’âge, le sexe, la localisation, le type et le grade histologique, et les récepteurs hormonaux. Un total de 3044 cas de cancers du sein a été recensé, soit une fréquence annuelle de 304,4 cas en moyenne. Le sexe féminin était le plus représenté avec 2971 cas (97,60%) et les hommes avec 73 cas (2,40%), soit un sexe ratio (H/F) de 0,02. L’âge moyen des patients était de 46±15,87 ans, avec des extrêmes de 13 et 95 ans. Selon la localisation, le sein gauche était atteint dans 1244 cas (52%) et le sein droit dans 1115 cas (47%). Au plan histologique, on retrouvait essentiellement des carcinomes avec 96,50% des cas, des sarcomes 1,39%, des lymphomes 1,07% et la maladie de Paget du mamelon, 1,03%. Les tumeurs épithéliales étaient infiltrantes dans 2049 cas (84,46%), avec une prédominance du carcinome canalaire infiltrant (1870 cas) et non infiltrantes dans 377 cas (15,54%). Le grade histo-pronostic de SBR avait révélé une prédominance du grade II dans 66% des cas. Les cancers du sein restent une pathologie fréquente au Cameroun et atteignent principalement la population féminine en âge de procréer. Ils sont caractérisés par la prédominance du carcinome canalaire infiltrant. PMID:26523182

Concepts for the evolution of the Space Station Program

NASA Technical Reports Server (NTRS)

Michaud, Roger B.; Miller, Ladonna J.; Primeaux, Gary R.

1986-01-01

An evaluation is made of innovative but pragmatic waste management, interior and exterior orbital module construction, Space Shuttle docking, orbital repair operation, and EVA techniques applicable to the NASA Space Station program over the course of its evolution. Accounts are given of the Space Shuttle's middeck extender module, an on-orbit module assembly technique employing 'Pringles' stack-transportable conformal panels, a flexible Shuttle/Space Station docking tunnel, an 'expandable dome' for transfer of objects into the Space Station, and a Space Station dual-hatch system. For EVA operations, pressurized bubbles with articulating manipulator arms and EVA hard suits incorporating maneuvering, life support and propulsion capabilities, as well as an EVA gas propulsion system, are proposed. A Space Station ultrasound cleaning system is also discussed.

Generation of high-order Bessel vortex beam carrying orbital angular momentum using multilayer amplitude-phase-modulated surfaces in radiofrequency domain

NASA Astrophysics Data System (ADS)

Kou, Na; Yu, Shixing; Li, Long

2017-01-01

A high-order Bessel vortex beam carrying orbital angular momentum (OAM) is generated by using multilayer amplitude-phase-modulated surfaces (APMSs) at 10 GHz. The APMS transmitarray is composed of four-layer conformal square-loop (FCSL) surfaces with both amplitude and phase modulation. The APMS can transform a quasi-spherical wave emitted from the feeding source into a pseudo non-diffractive high-order Bessel vortex beam with OAM. The APMS for a second-order Bessel beam carrying OAM in the n = 2 mode is designed, fabricated, and measured. Full-wave simulation and measurement results confirm that Bessel vortex beams with OAM can be effectively generated using the proposed APMS transmitarray.

Feasibility of an online adaptive replanning method for cranial frameless intensity-modulated radiosurgery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Calvo, Juan Francisco, E-mail: jfcdrr@gmail.com; San José, Sol; Garrido, LLuís

2013-10-01

To introduce an approach for online adaptive replanning (i.e., dose-guided radiosurgery) in frameless stereotactic radiosurgery, when a 6-dimensional (6D) robotic couch is not available in the linear accelerator (linac). Cranial radiosurgical treatments are planned in our department using intensity-modulated technique. Patients are immobilized using thermoplastic mask. A cone-beam computed tomography (CBCT) scan is acquired after the initial laser-based patient setup (CBCT{sub setup}). The online adaptive replanning procedure we propose consists of a 6D registration-based mapping of the reference plan onto actual CBCT{sub setup}, followed by a reoptimization of the beam fluences (“6D plan”) to achieve similar dosage as originally wasmore » intended, while the patient is lying in the linac couch and the original beam arrangement is kept. The goodness of the online adaptive method proposed was retrospectively analyzed for 16 patients with 35 targets treated with CBCT-based frameless intensity modulated technique. Simulation of reference plan onto actual CBCT{sub setup}, according to the 4 degrees of freedom, supported by linac couch was also generated for each case (4D plan). Target coverage (D99%) and conformity index values of 6D and 4D plans were compared with the corresponding values of the reference plans. Although the 4D-based approach does not always assure the target coverage (D99% between 72% and 103%), the proposed online adaptive method gave a perfect coverage in all cases analyzed as well as a similar conformity index value as was planned. Dose-guided radiosurgery approach is effective to assure the dose coverage and conformity of an intracranial target volume, avoiding resetting the patient inside the mask in a “trial and error” way so as to remove the pitch and roll errors when a robotic table is not available.« less

Field-induced structural control of COx molecules adsorbed on graphene

NASA Astrophysics Data System (ADS)

Matsubara, Manaho; Okada, Susumu

2018-05-01

Using the density functional theory combined with both the van der Waals correction and the effective screening medium method, we investigate the energetics and electronic structures of CO and CO2 molecules adsorbed on graphene surfaces in the field-effect-transistor structure with respect to the external electric field by the excess electrons/holes. The binding energies of CO and CO2 molecules to graphene monotonically increase with increasing hole and electron concentrations. The increase occurs regardless of the molecular conformations to graphene and the counter electrode, indicating that the carrier injection substantially enhances the molecular adsorption on graphene. Injected carriers also modulate the stable molecular conformation, which is metastable in the absence of an electric field.

A novel role for the integrin-binding III-10 module in fibronectin matrix assembly.

PubMed

Hocking, D C; Smith, R K; McKeown-Longo, P J

1996-04-01

Fibronectin matrix assembly is a cell-dependent process which is upregulated in tissues at various times during development and wound repair to support the functions of cell adhesion, migration, and differentiation. Previous studies have demonstrated that the alpha 5 beta 1 integrin and fibronectin's amino terminus and III-1 module are important in fibronectin polymerization. We have recently shown that fibronectin's III-1 module contains a conformationally sensitive binding site for fibronectin's amino terminus (Hocking, D.C., J. Sottile, and P.J. McKeown-Longo. 1994. J. Biol. Chem. 269: 19183-19191). The present study was undertaken to define the relationship between the alpha 5 beta 1 integrin and fibronectin polymerization. Solid phase binding assays using recombinant III-10 and III-1 modules of human plasma fibronectin indicated that the III-10 module contains a conformation-dependent binding site for the III-1 module of fibronectin. Unfolded III-10 could support the formation of a ternary complex containing both III-1 and the amino-terminal 70-kD fragment, suggesting that the III-1 module can support the simultaneous binding of III-10 and 70 kD. Both unfolded III-10 and unfolded III-1 could support fibronectin binding, but only III-10 could promote the formation of disulfide-bonded multimers of fibronectin in the absence of cells. III-10-dependent multimer formation was inhibited by both the anti-III-1 monoclonal antibody, 9D2, and amino-terminal fragments of fibronectin. A fragment of III-10, termed III-10/A, was able to block matrix assembly in fibroblast monolayers. Similar results were obtained using the III-10A/RGE fragment, in which the RGD site had been mutated to RGE, indicating that III-I0/A was blocking matrix assembly by a mechanism distinct from disruption of integrin binding. Texas red-conjugated recombinant III-1,2 localized to beta 1-containing sites of focal adhesions on cells plated on fibronectin or the III-9,10 modules of fibronectin. Monoclonal antibodies against the III-1 or the III-9,10 modules of fibronectin blocked binding of III-1,2 to cells without disrupting focal adhesions. These data suggest that a role of the alpha 5 beta 1 integrin in matrix assembly is to regulate a series of sequential self-interactions which result in the polymerization of fibronectin.

Positively selected FimH residues enhance virulence during urinary tract infection by altering FimH conformation.

PubMed

Schwartz, Drew J; Kalas, Vasilios; Pinkner, Jerome S; Chen, Swaine L; Spaulding, Caitlin N; Dodson, Karen W; Hultgren, Scott J

2013-09-24

Chaperone-usher pathway pili are a widespread family of extracellular, Gram-negative bacterial fibers with important roles in bacterial pathogenesis. Type 1 pili are important virulence factors in uropathogenic Escherichia coli (UPEC), which cause the majority of urinary tract infections (UTI). FimH, the type 1 adhesin, binds mannosylated glycoproteins on the surface of human and murine bladder cells, facilitating bacterial colonization, invasion, and formation of biofilm-like intracellular bacterial communities. The mannose-binding pocket of FimH is invariant among UPEC. We discovered that pathoadaptive alleles of FimH with variant residues outside the binding pocket affect FimH-mediated acute and chronic pathogenesis of two commonly studied UPEC strains, UTI89 and CFT073. In vitro binding studies revealed that, whereas all pathoadaptive variants tested displayed the same high affinity for mannose when bound by the chaperone FimC, affinities varied when FimH was incorporated into pilus tip-like, FimCGH complexes. Structural studies have shown that FimH adopts an elongated conformation when complexed with FimC, but, when incorporated into the pilus tip, FimH can adopt a compact conformation. We hypothesize that the propensity of FimH to adopt the elongated conformation in the tip corresponds to its mannose binding affinity. Interestingly, FimH variants, which maintain a high-affinity conformation in the FimCGH tip-like structure, were attenuated during chronic bladder infection, implying that FimH's ability to switch between conformations is important in pathogenesis. Our studies argue that positively selected residues modulate fitness during UTI by affecting FimH conformation and function, providing an example of evolutionary tuning of structural dynamics impacting in vivo survival.

Inverse-optimized 3D conformal planning: Minimizing complexity while achieving equivalence with beamlet IMRT in multiple clinical sites

PubMed Central

Fraass, Benedick A.; Steers, Jennifer M.; Matuszak, Martha M.; McShan, Daniel L.

2012-01-01

Purpose: Inverse planned intensity modulated radiation therapy (IMRT) has helped many centers implement highly conformal treatment planning with beamlet-based techniques. The many comparisons between IMRT and 3D conformal (3DCRT) plans, however, have been limited because most 3DCRT plans are forward-planned while IMRT plans utilize inverse planning, meaning both optimization and delivery techniques are different. This work avoids that problem by comparing 3D plans generated with a unique inverse planning method for 3DCRT called inverse-optimized 3D (IO-3D) conformal planning. Since IO-3D and the beamlet IMRT to which it is compared use the same optimization techniques, cost functions, and plan evaluation tools, direct comparisons between IMRT and simple, optimized IO-3D plans are possible. Though IO-3D has some similarity to direct aperture optimization (DAO), since it directly optimizes the apertures used, IO-3D is specifically designed for 3DCRT fields (i.e., 1–2 apertures per beam) rather than starting with IMRT-like modulation and then optimizing aperture shapes. The two algorithms are very different in design, implementation, and use. The goals of this work include using IO-3D to evaluate how close simple but optimized IO-3D plans come to nonconstrained beamlet IMRT, showing that optimization, rather than modulation, may be the most important aspect of IMRT (for some sites). Methods: The IO-3D dose calculation and optimization functionality is integrated in the in-house 3D planning/optimization system. New features include random point dose calculation distributions, costlet and cost function capabilities, fast dose volume histogram (DVH) and plan evaluation tools, optimization search strategies designed for IO-3D, and an improved, reimplemented edge/octree calculation algorithm. The IO-3D optimization, in distinction to DAO, is designed to optimize 3D conformal plans (one to two segments per beam) and optimizes MLC segment shapes and weights with various user-controllable search strategies which optimize plans without beamlet or pencil beam approximations. IO-3D allows comparisons of beamlet, multisegment, and conformal plans optimized using the same cost functions, dose points, and plan evaluation metrics, so quantitative comparisons are straightforward. Here, comparisons of IO-3D and beamlet IMRT techniques are presented for breast, brain, liver, and lung plans. Results: IO-3D achieves high quality results comparable to beamlet IMRT, for many situations. Though the IO-3D plans have many fewer degrees of freedom for the optimization, this work finds that IO-3D plans with only one to two segments per beam are dosimetrically equivalent (or nearly so) to the beamlet IMRT plans, for several sites. IO-3D also reduces plan complexity significantly. Here, monitor units per fraction (MU/Fx) for IO-3D plans were 22%–68% less than that for the 1 cm × 1 cm beamlet IMRT plans and 72%–84% than the 0.5 cm × 0.5 cm beamlet IMRT plans. Conclusions: The unique IO-3D algorithm illustrates that inverse planning can achieve high quality 3D conformal plans equivalent (or nearly so) to unconstrained beamlet IMRT plans, for many sites. IO-3D thus provides the potential to optimize flat or few-segment 3DCRT plans, creating less complex optimized plans which are efficient and simple to deliver. The less complex IO-3D plans have operational advantages for scenarios including adaptive replanning, cases with interfraction and intrafraction motion, and pediatric patients. PMID:22755717

Evaluation of a mixed beam therapy for post-mastectomy breast cancer patients: bolus electron conformal therapy combined with intensity modulated photon radiotherapy and volumetric modulated photon arc therapy.

PubMed

Zhang, Rui; Heins, David; Sanders, Mary; Guo, Beibei; Hogstrom, Kenneth

2018-05-10

The purpose of this study was to assess the potential benefits and limitations of a mixed beam therapy, which combined bolus electron conformal therapy (BECT) with intensity modulated photon radiotherapy (IMRT) and volumetric modulated photon arc therapy (VMAT), for left-sided post-mastectomy breast cancer patients. Mixed beam treatment plans were produced for nine post-mastectomy radiotherapy (PMRT) patients previously treated at our clinic with VMAT alone. The mixed beam plans consisted of 40 Gy to the chest wall area using BECT, 40 Gy to the supraclavicular area using parallel opposed IMRT, and 10 Gy to the total planning target volume (PTV) by optimizing VMAT on top of the BECT+IMRT dose distribution. The treatment plans were created in a commercial treatment planning system (TPS), and all plans were evaluated based on PTV coverage, dose homogeneity index (DHI), conformity index (CI), dose to organs at risk (OARs), normal tissue complication probability (NTCP), and secondary cancer complication probability (SCCP). The standard VMAT alone planning technique was used as the reference for comparison. Both techniques produced clinically acceptable PMRT plans but with a few significant differences: VMAT showed significantly better CI (0.70 vs. 0.53, p < 0.001) and DHI (0.12 vs. 0.20, p < 0.001) over mixed beam therapy. For normal tissues, mixed beam therapy showed better OAR sparing and significantly reduced NTCP for cardiac mortality (0.23% vs. 0.80%, p = 0.01) and SCCP for contralateral breast (1.7% vs. 3.1% based on linear model, and 1.2% vs. 1.9% based on linear-exponential model, p < 0.001 in both cases), but showed significantly higher mean (50.8 Gy vs. 49.3 Gy, p < 0.001) and maximum skin doses (59.7 Gy vs. 53.3 Gy, p < 0.001) compared with VMAT. Patients with more tissue (minimum distance between the distal PTV surface and lung approximately > 0.5 cm and volume of tissue between the distal PTV surface and heart or lung approximately > 250 cm 3 ) between distal PTV surface and lung may benefit the most from mixed beam therapy. This work has demonstrated that mixed beam therapy (BECT+IMRT : VMAT = 4 : 1) produces clinically acceptable plans having reduced OAR doses and risks of side effects compared with VMAT. Even though VMAT alone produces more homogenous and conformal dose distributions, mixed beam therapy remains as a viable option for treating post-mastectomy patients, possibly leading to reduced normal tissue complications. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Modulation of kinase-inhibitor interactions by auxiliary protein binding: Crystallography studies on Aurora A interactions with VX-680 and with TPX2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Baoguang; Smallwood, Angela; Yang, Jingsong

2008-10-24

VX-680, also known as MK-0457, is an ATP-competitive small molecule inhibitor of the Aurora kinases that has entered phase II clinical trials for the treatment of cancer. We have solved the cocrystal structure of AurA/TPX2/VX-680 at 2.3 {angstrom} resolution. In the crystal structure, VX-680 binds to the active conformation of AurA. The glycine-rich loop in AurA adopts a unique bent conformation, forming a {pi}-{pi} interaction with the phenyl group of VX-680. In contrast, in the published AurA/VX-680 structure, VX-680 binds to AurA in the inactive conformation, interacting with a hydrophobic pocket only present in the inactive conformation. These data suggestmore » that TPX2, a protein cofactor, can alter the binding mode of VX-680 with AurA. More generally, the presence of physiologically relevant cofactor proteins can alter the kinetics, binding interactions, and inhibition of enzymes, and studies with these multiprotein complexes may be beneficial to the discovery and optimization of enzyme inhibitors as therapeutic agents.« less

Change in single cystathionine β-synthase domain-containing protein from a bent to flat conformation upon adenosine monophosphate binding.

PubMed

Jeong, Byung-Cheon; Park, Si Hoon; Yoo, Kyoung Shin; Shin, Jeong Sheop; Song, Hyun Kyu

2013-07-01

Cystathionine β-synthase (CBS) domains are small intracellular modules that can act as binding domains for adenosine derivatives, and they may regulate the activity of associated enzymes or other functional domains. Among these, the single CBS domain-containing proteins, CBSXs, from Arabidopsis thaliana, have recently been identified as redox regulators of the thioredoxin system. Here, the crystal structure of CBSX2 in complex with adenosine monophosphate (AMP) is reported at 2.2Å resolution. The structure of dimeric CBSX2 with bound-AMP is shown to be approximately flat, which is in stark contrast to the bent form of apo-CBSXs. This conformational change in quaternary structure is triggered by a local structural change of the unique α5 helix, and by moving each loop P into an open conformation to accommodate incoming ligands. Furthermore, subtle rearrangement of the dimer interface triggers movement of all subunits, and consequently, the bent structure of the CBSX2 dimer becomes a flat structure. This reshaping of the structure upon complex formation with adenosine-containing ligand provides evidence that ligand-induced conformational reorganization of antiparallel CBS domains is an important regulatory mechanism. Copyright © 2013 Elsevier Inc. All rights reserved.

Dynamic Conformations of Nucleosome Arrays in Solution from Small-Angle X-ray Scattering

NASA Astrophysics Data System (ADS)

Howell, Steven C.

Chromatin conformation and dynamics remains unsolved despite the critical role of the chromatin in fundamental genetic functions such as transcription, replication, and repair. At the molecular level, chromatin can be viewed as a linear array of nucleosomes, each consisting of 147 base pairs (bp) of double-stranded DNA (dsDNA) wrapped around a protein core and connected by 10 to 90 bp of linker dsDNA. Using small-angle X-ray scattering (SAXS), we investigated how the conformations of model nucleosome arrays in solution are modulated by ionic condition as well as the effect of linker histone proteins. To facilitate ensemble modeling of these SAXS measurements, we developed a simulation method that treats coarse-grained DNA as a Markov chain, then explores possible DNA conformations using Metropolis Monte Carlo (MC) sampling. This algorithm extends the functionality of SASSIE, a program used to model intrinsically disordered biological molecules, adding to the previous methods for simulating protein, carbohydrates, and single-stranded DNA. Our SAXS measurements of various nucleosome arrays together with the MC generated models provide valuable solution structure information identifying specific differences from the structure of crystallized arrays.

Immunoglobulin G1 Fc domain motions: implications for Fc engineering

PubMed Central

Frank, Martin; Walker, Ross C.; Lanzilotta, William N.; Prestegard, James H.; Barb, Adam W.

2014-01-01

The fragment crystallizable (Fc) region links the key pathogen identification and destruction properties of immunoglobulin G(IgG). Pathogen opsonization positions Fcs to activate pro-inflammatory Fcγ receptors (FcγRs) on immune cells. The cellular response and committal to a damaging, though protective, immune response is tightly controlled at multiple levels. Control mechanisms are diverse and in many cases unclear, but one frequently suggested contribution originates in Fcγ receptor affinity being modulated through shifts in Fc conformational sampling. Here we report a previously unseen IgG1 Fc conformation. This observation motivated an extensive molecular dynamics (MD) investigation of polypeptide and glycan motions that revealed greater amplitude of motion for the N-terminal Cγ2 domains and N-glycan than previously observed. Residues in the Cγ2/Cγ3 interface and disulphide-bonded hinge were identified as influencing the Cγ2 motion. Our results are consistent with a model of Fc that is structurally dynamic. Conformational states that are competent to bind immune-stimulating FcγRs interconverted with Fc conformations distinct from those observed in FcγR complexes, which may represent a transient, nonbinding population. PMID:24522230

Cations Form Sequence Selective Motifs within DNA Grooves via a Combination of Cation-Pi and Ion-Dipole/Hydrogen Bond Interactions

PubMed Central

Stewart, Mikaela; Dunlap, Tori; Dourlain, Elizabeth; Grant, Bryce; McFail-Isom, Lori

2013-01-01

The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl+) and the polarized first hydration shell waters of divalent cations (Mg2+, Ca2+) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves. PMID:23940752

Conformational Analysis on structural perturbations of the zinc finger NEMO

NASA Astrophysics Data System (ADS)

Godwin, Ryan; Salsbury, Freddie; Salsbury Group Team

2014-03-01

The NEMO (NF-kB Essential Modulator) Zinc Finger protein (2jvx) is a functional Ubiquitin-binding domain, and plays a role in signaling pathways for immune/inflammatory responses, apoptosis, and oncogenesis [Cordier et al., 2008]. Characterized by 3 cysteines and 1 histidine residue at the active site, the biologically occurring, bound zinc configuration is a stable structural motif. Perturbations of the zinc binding residues suggest conformational changes in the 423-atom protein characterized via analysis of all-atom molecular dynamics simulations. Structural perturbations include simulations with and without a zinc ion and with and without de-protonated cysteines, resulting in four distinct configurations. Simulations of various time scales show consistent results, yet the longest, GPU driven, microsecond runs show more drastic structural and dynamic fluctuations when compared to shorter duration time-scales. The last cysteine residue (26 of 28) and the helix on which it resides exhibit a secondary, locally unfolded conformation in addition to its normal bound conformation. Combined analytics elucidate how the presence of zinc and/or protonated cysteines impact the dynamics and energetic fluctuations of NEMO. Comprehensive Cancer Center of Wake Forest University Computational Biosciences shared resource supported by NCI CCSG P30CA012197.

The Structural Basis of ATP as an Allosteric Modulator

PubMed Central

Wang, Qi; Shen, Qiancheng; Li, Shuai; Nussinov, Ruth; Zhang, Jian

2014-01-01

Adenosine-5’-triphosphate (ATP) is generally regarded as a substrate for energy currency and protein modification. Recent findings uncovered the allosteric function of ATP in cellular signal transduction but little is understood about this critical behavior of ATP. Through extensive analysis of ATP in solution and proteins, we found that the free ATP can exist in the compact and extended conformations in solution, and the two different conformational characteristics may be responsible for ATP to exert distinct biological functions: ATP molecules adopt both compact and extended conformations in the allosteric binding sites but conserve extended conformations in the substrate binding sites. Nudged elastic band simulations unveiled the distinct dynamic processes of ATP binding to the corresponding allosteric and substrate binding sites of uridine monophosphate kinase, and suggested that in solution ATP preferentially binds to the substrate binding sites of proteins. When the ATP molecules occupy the allosteric binding sites, the allosteric trigger from ATP to fuel allosteric communication between allosteric and functional sites is stemmed mainly from the triphosphate part of ATP, with a small number from the adenine part of ATP. Taken together, our results provide overall understanding of ATP allosteric functions responsible for regulation in biological systems. PMID:25211773

Asymmetric breathing motions of nucleosomal DNA and the role of histone tails

NASA Astrophysics Data System (ADS)

Chakraborty, Kaushik; Loverde, Sharon M.

2017-08-01

The most important packing unit of DNA in the eukaryotic cell is the nucleosome. It undergoes large-scale structural re-arrangements during different cell cycles. For example, the disassembly of the nucleosome is one of the key steps for DNA replication, whereas reassembly occurs after replication. Thus, conformational dynamics of the nucleosome is crucial for different DNA metabolic processes. We perform three different sets of atomistic molecular dynamics simulations of the nucleosome core particle at varying degrees of salt conditions for a total of 0.7 μs simulation time. We find that the conformational dynamics of the nucleosomal DNA tails are oppositely correlated from each other during the initial breathing motions. Furthermore, the strength of the interaction of the nucleosomal DNA tail with the neighboring H2A histone tail modulates the conformational state of the nucleosomal DNA tail. With increasing salt concentration, the degree of asymmetry in the conformation of the nucleosomal DNA tails decreases as both tails tend to unwrap. This direct correlation between the asymmetric breathing motions of the DNA tails and the H2A histone tails, and its decrease at higher salt concentrations, may play a significant role in the molecular pathway of unwrapping.

Cations form sequence selective motifs within DNA grooves via a combination of cation-pi and ion-dipole/hydrogen bond interactions.

PubMed

Stewart, Mikaela; Dunlap, Tori; Dourlain, Elizabeth; Grant, Bryce; McFail-Isom, Lori

2013-01-01

The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl⁺) and the polarized first hydration shell waters of divalent cations (Mg²⁺, Ca²⁺) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves.

NMR investigations of molecular dynamics

NASA Astrophysics Data System (ADS)

Palmer, Arthur

2011-03-01

NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

Modélisation par éléments finis 3D du champ magnétostatique dans les enroulements des réactances cuirassées de grande puissance. Comparaison avec le calcul en 2D

NASA Astrophysics Data System (ADS)

Ngnegueu, Triomphant; Terme, Claude; Mailhot, Michel

1993-03-01

In this paper, the finite element method is applied for the computation of the magnetostatic field in the windings of a shell-form reactor. The modeling is carried out in 3D, using FLUX3D, a software developed at the Laboratoire d'Electrotechnique de Grenoble. The results are compared to those obtained in 2D. These calculation results are also compared to some test results. Dans cet article, nous décrivons une application de la méthode des éléments finis pour la modélisation du champ magnétostatique dans les enroulements d'une réactance cuirassée de grande puissance. La modélisation est conduite en 3D, en utilisant le logiciel FLUX3D. Les résultats du calcul sont comparés avec ceux obtenus en 2D. Quelques comparaisons sont aussi effectuées avec des résultats de mesure.

Conversion of Natively Unstructured α-Synuclein to Its α-Helical Conformation Significantly Attenuates Production of Reactive Oxygen Species

PubMed Central

Zhou, Binbin; Hao, Yuanqiang; Wang, Chengshan; Li, Ding; Liu, You-Nian; Zhou, Feimeng

2012-01-01

The intracellular α-synuclein (α-syn) protein, whose conformational change and aggregation have been closely linked to the pathology of Parkingson’s disease (PD), is highly populated at the presynaptic termini and remains there in the α-helical conformation. In this study, circular dichroism confirmed that natively unstructured α-syn in aqueous solution was transformed to its α-helical conformation upon addition of trifluoroethanol (TFE). Electrochemical and UV–visible spectroscopic experiments reveal that both Cu(I) and Cu(II) are stabilized, with the former being stabilized by about two orders of magnitude. Compared to unstructured α-syn (Binolfi et al., J. Am. Chem. Soc. 133 (2011) 194–196), α-helical α-syn stabilizes Cu(I) by more than three orders of magnitude. Through the measurements of H2O2 and hydroxyl radicals (OH•) in solutions containing different forms of Cu(II) (free and complexed by unstructured or α-helical α-syn), we demonstrate that the significantly enhanced Cu(I) binding affinity helps inhibit the production of highly toxic reactive oxygen species, especially the hydroxyl radicals. Our study provides strong evidence that, as a possible means to prevent neuronal cell damage, conversion of the natively unstructured α-syn to its α-helical conformation in vivo could significantly attenuate the copper-modulated ROS production. PMID:23123341

The Differential Response of Proteins to Macromolecular Crowding

PubMed Central

Candotti, Michela; Orozco, Modesto

2016-01-01

The habitat in which proteins exert their function contains up to 400 g/L of macromolecules, most of which are proteins. The repercussions of this dense environment on protein behavior are often overlooked or addressed using synthetic agents such as poly(ethylene glycol), whose ability to mimic protein crowders has not been demonstrated. Here we performed a comprehensive atomistic molecular dynamic analysis of the effect of protein crowders on the structure and dynamics of three proteins, namely an intrinsically disordered protein (ACTR), a molten globule conformation (NCBD), and a one-fold structure (IRF-3) protein. We found that crowding does not stabilize the native compact structure, and, in fact, often prevents structural collapse. Poly(ethylene glycol) PEG500 failed to reproduce many aspects of the physiologically-relevant protein crowders, thus indicating its unsuitability to mimic the cell interior. Instead, the impact of protein crowding on the structure and dynamics of a protein depends on its degree of disorder and results from two competing effects: the excluded volume, which favors compact states, and quinary interactions, which favor extended conformers. Such a viscous environment slows down protein flexibility and restricts the conformational landscape, often biasing it towards bioactive conformations but hindering biologically relevant protein-protein contacts. Overall, the protein crowders used here act as unspecific chaperons that modulate the protein conformational space, thus having relevant consequences for disordered proteins. PMID:27471851

Lectins as probes for assessing the accessibility of N-linked glycans in relation to the conformational changes of fibronectin.

PubMed

Agniel, Rémy; Vendrely, Charlotte; Poulouin, Laurent; Bascetin, Rümeyza; Benachour, Hamanou; Gallet, Olivier; Leroy-Dudal, Johanne

2015-12-01

Fibronectin, a ≈ 450-kDa protein with 4-9% (w/w) glycosylation, is a key component of extracellular matrices and has a high conformational lability regarding its functions. However, the accessibility and the role of glycosylated moieties associated with the conformational changes of fibronectin are poorly understood. Using lectins as probes, we developed an approach comprising dynamic light scattering, turbidimetry measurements, and isothermal titration calorimetry to assess the accessibility of glycosylated moieties of fibronectin undergoing thermal-induced conformational changes. Among a set of 14 lectins, fibronectin mainly reacted with mannose-binding lectins, specifically concanavalin A. When temperature was raised from 25 to 50 °C, fibronectin underwent progressive unfolding, but the conformation of concanavalin A was unaffected. Dynamic light scattering, turbidimetry measurements, and isothermal titration calorimetry showed increased concanavalin A binding to fibronectin during progressive thermal-induced unfolding of the protein core. Such data suggest that mannosylated residues are progressively exposed as fibronectin unfolds. Because oligosaccharide moieties can be differently exposed to cells, and the cell's responses could be modified physiologically or pathologically, modulation of fibronectin sugar chains could be relevant to its biological functions. Thus, lectins might be useful tools to probe the glycosylation accessibility accompanying changes in protein core folding, for which a better understanding would be of value for biological and biomedical research. Copyright © 2015 John Wiley & Sons, Ltd.

Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis.

PubMed

Hamelberg, Donald; Shen, Tongye; McCammon, J Andrew

2005-02-16

The presence of serine/threonine-proline motifs in proteins provides a conformational switching mechanism of the backbone through the cis/trans isomerization of the peptidyl-prolyl (omega) bond. The reversible phosphorylation of the serine/threonine modulates this switching in regulatory proteins to alter signaling and transcription. However, the mechanism is not well understood. This is partly because cis/trans isomerization is a very slow process and, hence, difficult to study. We have used our accelerated molecular dynamics method to study the cis/trans proline isomerization, preferred backbone conformation of a serine-proline motif, and the effects of phosphorylation of the serine residue. We demonstrate that, unlike normal molecular dynamics, the accelerated molecular dynamics allows for the system to escape very easily from the trans isomer to cis isomer, and vice versa. Moreover, for both the unphosphorylated and phosphorylated peptides, the statistical thermodynamic properties are recaptured, and the results are consistent with experimental values. Isomerization of the proline omega bond is shown to be asymmetric and strongly dependent on the psi backbone angle before and after phosphorylation. The rates of escape decrease after phosphorylation. Also, the alpha-helical backbone conformation is more favored after phosphorylation. This accelerated molecular dynamics approach provides a general approach for enhancing the conformational transitions of molecular systems without having prior knowledge of the location of the minima and barriers on the potential-energy landscape.

Conformational and hydration properties modulate ice recognition by type I antifreeze protein and its mutants.

PubMed

Chakraborty, Sandipan; Jana, Biman

2017-05-10

The mechanism of ice recognition by antifreeze protein (AFP) is a topic of recent interest. Here, using equilibrium simulations and free energy calculations, we provide structural rationale to the observed experimental anomalies on type I AFP (wfAFP isoform HPLC6) and its mutants as well as probe the molecular origin of ice recognition by them. Our results clearly demonstrate that the interplay between the conformational and hydration properties dictates the ice binding ability of type I AFP and its mutants. We find that HPLC6 exists as a highly stable long helix which adsorbs on the ice surface through the ordered water cages around the CH 3 group of threonine (THR) residues, rather than directly binding to the ice surface via threonine (THR) through hydrogen bonding. Upon mutating THR with serine (SER), the straight helix conformation of HPLC6 disappears and the most stable conformation is a kinked helix devoid of ice binding ability. Free energy calculations reveal that there is a dynamic equilibrium between straight and bent helical conformations in the case of a valine (VAL) mutant. The straight long helical form of the VAL mutant also has the ability to form an ordered water cage structure around the CH 3 groups of the VAL residues and thereby efficiently adsorbs on an ice plane similar to the wild type AFP.

Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

PubMed Central

Quarta, Giulio; Sin, Ken; Schlick, Tamar

2012-01-01

Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design. PMID:22359488

Protonation-dependent conformational dynamics of the multidrug transporter EmrE

PubMed Central

Dastvan, Reza; Mishra, Smriti; Meiler, Jens; Mchaourab, Hassane S.

2016-01-01

The small multidrug transporter from Escherichia coli, EmrE, couples the energetically uphill extrusion of hydrophobic cations out of the cell to the transport of two protons down their electrochemical gradient. Although principal mechanistic elements of proton/substrate antiport have been described, the structural record is limited to the conformation of the substrate-bound state, which has been shown to undergo isoenergetic alternating access. A central but missing link in the structure/mechanism relationship is a description of the proton-bound state, which is an obligatory intermediate in the transport cycle. Here we report a systematic spin labeling and double electron electron resonance (DEER) study that uncovers the conformational changes of EmrE subsequent to protonation of critical acidic residues in the context of a global description of ligand-induced structural rearrangements. We find that protonation of E14 leads to extensive rotation and tilt of transmembrane helices 1–3 in conjunction with repacking of loops, conformational changes that alter the coordination of the bound substrate and modulate its access to the binding site from the lipid bilayer. The transport model that emerges from our data posits a proton-bound, but occluded, resting state. Substrate binding from the inner leaflet of the bilayer releases the protons and triggers alternating access between inward- and outward-facing conformations of the substrate-loaded transporter, thus enabling antiport without dissipation of the proton gradient. PMID:26787875

Simulation of reflectometry Bragg backscattering spectral responses in the absence of a cutoff layer.

PubMed

da Silva, F; da Graça, S; Heuraux, S; Conway, G D

2010-10-01

Experimental reflectometry signals obtained in the absence of a cutoff layer, with the possibility of interferometric operation excluded, show a coherent and recurrent frequency spectrum signature similar to an Alfvén cascade signature. A possible explanation resides in the modulation of a resonant Bragg backscattering response by an Alfvén mode structure located at the center of the plasma whose frequency of oscillation modulates the backscattered signal in a conformable way. This situation is modeled and simulated using an O-mode full-wave Maxwell finite-difference time-domain code and the resulting signatures are discussed.

Intensity-modulated radiation therapy: a review with a physics perspective.

PubMed

Cho, Byungchul

2018-03-01

Intensity-modulated radiation therapy (IMRT) has been considered the most successful development in radiation oncology since the introduction of computed tomography into treatment planning that enabled three-dimensional conformal radiotherapy in 1980s. More than three decades have passed since the concept of inverse planning was first introduced in 1982, and IMRT has become the most important and common modality in radiation therapy. This review will present developments in inverse IMRT treatment planning and IMRT delivery using multileaf collimators, along with the associated key concepts. Other relevant issues and future perspectives are also presented.

The Molecular Determinants of Small-Molecule Ligand Binding at P2X Receptors

PubMed Central

Pasqualetto, Gaia; Brancale, Andrea; Young, Mark T.

2018-01-01

P2X receptors are trimeric eukaryotic ATP-gated cation channels. Extracellular ATP—their physiological ligand—is released as a neurotransmitter and in conditions of cell damage such as inflammation, and substantial evidence implicates P2X receptors in diseases including neuropathic pain, cancer, and arthritis. In 2009, the first P2X crystal structure, Danio rerio P2X4 in the apo- state, was published, and this was followed in 2012 by the ATP-bound structure. These structures transformed our understanding of the conformational changes induced by ATP binding and the mechanism of ligand specificity, and enabled homology modeling of mammalian P2X receptors for ligand docking and rational design of receptor modulators. P2X receptors are attractive drug targets, and a wide array of potent, subtype-selective modulators (mostly antagonists) have been developed. In 2016, crystal structures of human P2X3 in complex with the competitive antagonists TNP-ATP and A-317491, and Ailuropoda melanoleuca P2X7 in complex with a series of allosteric antagonists were published, giving fascinating insights into the mechanism of channel antagonism. In this article we not only summarize current understanding of small-molecule modulator binding at P2X receptors, but also use this information in combination with previously published structure-function data and molecular docking experiments, to hypothesize a role for the dorsal fin loop region in differential ATP potency, and describe novel, testable binding conformations for both the semi-selective synthetic P2X7 agonist 2′-(3′)-O-(4-benzoyl)benzoyl ATP (BzATP), and the P2X4-selective positive allosteric modulator ivermectin. We find that the distal benzoyl group of BzATP lies in close proximity to Lys-127, a residue previously implicated in BzATP binding to P2X7, potentially explaining the increased potency of BzATP at rat P2X7 receptors. We also present molecular docking of ivermectin to rat P2X4 receptors, illustrating a plausible binding conformation between the first and second transmembrane domains which not only tallies with previous mutagenesis studies, but would also likely have the effect of stabilizing the open channel structure, consistent with the mode of action of this positive allosteric modulator. From our docking simulations and analysis of sequence homology we propose a series of mutations likely to confer ivermectin sensitivity to human P2X1. PMID:29456508

A conserved Mediator–CDK8 kinase module association regulates Mediator–RNA polymerase II interaction

PubMed Central

Tsai, Kuang-Lei; Sato, Shigeo; Tomomori-Sato, Chieri; Conaway, Ronald C.; Conaway, Joan W.; Asturias, Francisco J.

2013-01-01

The CDK8 kinase module (CKM) is a conserved, dissociable Mediator subcomplex whose component subunits were genetically linked to the RNA polymerase II (RNAPII) carboxy-terminal domain (CTD) and individually recognized as transcriptional repressors before Mediator was identified as a preeminent complex in eukaryotic transcription regulation. We used macromolecular electron microscopy and biochemistry to investigate the subunit organization, structure, and Mediator interaction of the Saccharomyces cerevisiae CKM. We found that interaction of the CKM with Mediator’s Middle module interferes with CTD-dependent RNAPII binding to a previously unknown Middle module CTD-binding site targeted early on in a multi-step holoenzyme formation process. Taken together, our results reveal the basis for CKM repression, clarify the origin of the connection between CKM subunits and the CTD, and suggest that a combination of competitive interactions and conformational changes that facilitate holoenzyme formation underlie the Mediator mechanism. PMID:23563140

Prions, amyloids, and RNA: Pieces of a puzzle.

PubMed

Nizhnikov, Anton A; Antonets, Kirill S; Bondarev, Stanislav A; Inge-Vechtomov, Sergey G; Derkatch, Irina L

2016-05-03

Amyloids are protein aggregates consisting of fibrils rich in β-sheets. Growth of amyloid fibrils occurs by the addition of protein molecules to the tip of an aggregate with a concurrent change of a conformation. Thus, amyloids are self-propagating protein conformations. In certain cases these conformations are transmissible / infectious; they are known as prions. Initially, amyloids were discovered as pathological extracellular deposits occurring in different tissues and organs. To date, amyloids and prions have been associated with over 30 incurable diseases in humans and animals. However, a number of recent studies demonstrate that amyloids are also functionally involved in a variety of biological processes, from biofilm formation by bacteria, to long-term memory in animals. Interestingly, amyloid-forming proteins are highly overrepresented among cellular factors engaged in all stages of mRNA life cycle: from transcription and translation, to storage and degradation. Here we review rapidly accumulating data on functional and pathogenic amyloids associated with mRNA processing, and discuss possible significance of prion and amyloid networks in the modulation of key cellular functions.

Human Protein-disulfide Isomerase Is a Redox-regulated Chaperone Activated by Oxidation of Domain a′*

PubMed Central

Wang, Chao; Yu, Jiang; Huo, Lin; Wang, Lei; Feng, Wei; Wang, Chih-chen

2012-01-01

Protein-disulfide isomerase (PDI), with domains arranged as abb′xa′c, is a key enzyme and chaperone localized in the endoplasmic reticulum (ER) catalyzing oxidative folding and preventing misfolding/aggregation of proteins. It has been controversial whether the chaperone activity of PDI is redox-regulated, and the molecular basis is unclear. Here, we show that both the chaperone activity and the overall conformation of human PDI are redox-regulated. We further demonstrate that the conformational changes are triggered by the active site of domain a′, and the minimum redox-regulated cassette is located in b′xa′. The structure of the reduced bb′xa′ reveals for the first time that domain a′ packs tightly with both domain b′ and linker x to form one compact structural module. Oxidation of domain a′ releases the compact conformation and exposes the shielded hydrophobic areas to facilitate its high chaperone activity. Thus, the study unequivocally provides mechanistic insights into the redox-regulated chaperone activity of human PDI. PMID:22090031

Initial steps of inactivation at the K+ channel selectivity filter

PubMed Central

Thomson, Andrew S.; Heer, Florian T.; Smith, Frank J.; Hendron, Eunan; Bernèche, Simon; Rothberg, Brad S.

2014-01-01

K+ efflux through K+ channels can be controlled by C-type inactivation, which is thought to arise from a conformational change near the channel’s selectivity filter. Inactivation is modulated by ion binding near the selectivity filter; however, the molecular forces that initiate inactivation remain unclear. We probe these driving forces by electrophysiology and molecular simulation of MthK, a prototypical K+ channel. Either Mg2+ or Ca2+ can reduce K+ efflux through MthK channels. However, Ca2+, but not Mg2+, can enhance entry to the inactivated state. Molecular simulations illustrate that, in the MthK pore, Ca2+ ions can partially dehydrate, enabling selective accessibility of Ca2+ to a site at the entry to the selectivity filter. Ca2+ binding at the site interacts with K+ ions in the selectivity filter, facilitating a conformational change within the filter and subsequent inactivation. These results support an ionic mechanism that precedes changes in channel conformation to initiate inactivation. PMID:24733889

Structure of the full-length glucagon class B G protein-coupled receptor

PubMed Central

Zhang, Haonan; Qiao, Anna; Yang, Dehua; Yang, Linlin; Dai, Antao; de Graaf, Chris; Reedtz-Runge, Steffen; Dharmarajan, Venkatasubramanian; Zhang, Hui; Han, Gye Won; Grant, Thomas D.; Sierra, Raymond G.; Weierstall, Uwe; Nelson, Garrett; Liu, Wei; Wu, Yanhong; Ma, Limin; Cai, Xiaoqing; Lin, Guangyao; Wu, Xiaoai; Geng, Zhi; Dong, Yuhui; Song, Gaojie; Griffin, Patrick R.; Lau, Jesper; Cherezov, Vadim; Yang, Huaiyu; Hanson, Michael A.; Stevens, Raymond C.; Zhao, Qiang; Jiang, Hualiang; Wang, Ming-Wei; Wu, Beili

2017-01-01

The human glucagon receptor (GCGR) belongs to the class B G protein-coupled receptor (GPCR) family and plays a key role in glucose homeostasis and the pathophysiology of type 2 diabetes. Here we report the 3.0 Å crystal structure of full-length GCGR containing both extracellular domain (ECD) and transmembrane domain (TMD) in an inactive conformation. The two domains are connected by a 12-residue segment termed the ‘stalk’, which adopts a β-strand conformation, instead of forming an α-helix as observed in the previously solved structure of GCGR-TMD. The first extracellular loop (ECL1) exhibits a β-hairpin conformation and interacts with the stalk to form a compact β-sheet structure. Hydrogen/deuterium exchange, disulfide cross-linking and molecular dynamics studies suggest that the stalk and ECL1 play critical roles in modulating peptide ligand binding and receptor activation. These insights into the full-length GCGR structure deepen our understanding about the signaling mechanisms of class B GPCRs. PMID:28514451

Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase

PubMed Central

Garcin, Elsa D.; Arvai, Andrew S.; Rosenfeld, Robin J.; Kroeger, Matt D.; Crane, Brian R.; Andersson, Gunilla; Andrews, Glen; Hamley, Peter J.; Mallinder, Philip R.; Nicholls, David J.; St-Gallay, Stephen A.; Tinker, Alan C.; Gensmantel, Nigel P.; Mete, Antonio; Cheshire, David R.; Connolly, Stephen; Stuehr, Dennis J.; Åberg, Anders; Wallace, Alan V.; Tainer, John A.; Getzoff, Elizabeth D.

2008-01-01

Nitric oxide synthase (NOS) enzymes synthesize nitric oxide, a signal for vasodilatation and neurotransmission at low levels, and a defensive cytotoxin at higher levels. The high active-site conservation among all three NOS isozymes hinders the design of selective NOS inhibitors to treat inflammation, arthritis, stroke, septic shock, and cancer. Our structural and mutagenesis results identified an isozyme-specific induced-fit binding mode linking a cascade of conformational changes to a novel specificity pocket. Plasticity of an isozyme-specific triad of distant second- and third-shell residues modulates conformational changes of invariant first-shell residues to determine inhibitor selectivity. To design potent and selective NOS inhibitors, we developed the anchored plasticity approach: anchor an inhibitor core in a conserved binding pocket, then extend rigid bulky substituents towards remote specificity pockets, accessible upon conformational changes of flexible residues. This approach exemplifies general principles for the design of selective enzyme inhibitors that overcome strong active-site conservation. PMID:18849972

Chain-Length-Dependent Exciton Dynamics in Linear Oligothiophenes Probed Using Ensemble and Single-Molecule Spectroscopy.

PubMed

Kim, Tae-Woo; Kim, Woojae; Park, Kyu Hyung; Kim, Pyosang; Cho, Jae-Won; Shimizu, Hideyuki; Iyoda, Masahiko; Kim, Dongho

2016-02-04

Exciton dynamics in π-conjugated molecular systems is highly susceptible to conformational disorder. Using time-resolved and single-molecule spectroscopic techniques, the effect of chain length on the exciton dynamics in a series of linear oligothiophenes, for which the conformational disorder increased with increasing chain length, was investigated. As a result, extraordinary features of the exciton dynamics in longer-chain oligothiophene were revealed. Ultrafast fluorescence depolarization processes were observed due to exciton self-trapping in longer and bent chains. Increase in exciton delocalization during dynamic planarization processes was also observed in the linear oligothiophenes via time-resolved fluorescence spectra but was restricted in L-10T because of its considerable conformational disorder. Exciton delocalization was also unexpectedly observed in a bent chain using single-molecule fluorescence spectroscopy. Such delocalization modulates the fluorescence spectral shape by attenuating the 0-0 peak intensity. Collectively, these results provide significant insights into the exciton dynamics in conjugated polymers.

Residues in the membrane-spanning domain core modulate conformation and fusogenicity of the HIV-1 envelope glycoprotein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shang Liang; Hunter, Eric, E-mail: eric.hunter2@emory.ed

2010-09-01

The membrane-spanning domain (MSD) of human immunodeficiency virus type I (HIV-1) envelope glycoprotein (Env) is critical for its biological activity. Initial studies have defined an almost invariant 'core' structure in the MSD and demonstrated that it is crucial for anchoring Env in the membrane and virus entry. We show here that amino acid substitutions in the MSD 'core' do not influence specific virus-cell attachment, nor CD4 receptor and CXCR4 coreceptor recognition by Env. However, substitutions within the MSD 'core' delayed the kinetics and reduced the efficiency of cell-cell fusion mediated by Env. Although we observed no evidence that membrane fusionmore » mediated by the MSD core mutants was arrested at a hemifusion stage, impaired Env fusogenicity was correlated with minor conformational changes in the V2, C1, and C5 regions in gp120 and the immunodominant loop in gp41. These changes could delay initiation of the conformational changes required in the fusion process.« less

Forster Resonance Energy Transfer and Conformational Stability of Proteins: An Advanced Biophysical Module for Physical Chemistry Students

ERIC Educational Resources Information Center

Sanchez, Katheryn M.; Schlamadinger, Diana E.; Gable, Jonathan E.; Kim, Judy E.

2008-01-01

Protein folding is an exploding area of research in biophysics and physical chemistry. Here, we describe the integration of several techniques, including absorption spectroscopy, fluorescence spectroscopy, and Forster resonance energy transfer (FRET) measurements, to probe important topics in protein folding. Cytochrome c is used as a model…

SU-E-T-410: Evaluation of Treatment Modalities for Stereotactic Lung Radiation Therapy: A Phantom Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohatt, D; Malhotra, H

Purpose: To evaluate and verify the accuracy of alternative treatment modalities for stereotactic lung therapy with end-to-end testing. We compared three dimensional conformal therapy (3DCRT), dynamic conformal arc therapy (DCAT), intensity modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT) treatment using 6 MV, 6 MV flattening filter free (FFF) and 10 MV FFF photons. Methods: A QUASAR respiratory motion phantom was utilized with custom ion chamber and gafchromatic EBT2 film inserts. The phantom contained a low density lung medium with a cylindrical polystyrene tumor (35 cc). Pseudo representative structures for various organs at risk (OAR) were created. Allmore » treatment plans were created using Eclipse ver. 11 using the same image and structure sets, and delivered via Varian TrueBeam STx linear accelerator equipped with high definition MLC. Evaluation of plan quality followed ROTG 0813 criterion for conformity index (CI100%), high dose spillage, D2cm, and R50%. Results: All treatment plans met the OAR dose constraints per protocol and could be delivered without any beam hold offs or other interlocks and hence were deemed clinically safe. For equivalent beam energies, target conformity was improved for all modalities when switching to FFF mode. Treatment efficiency increased for VMAT FFF by a factor of 3–4 over IMRT, and up to factor of 7 when compared to 3DCRT. Pass rates were > 97% for all treatment using gamma criteria of 3%, 3mm. Absolute dose at iso-center was verified with ion chamber, and found to be within 2% of the treatment planning system. Conclusion: The higher dose rate associated with FFF not only reduces delivery times, but in most cases enhances plan quality. The one modality with succeeding best results for all RTOG criterions was VMAT 6 MV FFF. This end-to-end testing provides necessary confidence in the entire dose delivery chain for lung SBRT patients.« less

Cholesterol accelerates the binding of Alzheimer's β-amyloid peptide to ganglioside GM1 through a universal hydrogen-bond-dependent sterol tuning of glycolipid conformation

PubMed Central

Fantini, Jacques; Yahi, Nouara; Garmy, Nicolas

2013-01-01

Age-related alterations of membrane lipids in brain cell membranes together with high blood cholesterol are considered as major risk factors for Alzheimer's disease. Yet the molecular mechanisms by which these factors increase Alzheimer's risk are mostly unknown. In lipid raft domains of the plasma membrane, neurotoxic Alzheimer's beta-amyloid (Abeta) peptides interact with both cholesterol and ganglioside GM1. Recent data also suggested that cholesterol could stimulate the binding of Abeta to GM1 through conformational modulation of the ganglioside headgroup. Here we used a combination of physicochemical and molecular modeling approaches to decipher the mechanisms of cholesterol-assisted binding of Abeta to GM1. With the aim of decoupling the effect of cholesterol on GM1 from direct Abeta-cholesterol interactions, we designed a minimal peptide (Abeta5-16) containing the GM1-binding domain but lacking the amino acid residues involved in cholesterol recognition. Using the Langmuir technique, we showed that cholesterol (but not phosphatidylcholine or sphingomyelin) significantly accelerates the interaction of Abeta5-16 with GM1. Molecular dynamics simulations suggested that Abeta5-16 interacts with a cholesterol-stabilized dimer of GM1. The main structural effect of cholesterol is to establish a hydrogen-bond between its own OH group and the glycosidic-bond linking ceramide to the glycone part of GM1, thereby inducing a tilt in the glycolipid headgroup. This fine conformational tuning stabilizes the active conformation of the GM1 dimer whose headgroups, oriented in two opposite directions, form a chalice-shaped receptacle for Abeta. These data give new mechanistic insights into the stimulatory effect of cholesterol on Abeta/GM1 interactions. They also support the emerging concept that cholesterol is a universal modulator of protein-glycolipid interactions in the broader context of membrane recognition processes. PMID:23772214

A planning comparison of 3-dimensional conformal multiple static field, conformal arc, and volumetric modulated arc therapy for the delivery of stereotactic body radiotherapy for early stage lung cancer.

PubMed

Dickey, Mike; Roa, Wilson; Drodge, Suzanne; Ghosh, Sunita; Murray, Brad; Scrimger, Rufus; Gabos, Zsolt

2015-01-01

The primary objective of this study was to compare dosimetric variables as well as treatment times of multiple static fields (MSFs), conformal arcs (CAs), and volumetric modulated arc therapy (VMAT) techniques for the treatment of early stage lung cancer using stereotactic body radiotherapy (SBRT). Treatments of 23 patients previously treated with MSF of 48Gy to 95% of the planning target volume (PTV) in 4 fractions were replanned using CA and VMAT techniques. Dosimetric parameters of the Radiation Therapy Oncology Group (RTOG) 0915 trial were evaluated, along with the van׳t Riet conformation number (CN), monitor units (MUs), and actual and calculated treatment times. Paired t-tests for noninferiority were used to compare the 3 techniques. CA had significant dosimetric improvements over MSF for the ratio of the prescription isodose volume to PTV (R100%, p < 0.0001), the maximum dose 2cm away from the PTV (D2cm, p = 0.005), and van׳t Riet CN (p < 0.0001). CA was not statistically inferior to MSF for the 50% prescription isodose volume to PTV (R50%, p = 0.05). VMAT was significantly better than CA for R100% (p < 0.0001), R50% (p < 0.0001), D2cm (p = 0.006), and CN (p < 0.0001). CA plans had significantly shorter treatment times than those of VMAT (p < 0.0001). Both CA and VMAT planning showed significant dosimetric improvements and shorter treatment times over those of MSF. VMAT showed the most favorable dosimetry of all 3 techniques; however, the dosimetric effect of tumor motion was not evaluated. CA plans were significantly faster to treat, and minimize the interplay of tumor motion and dynamic multileaf collimator (MLC) motion effects. Given these results, CA has become the treatment technique of choice at our facility. Copyright © 2015 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.

A planning comparison of 7 irradiation options allowed in RTOG 1005 for early-stage breast cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Guang-Pei, E-mail: gpchen@mcw.edu; Liu, Feng; White, Julia

2015-04-01

This study compared the 7 treatment plan options in achieving the dose-volume criteria required by the Radiation Therapy Oncology Group (RTOG) 1005 protocol. Dosimetry plans were generated for 15 representative patients with early-stage breast cancer (ESBC) based on the protocol-required dose-volume criteria for each of the following 7 treatment options: 3D conformal radiotherapy (3DCRT), whole-breast irradiation (WBI) plus 3DCRT lumpectomy boost, 3DCRT WBI plus electron boost, 3DCRT WBI plus intensity-modulated radiation therapy (IMRT) boost, IMRT WBI plus 3DCRT boost, IMRT WBI plus electron boost, IMRT WBI plus IMRT boost, and simultaneous integrated boost (SIB) with IMRT. A variety of dose-volumemore » parameters, including target dose conformity and uniformity and normal tissue sparing, were compared for these plans. For the patients studied, all plans met the required acceptable dose-volume criteria, with most of them meeting the ideal criteria. When averaged over patients, most dose-volume goals for all plan options can be achieved with a positive gap of at least a few tenths of standard deviations. The plans for all 7 options are generally comparable. The dose-volume goals required by the protocol can in general be easily achieved. IMRT WBI provides better whole-breast dose uniformity than 3DCRT WBI does, but it causes no significant difference for the dose conformity. All plan options are comparable for lumpectomy dose uniformity and conformity. Patient anatomy is always an important factor when whole-breast dose uniformity and conformity and lumpectomy dose conformity are considered.« less

BamA POTRA Domain Interacts with a Native Lipid Membrane Surface.

PubMed

Fleming, Patrick J; Patel, Dhilon S; Wu, Emilia L; Qi, Yifei; Yeom, Min Sun; Sousa, Marcelo Carlos; Fleming, Karen G; Im, Wonpil

2016-06-21

The outer membrane of Gram-negative bacteria is an asymmetric membrane with lipopolysaccharides on the external leaflet and phospholipids on the periplasmic leaflet. This outer membrane contains mainly β-barrel transmembrane proteins and lipidated periplasmic proteins (lipoproteins). The multisubunit protein β-barrel assembly machine (BAM) catalyzes the insertion and folding of the β-barrel proteins into this membrane. In Escherichia coli, the BAM complex consists of five subunits, a core transmembrane β-barrel with a long periplasmic domain (BamA) and four lipoproteins (BamB/C/D/E). The BamA periplasmic domain is composed of five globular subdomains in tandem called POTRA motifs that are key to BAM complex formation and interaction with the substrate β-barrel proteins. The BAM complex is believed to undergo conformational cycling while facilitating insertion of client proteins into the outer membrane. Reports describing variable conformations and dynamics of the periplasmic POTRA domain have been published. Therefore, elucidation of the conformational dynamics of the POTRA domain in full-length BamA is important to understand the function of this molecular complex. Using molecular dynamics simulations, we present evidence that the conformational flexibility of the POTRA domain is modulated by binding to the periplasmic surface of a native lipid membrane. Furthermore, membrane binding of the POTRA domain is compatible with both BamB and BamD binding, suggesting that conformational selection of different POTRA domain conformations may be involved in the mechanism of BAM-facilitated insertion of outer membrane β-barrel proteins. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2

PubMed Central

Pisani, Pasquale; Rastelli, Giulio

2016-01-01

Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human kinome. PMID:27100206

Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2.

PubMed

Pisani, Pasquale; Caporuscio, Fabiana; Carlino, Luca; Rastelli, Giulio

2016-01-01

Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human kinome.

Computational and experimental analysis of short peptide motifs for enzyme inhibition.

PubMed

Fu, Jinglin; Larini, Luca; Cooper, Anthony J; Whittaker, John W; Ahmed, Azka; Dong, Junhao; Lee, Minyoung; Zhang, Ting

2017-01-01

The metabolism of living systems involves many enzymes that play key roles as catalysts and are essential to biological function. Searching ligands with the ability to modulate enzyme activities is central to diagnosis and therapeutics. Peptides represent a promising class of potential enzyme modulators due to the large chemical diversity, and well-established methods for library synthesis. Peptides and their derivatives are found to play critical roles in modulating enzymes and mediating cellular uptakes, which are increasingly valuable in therapeutics. We present a methodology that uses molecular dynamics (MD) and point-variant screening to identify short peptide motifs that are critical for inhibiting β-galactosidase (β-Gal). MD was used to simulate the conformations of peptides and to suggest short motifs that were most populated in simulated conformations. The function of the simulated motifs was further validated by the experimental point-variant screening as critical segments for inhibiting the enzyme. Based on the validated motifs, we eventually identified a 7-mer short peptide for inhibiting an enzyme with low μM IC50. The advantage of our methodology is the relatively simplified simulation that is informative enough to identify the critical sequence of a peptide inhibitor, with a precision comparable to truncation and alanine scanning experiments. Our combined experimental and computational approach does not rely on a detailed understanding of mechanistic and structural details. The MD simulation suggests the populated motifs that are consistent with the results of the experimental alanine and truncation scanning. This approach appears to be applicable to both natural and artificial peptides. With more discovered short motifs in the future, they could be exploited for modulating biocatalysis, and developing new medicine.

Insights into the Modulation of Dopamine Transporter Function by Amphetamine, Orphenadrine, and Cocaine Binding

PubMed Central

Cheng, Mary Hongying; Block, Ethan; Hu, Feizhuo; Cobanoglu, Murat Can; Sorkin, Alexander; Bahar, Ivet

2015-01-01

Human dopamine (DA) transporter (hDAT) regulates dopaminergic signaling in the central nervous system by maintaining the synaptic concentration of DA at physiological levels, upon reuptake of DA into presynaptic terminals. DA translocation involves the co-transport of two sodium ions and the channeling of a chloride ion, and it is achieved via alternating access between outward-facing (OF) and inward-facing states of DAT. hDAT is a target for addictive drugs, such as cocaine, amphetamine (AMPH), and therapeutic antidepressants. Our recent quantitative systems pharmacology study suggested that orphenadrine (ORPH), an anticholinergic agent and anti-Parkinson drug, might be repurposable as a DAT drug. Previous studies have shown that DAT-substrates like AMPH or -blockers like cocaine modulate the function of DAT in different ways. However, the molecular mechanisms of modulation remained elusive due to the lack of structural data on DAT. The newly resolved DAT structure from Drosophila melanogaster opens the way to a deeper understanding of the mechanism and time evolution of DAT–drug/ligand interactions. Using a combination of homology modeling, docking analysis, molecular dynamics simulations, and molecular biology experiments, we performed a comparative study of the binding properties of DA, AMPH, ORPH, and cocaine and their modulation of hDAT function. Simulations demonstrate that binding DA or AMPH drives a structural transition toward a functional form predisposed to translocate the ligand. In contrast, ORPH appears to inhibit DAT function by arresting it in the OF open conformation. The analysis shows that cocaine and ORPH competitively bind DAT, with the binding pose and affinity dependent on the conformational state of DAT. Further assays show that the effect of ORPH on DAT uptake and endocytosis is comparable to that of cocaine. PMID:26106364

Influence of jaw tracking in intensity-modulated and volumetric-modulated arc radiotherapy for head and neck cancers: a dosimetric study.

PubMed

Mani, Karthick Raj; Upadhayay, Sagar; Das, K J Maria

2017-03-01

To Study the dosimetric advantage of the Jaw tracking technique in intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc therapy (VMAT) for Head and Neck Cancers. We retrospectively selected 10 previously treated head and neck cancer patients stage (T1/T2, N1, M0) in this study. All the patients were planned for IMRT and VMAT with simultaneous integrated boost technique. IMRT and VMAT plans were performed with jaw tracking (JT) and with static jaw (SJ) technique by keeping the same constraints and priorities for a particular patient. Target conformity, dose to the critical structures and low dose volumes were recorded and analyzed for IMRT and VMAT plans with and without JT for all the patients. The conformity index average of all patients followed by standard deviation ([Formula: see text] ± [Formula: see text]) of the JT-IMRT, SJ-IMRT, JT-VMAT, and SJ-VMAT were 1.72 ± 0.56, 1.67 ± 0.57, 1.83 ± 0.65, and 1.85 ± 0.64, and homogeneity index were 0.059 ± 0.05, 0.064 ± 0.05, 0.064 ± 0.04, and 0.064 ± 0.05. JT-IMRT shows significant mean reduction in right parotid and left parotid shows of 7.64% (p < 0.001) and 7.45% (p < 0.001) compare to SJ-IMRT. JT-IMRT plans also shows considerable dose reduction to thyroid, inferior constrictors, spinal cord and brainstem compared to the SJ-IMRT plans. Significant dose reductions were observed for critical structure in the JT-IMRT compared to SJ-IMRT technique. In JT-VMAT plans dose reduction to the critical structure were not significant compared to the SJ-IMRT due to relatively lesser monitor units.

Optimal Normal Tissue Sparing in Craniospinal Axis Irradiation Using IMRT With Daily Intrafractionally Modulated Junction(s)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kusters, Johannes M.A.M.; Louwe, Rob J.W.; Kollenburg, Peter G.M. van

2011-12-01

Purpose: To develop a treatment technique for craniospinal irradiation using intensity-modulated radiotherapy (IMRT) with improved dose homogeneity at the field junction(s), increased target volume conformity, and minimized dose to the organs at risk (OARs). Methods and Materials: Five patients with high-risk medulloblastoma underwent CT simulation in supine position. For each patient, an IMRT plan with daily intrafractionally modulated junction(s) was generated, as well as a treatment plan based on conventional three-dimensional planning (3DCRT). A dose of 39.6 Gy in 22 daily fractions of 1.8 Gy was prescribed. Dose-volume parameters for target volumes and OARs were compared for the two techniques.more » Results: The maximum dose with IMRT was <107% in all patients. V{sub <95} and V{sub >107} were <1 cm{sup 3} for IMRT compared with 3-9 cm{sup 3} for the craniospinal and 26-43 cm{sup 3} for the spinal-spinal junction with 3DCRT. These observations corresponded with a lower homogeneity index and a higher conformity index for the spinal planning target volume with IMRT. IMRT provided considerable sparing of acute and late reacting tissues. V{sub 75} for the esophagus, gastroesophageal junction, and intestine was 81%, 81%, and 22% with 3DCRT versus 5%, 0%, and 1% with IMRT, respectively. V{sub 75} for the heart and thyroid was 42% and 32% vs. 0% with IMRT. Conclusion: IMRT with daily intrafractionally modulated junction results in a superior target coverage and junction homogeneity compared with 3DCRT. A significant dose reduction can be obtained for acute as well as late-reacting tissues.« less

The conformational flexibility of the carboxy terminal residues 105–114 is a key modulator of the catalytic activity and stability of Macrophage Migration Inhibitory Factor (MIF)†

PubMed Central

El-Turk, Farah; Cascella, Michele; Ouertatani-Sakouhi, Hajer; Narayanan, Raghavendran Lakshmi; Leng, Lin; Bucala, Richard; Hweckstetter, Markus; Rothlisberger, Ursula; Lashuel, Hilal A.

2013-01-01

Macrophage migration inhibitory factor (MIF) is a multifunctional protein and a major mediator of innate immunity. Although X-ray crystallography revealed that MIF exists as a homotrimer, its oligomerization state in vivo as well as the factors governing its oligomerization and stability remain poorly understood. The C-terminal region of MIF is highly conserved and participates in several intramolecular interactions that suggest a role in modulating the stability and biochemical activity of MIF. To determine the importance of these interactions, point mutations (A48P, L46A), insertions (P107) at the monomer-monomer interfaces, and C-terminal deletion (Δ110-114NSTFA and Δ105–114NVGWNNSTFA) variants were designed and their structural properties, thermodynamic stability, oligomerization state, catalytic activity and receptor binding were characterized using a battery of biophysical methods. The C-terminal deletion mutants ΔC5 huMIF1-109 and ΔC10 huMIF1-104 were enzymatically inactive and thermodynamically less stable than wild type MIF. Analytical ultracentrifugation studies demonstrate that both C-terminal mutants sediment as trimers and exhibit similar binding to CD74 as the wild type protein. Disrupting the conformation of the C-terminal region 105–114 and increasing its conformational flexibility through the insertion of a proline residue at position 107 was sufficient to reproduce the structural, biochemical and thermodynamic properties of the deletion mutants. P107 MIF forms an enzymatically inactive trimer and exhibits reduced thermodynamic stability relative to the wild type protein. To provide a rationale for the changes induced by these mutations at the molecular level, we also performed molecular dynamics simulations on these mutants in comparison to the wild type MIF. Together, our studies demonstrate that inter-subunit interactions involving the C-terminal region 105–114, including a salt-bridge interaction between Arg73 of one monomer and the carboxy terminus of a neighbouring monomer, play critical roles in modulating tertiary structure stabilization, enzymatic activity, and thermodynamic stability of MIF, but not its oligomerization state and receptor binding properties. Our results suggest that targeting the C-terminal region could provide new strategies for allosteric modulation of MIF enzymatic activity and the development of novel inhibitors of MIF tautomerase activity. PMID:18795803

Conformational Changes of an Interdomain Linker Mediate Mechanical Signal Transmission in Sensor Kinase BvgS

PubMed Central

Lesne, Elodie; Dupré, Elian; Locht, Camille

2017-01-01

ABSTRACT The whooping cough agent, Bordetella pertussis, controls the expression of its large virulence regulon in a coordinated manner through the two-component system BvgAS. BvgS is a dimeric, multidomain sensor kinase. Each monomer comprises, in succession, tandem periplasmic Venus flytrap (VFT) domains, a transmembrane segment, a cytoplasmic Per-Arnt-Sim (PAS) domain, a kinase module, and additional phosphorelay domains. BvgS shifts between kinase and phosphatase modes of activity in response to chemical modulators that modify the clamshell motions of the VFT domains. We have shown previously that this regulation involves a shift between distinct states of conformation and dynamics of the two-helix coiled-coil linker preceding the enzymatic module. In this work, we determined the mechanism of signal transduction across the membrane via a first linker, which connects the VFT and PAS domains of BvgS, using extensive cysteine cross-linking analyses and other approaches. Modulator perception by the periplasmic domains appears to trigger a small, symmetrical motion of the transmembrane segments toward the periplasm, causing rearrangements of the noncanonical cytoplasmic coiled coil that follows. As a consequence, the interface of the PAS domains is modified, which affects the second linker and eventually causes the shift of enzymatic activity. The major features of this first linker are well conserved among BvgS homologs, indicating that the mechanism of signal transduction unveiled here is likely to be generally relevant for this family of sensor kinases. IMPORTANCE Bordetella pertussis produces virulence factors coordinately regulated by the two-component system BvgAS. BvgS is a sensor kinase, and BvgA is a response regulator that activates gene transcription when phosphorylated by BvgS. Sensor kinases homologous to BvgS are also found in other pathogens. Our goal is to decipher the mechanisms of BvgS signaling, since these sensor kinases may represent new targets for antibacterial agents. Signal perception by the sensor domains of BvgS triggers small motions of the helical linker region underneath. The protein domain that follows this linker undergoes a large conformational change that amplifies the initial signal, causing a shift of activity from kinase to phosphatase. Because BvgS homologs harbor similar regions, these signaling mechanisms are likely to apply generally to that family of sensor kinases. PMID:28507245

Glucocorticoid receptor modulators.

PubMed

Meijer, Onno C; Koorneef, Lisa L; Kroon, Jan

2018-06-01

The glucocorticoid hormone cortisol acts throughout the body to support circadian processes and adaptation to stress. The glucocorticoid receptor is the target of cortisol and of synthetic glucocorticoids, which are used widely in the clinic. Both agonism and antagonism of the glucocorticoid receptor may be beneficial in disease, but given the wide expression of the receptor and involvement in various processes, beneficial effects are often accompanied by unwanted side effects. Selective glucocorticoid receptor modulators are ligands that induce a receptor conformation that allows activation of only a subset of downstream signaling pathways. Such molecules thereby combine agonistic and antagonistic properties. Here we discuss the mechanisms underlying selective receptor modulation and their promise in treating diseases in several organ systems where cortisol signaling plays a role. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Anthranilate-Activating Modules from Fungal Nonribosomal Peptide Assembly Lines†

PubMed Central

Ames, Brian D.; Walsh, Christopher T.

2010-01-01

Fungal natural products containing benzodiazepinone- and quinazolinone-fused ring systems can be assembled by nonribosomal peptide synthetases (NRPS) using the conformationally restricted β-amino acid anthranilate as one of the key building blocks. We validated that the first module of the acetylaszonalenin synthetase of Neosartorya fischeri NRRL 181 activates anthranilate to anthranilyl-AMP. With this as starting point, we then used bioinformatic predictions about fungal adenylation domain selectivities to identify and confirm an anthranilate-activating module in the fumiquinazoline A producer Aspergillus fumigatus Af293 as well as a second anthranilate-activating NRPS in N. fischeri. This establishes an anthranilate adenylation domain code for fungal NRPS and should facilitate detection and cloning of gene clusters for benzodiazepine- and quinazoline-containing polycyclic alkaloids with a wide range of biological activities. PMID:20225828

Light attenuation versus evolved carbon (AVEC) - A new way to look at elemental and organic carbon analysis

NASA Astrophysics Data System (ADS)

Nicolosi, E. M. G.; Quincey, P.; Font, A.; Fuller, G. W.

2018-02-01

The Attenuation Versus Evolved Carbon (AVEC) plot is a new way to represent thermal-optical organic carbon/elemental carbon (OC/EC) analysis data. The accumulated carbon concentration is plotted against the attenuation (ln (I0/I)). Unlike the thermogram, it provides information about the sample properties rather than the instantaneous instrument sensor status. The plot can be used to refine the determination of OC and EC split point, either from consideration of laser instability or transit time within the instrument; to investigate the optical properties of the particles; and to spot the early evolution of pyrolysed carbon (PC) and/or EC during the inert phase. 168 samples from three sites were studied. The gradient of the AVEC plot curve in the oxygenated phase provides information about the mass absorption cross section (σ) of the particles leaving the filter. The σ of the PC generated in the higher temperature Quartz protocol was greater than the PC generated in the lower temperature EUSAAR_2 protocol. Also, in both cases the PC evolved at a lower temperature in the oxygenated phase than the native EC. To minimise the shadowing effect, σ was also measured for the particles leaving the filter at the end of the analysis. These σ values, which are expected to be a combination of inherent σ together with fixed instrumental factors, were consistent between the different sites (45 ± 10 m2 g-1 in rural samples, 42 ± 8 m2 g-1 in urban samples and 35 ± 14 m2 g-1 in roadside samples). The AVEC plot can be generated from the data routinely produced by the analytical instrument using the R-code supplied in the supplementary material.

The feasibility and benefits of using volumetric arc therapy in patients with brain metastases: a systematic review.

PubMed

Andrevska, Adriana; Knight, Kellie A; Sale, Charlotte A

2014-12-01

Radiotherapy management of patients with brain metastases most commonly involve a whole-brain radiation therapy (WBRT) regime, as well as newer techniques such as stereotactic radiosurgery (SRS) and intensity modulated radiotherapy (IMRT). The long treatment times incurred by these techniques indicates the need for a novel technique that has shorter treatment times, whilst still producing highly conformal treatment with the potential to deliver escalated doses to the target area. Volumetric modulated arc therapy (VMAT) is a dynamic, highly conformal technique that may deliver high doses of radiation through a single gantry arc and reduce overall treatment times. The aim of this systematic review is to determine the feasibility and benefits of VMAT treatment in regard to overall survival rates and local control in patients with brain metastases, in comparison with patients treated with WBRT, SRS and IMRT. A search of the literature identified 23 articles for the purpose of this review. Articles were included on the basis they were human-based studies, with sample sizes of more than five patients who were receiving treatment for 1-10 metastatic brain lesions. VMAT was found to be highly conformal, have a reduced treatment delivery time and incurred no significant toxicities in comparison with WBRT, SRS and IMRT. Compared to other treatment techniques, VMAT proved to have fewer toxicities than conventional WBRT, shorter treatment times than SRS and similar dose distributions to IMRT plans. Future prospective studies are needed to accurately assess the prognostic benefits of VMAT as well as the occurrence of late toxicities.

Both the cis-trans equilibrium and isomerization dynamics of a single proline amide modulate β2-microglobulin amyloid assembly

PubMed Central

Torbeev, Vladimir Yu.; Hilvert, Donald

2013-01-01

The human protein β2-microglobulin (β2m) aggregates as amyloid fibrils in patients undergoing long-term hemodialysis. Isomerization of Pro32 from its native cis to a nonnative trans conformation is thought to trigger β2m misfolding and subsequent amyloid assembly. To examine this hypothesis, we systematically varied the free-energy profile of proline cis-trans isomerization by replacing Pro32 with a series of 4-fluoroprolines via total chemical synthesis. We show that β2m’s stability, (un)folding, and aggregation properties are all influenced by the rate and equilibrium of Pro32 cis-trans isomerization. As anticipated, the β2m monomer was either stabilized or destabilized by respective incorporation of (2S,4S)-fluoroproline, which favors the native cis amide bond, or the stereoisomeric (2S,4R)-fluoroproline, which disfavors this conformation. However, substitution of Pro32 with 4,4-difluoroproline, which has nearly the same cis-trans preference as proline but an enhanced isomerization rate, caused pronounced destabilization of the protein and increased oligomerization at neutral pH. More remarkably, these subtle alterations in chemical composition—incorporation of one or two fluorine atoms into a single proline residue in the 99 amino acid long protein—modulated the aggregation properties of β2m, inducing the formation of polymorphically distinct amyloid fibrils. These results highlight the importance of conformational dynamics for molecular assembly of an amyloid cross-β structure and provide insights into mechanistic aspects of Pro32 cis-trans isomerism in β2m aggregation. PMID:24262149

Both the cis-trans equilibrium and isomerization dynamics of a single proline amide modulate β2-microglobulin amyloid assembly.

PubMed

Torbeev, Vladimir Yu; Hilvert, Donald

2013-12-10

The human protein β2-microglobulin (β2m) aggregates as amyloid fibrils in patients undergoing long-term hemodialysis. Isomerization of Pro32 from its native cis to a nonnative trans conformation is thought to trigger β2m misfolding and subsequent amyloid assembly. To examine this hypothesis, we systematically varied the free-energy profile of proline cis-trans isomerization by replacing Pro32 with a series of 4-fluoroprolines via total chemical synthesis. We show that β2m's stability, (un)folding, and aggregation properties are all influenced by the rate and equilibrium of Pro32 cis-trans isomerization. As anticipated, the β2m monomer was either stabilized or destabilized by respective incorporation of (2S,4S)-fluoroproline, which favors the native cis amide bond, or the stereoisomeric (2S,4R)-fluoroproline, which disfavors this conformation. However, substitution of Pro32 with 4,4-difluoroproline, which has nearly the same cis-trans preference as proline but an enhanced isomerization rate, caused pronounced destabilization of the protein and increased oligomerization at neutral pH. More remarkably, these subtle alterations in chemical composition--incorporation of one or two fluorine atoms into a single proline residue in the 99 amino acid long protein--modulated the aggregation properties of β2m, inducing the formation of polymorphically distinct amyloid fibrils. These results highlight the importance of conformational dynamics for molecular assembly of an amyloid cross-β structure and provide insights into mechanistic aspects of Pro32 cis-trans isomerism in β2m aggregation.

Calcium Ions Promote Superoxide Dismutase 1 (SOD1) Aggregation into Non-fibrillar Amyloid

PubMed Central

Leal, Sónia S.; Cardoso, Isabel; Valentine, Joan S.; Gomes, Cláudio M.

2013-01-01

Imbalance in metal ion homeostasis is a hallmark in neurodegenerative conditions involving protein deposition, and amyotrophic lateral sclerosis (ALS) is no exception. In particular, Ca2+ dysregulation has been shown to correlate with superoxide dismutase-1 (SOD1) aggregation in a cellular model of ALS. Here we present evidence that SOD1 aggregation is enhanced and modulated by Ca2+. We show that at physiological pH, Ca2+ induces conformational changes that increase SOD1 β-sheet content, as probed by far UV CD and attenuated total reflectance-FTIR, and enhances SOD1 hydrophobicity, as probed by ANS fluorescence emission. Moreover, dynamic light scattering analysis showed that Ca2+ boosts the onset of SOD1 aggregation. In agreement, Ca2+ decreases SOD1 critical concentration and nucleation time during aggregation kinetics, as evidenced by thioflavin T fluorescence emission. Attenuated total reflectance FTIR analysis showed that Ca2+ induced aggregates consisting preferentially of antiparallel β-sheets, thus suggesting a modulation effect on the aggregation pathway. Transmission electron microscopy and analysis with conformational anti-fibril and anti-oligomer antibodies showed that oligomers and amyloidogenic aggregates constitute the prevalent morphology of Ca2+-induced aggregates, thus indicating that Ca2+ diverts SOD1 aggregation from fibrils toward amorphous aggregates. Interestingly, the same heterogeneity of conformations is found in ALS-derived protein inclusions. We thus hypothesize that transient variations and dysregulation of cellular Ca2+ levels contribute to the formation of SOD1 aggregates in ALS patients. In this scenario, Ca2+ may be considered as a pathogenic effector in the formation of ALS proteinaceous inclusions. PMID:23861388

Volumetric Modulated Arc Radiotherapy for Vestibular Schwannomas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lagerwaard, Frank J.; Meijer, Otto W.M.; Hoorn, Elles A.P. van der

2009-06-01

Purpose: To evaluate volumetric modulated arc radiotherapy (RapidArc [RA]), a novel approach allowing for rapid treatment delivery, for the treatment of vestibular schwannoma (VS). Methods and Materials: The RA plans were generated for a small (0.5 cm{sup 3}), intermediate (2.8 cm{sup 3}), and large (14.8 cm{sup 3}) VS. The prescription dose was 12.5 Gy to the encompassing 80% isodose. The RA plans were compared with conventional radiosurgery plans using both a single dynamic conformal arc (1DCA) and five noncoplanar dynamic conformal arcs (5DCA). Conformity indices (CI) and dose-volume histograms of critical organs were compared. The RA plan for the medium-sizedmore » VS was measured in a phantom using Gafchromic EBT films and compared with calculated dose distributions. Results: The RA planning was completed within 30 min in all cases, and calculated treatment delivery time (after patient setup) was 5 min vs. 20 min for 5DCA. A superior CI was achieved with RA, with a substantial decrease in low-dose irradiation of the normal brain achieved relative to 5DCA plans. Maximum doses to critical organs were similar for RA and 5DCA but were higher for 1DCA. Film measurements showed the differences between calculated and measured doses to be smaller than 1.5% in the high-dose area and smaller than 3% in the low-dose area. Conclusion: The RA plans consistently achieved a higher CI and decrease in areas of low-dose irradiation. This, together with shorter treatment delivery times, has led to RA replacing our conventional five-arc radiosurgery technique for VS.« less

A 5-Year Investigation of Children's Adaptive Functioning Following Conformal Radiation Therapy for Localized Ependymoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Netson, Kelli L.; Conklin, Heather M.; Wu Shengjie

2012-09-01

Purpose: Conformal and intensity modulated radiation therapies have the potential to preserve cognitive outcomes in children with ependymoma; however, functional behavior remains uninvestigated. This longitudinal investigation prospectively examined intelligence quotient (IQ) and adaptive functioning during the first 5 years after irradiation in children diagnosed with ependymoma. Methods and Materials: The study cohort consisted of 123 children with intracranial ependymoma. Mean age at irradiation was 4.60 years (95% confidence interval [CI], 3.85-5.35). Serial neurocognitive evaluations, including an age-appropriate IQ measure and the Vineland Adaptive Behavior Scales (VABS), were completed before irradiation, 6 months after treatment, and annually for 5 years. Amore » total of 579 neurocognitive evaluations were included in these analyses. Results: Baseline IQ and VABS were below normative means (P<.05), although within the average range. Linear mixed models revealed stable IQ and VABS across the follow-up period, except for the VABS Communication Index, which declined significantly (P=.015). Annual change in IQ (-.04 points) did not correlate with annual change in VABS (-.90 to +.44 points). Clinical factors associated with poorer baseline performance (P<.05) included preirradiation chemotherapy, cerebrospinal fluid shunt placement, number and extent of surgical resections, and younger age at treatment. No clinical factors significantly affected the rate of change in scores. Conclusions: Conformal and intensity modulated radiation therapies provided relative sparing of functional outcomes including IQ and adaptive behaviors, even in very young children. Communication skills remained vulnerable and should be the target of preventive and rehabilitative interventions.« less

Inverse planning in three-dimensional conformal and intensity-modulated radiotherapy of mid-thoracic oesophageal cancer.

PubMed

Wu, V W C; Sham, J S T; Kwong, D L W

2004-07-01

The aim of this study is to demonstrate the use of inverse planning in three-dimensional conformal radiation therapy (3DCRT) of oesophageal cancer patients and to evaluate its dosimetric results by comparing them with forward planning of 3DCRT and inverse planning of intensity-modulated radiotherapy (IMRT). For each of the 15 oesophageal cancer patients in this study, the forward 3DCRT, inverse 3DCRT and inverse IMRT plans were produced using the FOCUS treatment planning system. The dosimetric results and the planner's time associated with each of the treatment plans were recorded for comparison. The inverse 3DCRT plans showed similar dosimetric results to the forward plans in the planning target volume (PTV) and organs at risk (OARs). However, they were inferior to that of the IMRT plans in terms of tumour control probability and target dose conformity. Furthermore, the inverse 3DCRT plans were less effective in reducing the percentage lung volume receiving a dose below 25 Gy when compared with the IMRT plans. The inverse 3DCRT plans delivered a similar heart dose as in the forward plans, but higher dose than the IMRT plans. The inverse 3DCRT plans significantly reduced the operator's time by 2.5 fold relative to the forward plans. In conclusion, inverse planning for 3DCRT is a reasonable alternative to the forward planning for oesophageal cancer patients with reduction of the operator's time. However, IMRT has the better potential to allow further dose escalation and improvement of tumour control.

Eddy current loss analysis of open-slot fault-tolerant permanent-magnet machines based on conformal mapping method

NASA Astrophysics Data System (ADS)

Ji, Jinghua; Luo, Jianhua; Lei, Qian; Bian, Fangfang

2017-05-01

This paper proposed an analytical method, based on conformal mapping (CM) method, for the accurate evaluation of magnetic field and eddy current (EC) loss in fault-tolerant permanent-magnet (FTPM) machines. The aim of modulation function, applied in CM method, is to change the open-slot structure into fully closed-slot structure, whose air-gap flux density is easy to calculate analytically. Therefore, with the help of Matlab Schwarz-Christoffel (SC) Toolbox, both the magnetic flux density and EC density of FTPM machine are obtained accurately. Finally, time-stepped transient finite-element method (FEM) is used to verify the theoretical analysis, showing that the proposed method is able to predict the magnetic flux density and EC loss precisely.

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry.

PubMed

Walzthoeni, Thomas; Joachimiak, Lukasz A; Rosenberger, George; Röst, Hannes L; Malmström, Lars; Leitner, Alexander; Frydman, Judith; Aebersold, Ruedi

2015-12-01

Chemical cross-linking in combination with mass spectrometry generates distance restraints of amino acid pairs in close proximity on the surface of native proteins and protein complexes. In this study we used quantitative mass spectrometry and chemical cross-linking to quantify differences in cross-linked peptides obtained from complexes in spatially discrete states. We describe a generic computational pipeline for quantitative cross-linking mass spectrometry consisting of modules for quantitative data extraction and statistical assessment of the obtained results. We used the method to detect conformational changes in two model systems: firefly luciferase and the bovine TRiC complex. Our method discovers and explains the structural heterogeneity of protein complexes using only sparse structural information.

One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites

DOE PAGES

Fischer, Marcus; Shoichet, Brian K.; Fraser, James S.

2015-05-28

Interrogating fragment libraries by X-ray crystallography is a powerful strategy for discovering allosteric ligands for protein targets. Cryocooling of crystals should theoretically increase the fraction of occupied binding sites and decrease radiation damage. However, it might also perturb protein conformations that can be accessed at room temperature. Using data from crystals measured consecutively at room temperature and at cryogenic temperature, we found that transient binding sites could be abolished at the cryogenic temperatures employed by standard approaches. Finally, changing the temperature at which the crystallographic data was collected could provide a deliberate perturbation to the equilibrium of protein conformations andmore » help to visualize hidden sites with great potential to allosterically modulate protein function.« less

A Conformance Test Suite for Arden Syntax Compilers and Interpreters.

PubMed

Wolf, Klaus-Hendrik; Klimek, Mike

2016-01-01

The Arden Syntax for Medical Logic Modules is a standardized and well-established programming language to represent medical knowledge. To test the compliance level of existing compilers and interpreters no public test suite exists. This paper presents the research to transform the specification into a set of unit tests, represented in JUnit. It further reports on the utilization of the test suite testing four different Arden Syntax processors. The presented and compared results reveal the status conformance of the tested processors. How test driven development of Arden Syntax processors can help increasing the compliance with the standard is described with two examples. In the end some considerations how an open source test suite can improve the development and distribution of the Arden Syntax are presented.

N-terminal segments modulate the α-helical propensities of the intrinsically disordered basic regions of bZIP proteins.

PubMed

Das, Rahul K; Crick, Scott L; Pappu, Rohit V

2012-02-17

Basic region leucine zippers (bZIPs) are modular transcription factors that play key roles in eukaryotic gene regulation. The basic regions of bZIPs (bZIP-bRs) are necessary and sufficient for DNA binding and specificity. Bioinformatic predictions and spectroscopic studies suggest that unbound monomeric bZIP-bRs are uniformly disordered as isolated domains. Here, we test this assumption through a comparative characterization of conformational ensembles for 15 different bZIP-bRs using a combination of atomistic simulations and circular dichroism measurements. We find that bZIP-bRs have quantifiable preferences for α-helical conformations in their unbound monomeric forms. This helicity varies from one bZIP-bR to another despite a significant sequence similarity of the DNA binding motifs (DBMs). Our analysis reveals that intramolecular interactions between DBMs and eight-residue segments directly N-terminal to DBMs are the primary modulators of bZIP-bR helicities. We test the accuracy of this inference by designing chimeras of bZIP-bRs to have either increased or decreased overall helicities. Our results yield quantitative insights regarding the relationship between sequence and the degree of intrinsic disorder within bZIP-bRs, and might have general implications for other intrinsically disordered proteins. Understanding how natural sequence variations lead to modulation of disorder is likely to be important for understanding the evolution of specificity in molecular recognition through intrinsically disordered regions (IDRs). Copyright © 2011 Elsevier Ltd. All rights reserved.

The Sensorless Pore Module of Voltage-gated K+ Channel Family 7 Embodies the Target Site for the Anticonvulsant Retigabine.

PubMed

Syeda, Ruhma; Santos, Jose S; Montal, Mauricio

2016-02-05

KCNQ (voltage-gated K(+) channel family 7 (Kv7)) channels control cellular excitability and underlie the K(+) current sensitive to muscarinic receptor signaling (the M current) in sympathetic neurons. Here we show that the novel anti-epileptic drug retigabine (RTG) modulates channel function of pore-only modules (PMs) of the human Kv7.2 and Kv7.3 homomeric channels and of Kv7.2/3 heteromeric channels by prolonging the residence time in the open state. In addition, the Kv7 channel PMs are shown to recapitulate the single-channel permeation and pharmacological specificity characteristics of the corresponding full-length proteins in their native cellular context. A mutation (W265L) in the reconstituted Kv7.3 PM renders the channel insensitive to RTG and favors the conductive conformation of the PM, in agreement to what is observed when the Kv7.3 mutant is heterologously expressed. On the basis of the new findings and homology models of the closed and open conformations of the Kv7.3 PM, we propose a structural mechanism for the gating of the Kv7.3 PM and for the site of action of RTG as a Kv7.2/Kv7.3 K(+) current activator. The results validate the modular design of human Kv channels and highlight the PM as a high-fidelity target for drug screening of Kv channels. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

The Sensorless Pore Module of Voltage-gated K+ Channel Family 7 Embodies the Target Site for the Anticonvulsant Retigabine*

PubMed Central

Syeda, Ruhma; Santos, Jose S.; Montal, Mauricio

2016-01-01

KCNQ (voltage-gated K+ channel family 7 (Kv7)) channels control cellular excitability and underlie the K+ current sensitive to muscarinic receptor signaling (the M current) in sympathetic neurons. Here we show that the novel anti-epileptic drug retigabine (RTG) modulates channel function of pore-only modules (PMs) of the human Kv7.2 and Kv7.3 homomeric channels and of Kv7.2/3 heteromeric channels by prolonging the residence time in the open state. In addition, the Kv7 channel PMs are shown to recapitulate the single-channel permeation and pharmacological specificity characteristics of the corresponding full-length proteins in their native cellular context. A mutation (W265L) in the reconstituted Kv7.3 PM renders the channel insensitive to RTG and favors the conductive conformation of the PM, in agreement to what is observed when the Kv7.3 mutant is heterologously expressed. On the basis of the new findings and homology models of the closed and open conformations of the Kv7.3 PM, we propose a structural mechanism for the gating of the Kv7.3 PM and for the site of action of RTG as a Kv7.2/Kv7.3 K+ current activator. The results validate the modular design of human Kv channels and highlight the PM as a high-fidelity target for drug screening of Kv channels. PMID:26627826

[Dynamics of biomacromolecules in coherent electromagnetic radiation field].

PubMed

Leshcheniuk, N S; Apanasevich, E E; Tereshenkov, V I

2014-01-01

It is shown that induced oscillations and periodic displacements of the equilibrium positions occur in biomacromolecules in the absence of electromagnetic radiation absorption, due to modulation of interaction potential between atoms and groups of atoms forming the non-valence bonds in macromolecules by the external electromagnetic field. Such "hyperoscillation" state causes inevitably the changes in biochemical properties of macromolecules and conformational transformation times.

Extended generation profile - E.B.I.C model application in the case of a PN junction

NASA Astrophysics Data System (ADS)

Guermazi, S.; Toureille, A.; Grill, C.; El Jani, B.

2000-01-01

We have developed a model for the calculation of the induced current due to an electron beam with an extended generation profile. Added to the absorbed and diffuse electrons in the depth distribution, the generation profile takes into account the lateral diffusion. The analytical expression of the electron beam induced current (EBIC) is obtained by solving the continuity equation in permanent regime by the Green function method. The induced current profile, obtained in the case of a ternary component (Ga{0.7}Al{0.3}As:N^+/Ga{0.7}Al{0.3}As:P) sulfur doped and prepared by organometallic compounds phase vapor epitaxy method, is compared to the theoretical profiles whose analytical expressions are given by Van Roosbroeck and Bresse. The experimental current profile, measured by S.E.M provided us to calculate the diffusion length of the minority carriers: L_p=1 μm in the N region and L_n=1.80 μm in the P region of the ternaire component. The theoretical curve obtained from the proposed model is in good agreement with the experimental one for a surface recombination velocity of 10^6 cm s^{-1}. Our results are found to be consistent compared to those obtained by other experimental techniques using the same samples. Nous avons développé un modèle de calcul du courant induit par un faisceau d'électrons avec un profil de génération élargi. Le profil de génération prend en compte la répartition spatiale de la diffusion et de l'absorption des électrons. L'expression analytique du courant induit (E.B.I.C) est déterminée par résolution de l'équation de continuité en régime permanent par la méthode des fonctions de Green. Le profil de courant induit obtenu dans le cas d'une jonction PN (Ga{0,7}Al{0,3}As:N^+/Ga{0,7}Al{0,3}As:P) dopée par le soufre et préparée par épitaxie à phase vapeur organo-métallique, est comparé au profil de courant théorique dont l'expression analytique est explicitée par Van Roosbroeck et Bresse. Le profil expérimental de courant E.B.I.C, mesuré par un microscope électronique à balayage, nous a permis de déterminer la longueur de diffusion des porteurs minoritaires L_p=1 μm dans la région N du composant ternaire et L_n=1,8 μm dans la région P de ce composant. La courbe théorique, tracée à partir du modèle proposé, est en bon accord avec la courbe expérimentale pour une vitesse de recombinaison à la surface de 10^6 cm s^{-1}. Ces résultats sont conformes avec ceux obtenus par d'autres techniques expérimentales sur les mêmes échantillons.

Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator).

PubMed

Godwin, Ryan C; Melvin, Ryan L; Gmeiner, William H; Salsbury, Freddie R

2017-01-31

Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein structure, dynamics, and ultimately function, as these pivotal regulatory proteins are increasingly important for protein engineering and therapeutic discovery. To better understand the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB essential modulator), as well as the role of zinc, we present results of 20 μs molecular dynamics trajectories, 5 μs for each of four active site configurations. Consistent with experimental evidence, the zinc ion is essential for mechanical stabilization of the functional, folded conformation. Hydrogen bond motifs are unique for deprotonated configurations yet overlap in protonated cases. Correlated motions and principal component analysis corroborate the similarity of the protonated configurations and highlight unique relationships of the zinc-bound configuration. We hypothesize a potential mechanism for zinc binding from results of the thiol configurations. The deprotonated, zinc-bound configuration alone predominantly maintains its tertiary structure throughout all 5 μs and alludes rare conformations potentially important for (im)proper zinc-finger-related protein-protein or protein-DNA interactions.

Uncovering the Role of Sgf73 in Maintaining SAGA Deubiquitinating Module Structure and Activity

DOE PAGES

Yan, Ming; Wolberger, Cynthia

2014-12-17

The SAGA (Spt-Ada-Gcn5-acetyltransferase) complex performs multiple functions in transcription activation including deubiquitinating histone H2B, which is mediated by a subcomplex called the deubiquitinating module (DUBm). The yeast DUBm comprises a catalytic subunit, Ubp8, and three additional subunits, Sgf11, Sus1 and Sgf73, all of which are required for DUBm activity. A portion of the non-globular Sgf73 subunit lies between the Ubp8 catalytic domain and the ZnF-UBP domain and has been proposed to contribute to deubiquitinating activity by maintaining the catalytic domain in an active conformation. We report structural and solution studies of the DUBm containing two different Sgf73 point mutations thatmore » disrupt deubiquitinating activity. We find that the Sgf73 mutations abrogate deubiquitinating activity by impacting the Ubp8 ubiquitin-binding fingers region and have an unexpected effect on the overall folding and stability of the DUBm complex. Finally, taken together, our data suggest a role for Sgf73 in maintaining both the organization and ubiquitin-binding conformation of Ubp8, thereby contributing to overall DUBm activity.« less

Mechanism of Positive Allosteric Modulators Acting on AMPA Receptors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin,R.; Clark, S.; Weeks, A.

2005-01-01

Ligand-gated ion channels involved in the modulation of synaptic strength are the AMPA, kainate, and NMDA glutamate receptors. Small molecules that potentiate AMPA receptor currents relieve cognitive deficits caused by neurodegenerative diseases such as Alzheimer's disease and show promise in the treatment of depression. Previously, there has been limited understanding of the molecular mechanism of action for AMPA receptor potentiators. Here we present cocrystal structures of the glutamate receptor GluR2 S1S2 ligand-binding domain in complex with aniracetam [1-(4-methoxybenzoyl)-2-pyrrolidinone] or CX614 (pyrrolidino-1, 3-oxazino benzo-1, 4-dioxan-10-one), two AMPA receptor potentiators that preferentially slow AMPA receptor deactivation. Both potentiators bind within the dimermore » interface of the nondesensitized receptor at a common site located on the twofold axis of molecular symmetry. Importantly, the potentiator binding site is adjacent to the 'hinge' in the ligand-binding core 'clamshell' that undergoes conformational rearrangement after glutamate binding. Using rapid solution exchange, patch-clamp electrophysiology experiments, we show that point mutations of residues that interact with potentiators in the cocrystal disrupt potentiator function. We suggest that the potentiators slow deactivation by stabilizing the clamshell in its closed-cleft, glutamate-bound conformation.« less

Ability of a beta-casein phosphopeptide to modulate the precipitation of calcium phosphate by forming amorphous dicalcium phosphate nanoclusters.

PubMed Central

Holt, C; Wahlgren, N M; Drakenberg, T

1996-01-01

The ability of casein in the form of colloidal-sized casein micelles to modulate the phase separation of calcium phosphate during milk secretion is adapted to produce nanometre-sized particles of calcium phosphate stabilized by a casein phosphopeptide (nanoclusters). The nanoclusters were prepared from an undersaturated solution of salts and the peptide by raising the pH homogeneously from about 5.5 to 6.7 with urea plus urease. Chemical analysis and IR spectroscopy showed that they comprise an amorphous dicalcium phosophate bound to the phosphopeptide. Multinuclear NMR spectroscopy of the cluster solutions showed that the small ions and free peptide in the solution were in a state of dynamic exchange with the nanoclusters. The peptide is linked to the calcium phosphate through its sequence of phosphorylated residues, but, in a proportion of adsorbed conformational states, the termini retain the conformational freedom of the unbound peptide. The ability of casein to form nanoclusters in milk suggests a more general mechanism for avoiding pathological calcification and regulating calcium flow in tissues and biological fluids exposed to or containing high concentrations of calcium. PMID:8615755

Conformation Change in a Self-recognizing Autotransporter Modulates Bacterial Cell-Cell Interaction*

PubMed Central

Girard, Victoria; Côté, Jean-Philippe; Charbonneau, Marie-Ève; Campos, Manuel; Berthiaume, Frédéric; Hancock, Mark A.; Siddiqui, Nadeem; Mourez, Michael

2010-01-01

Bacteria mostly live as multicellular communities, although they are unicellular organisms, yet the mechanisms that tie individual bacteria together are often poorly understood. The adhesin involved in diffuse adherence (AIDA-I) is an adhesin of diarrheagenic Escherichia coli strains. AIDA-I also mediates bacterial auto-aggregation and biofilm formation and thus could be important for the organization of communities of pathogens. Using purified protein and whole bacteria, we provide direct evidence that AIDA-I promotes auto-aggregation by interacting with itself. Using various biophysical and biochemical techniques, we observed a conformational change in the protein during AIDA-AIDA interactions, strengthening the notion that this is a highly specific interaction. The self-association of AIDA-I is of high affinity but can be modulated by sodium chloride. We observe that a bile salt, sodium deoxycholate, also prevents AIDA-I oligomerization and bacterial auto-aggregation. Thus, we propose that AIDA-I, and most likely other similar autotransporters such as antigen 43 (Ag43) and TibA, organize bacterial communities of pathogens through a self-recognition mechanism that is sensitive to the environment. This could permit bacteria to switch between multicellular and unicellular lifestyles to complete their infection. PMID:20123991

Using Surface Enhanced Raman Scattering to Analyze the Interactions of Protein Receptors with Bacterial Quorum Sensing Modulators

PubMed Central

2015-01-01

Many members of the LuxR family of quorum sensing (QS) transcriptional activators, including LasR of Pseudomonas aeruginosa, are believed to require appropriate acyl-homoserine lactone (acyl-HSL) ligands to fold into an active conformation. The failure to purify ligand-free LuxR homologues in nonaggregated form at the high concentrations required for their structural characterization has limited the understanding of the mechanisms by which QS receptors are activated. Surface-enhanced Raman scattering (SERS) is a vibrational spectroscopy technique that can be applied to study proteins at extremely low concentrations in their active state. The high sensitivity of SERS has allowed us to detect molecular interactions between the ligand-binding domain of LasR (LasRLBD) as a soluble apoprotein and modulators of P. aeruginosa QS. We found that QS activators and inhibitors produce differential SERS fingerprints in LasRLBD, and in combination with molecular docking analysis provide insight into the relevant interaction mechanism. This study reveals signal-specific structural changes in LasR upon ligand binding, thereby confirming the applicability of SERS to analyze ligand-induced conformational changes in proteins. PMID:25927541

Dosimetric Evaluation of Intensity Modulated Radiotherapy and 4-Field 3-D Conformal Radiotherapy in Prostate Cancer Treatment

PubMed Central

Uysal, Bora; Beyzadeoğlu, Murat; Sager, Ömer; Dinçoğlan, Ferrat; Demiral, Selçuk; Gamsız, Hakan; Sürenkök, Serdar; Oysul, Kaan

2013-01-01

Objective: The purpose of this dosimetric study is the targeted dose homogeneity and critical organ dose comparison of 7-field Intensity Modulated Radiotherapy (IMRT) and 3-D 4-field conformal radiotherapy. Study Design: Cross sectional study. Material and Methods: Twenty patients with low and moderate risk prostate cancer treated at Gülhane Military Medical School Radiation Oncology Department between January 2009 and December 2009 are included in this study. Two seperate dosimetric plans both for 7-field IMRT and 3D-CRT have been generated for each patient to comparatively evaluate the dosimetric status of both techniques and all the patients received 7-field IMRT. Results: Dose-comparative evaluation of two techniques revealed the superiority of IMRT technique with statistically significantly lower femoral head doses along with reduced critical organ dose-volume parameters of bladder V60 (the volume receiving 60 Gy) and rectal V40 (the volume receiving 40 Gy) and V60. Conclusion: It can be concluded that IMRT is an effective definitive management tool for prostate cancer with improved critical organ sparing and excellent dose homogenization in target organs of prostate and seminal vesicles. PMID:25207069

A Calmodulin C-Lobe Ca2+-Dependent Switch Governs Kv7 Channel Function.

PubMed

Chang, Aram; Abderemane-Ali, Fayal; Hura, Greg L; Rossen, Nathan D; Gate, Rachel E; Minor, Daniel L

2018-02-21

Kv7 (KCNQ) voltage-gated potassium channels control excitability in the brain, heart, and ear. Calmodulin (CaM) is crucial for Kv7 function, but how this calcium sensor affects activity has remained unclear. Here, we present X-ray crystallographic analysis of CaM:Kv7.4 and CaM:Kv7.5 AB domain complexes that reveal an Apo/CaM clamp conformation and calcium binding preferences. These structures, combined with small-angle X-ray scattering, biochemical, and functional studies, establish a regulatory mechanism for Kv7 CaM modulation based on a common architecture in which a CaM C-lobe calcium-dependent switch releases a shared Apo/CaM clamp conformation. This C-lobe switch inhibits voltage-dependent activation of Kv7.4 and Kv7.5 but facilitates Kv7.1, demonstrating that mechanism is shared by Kv7 isoforms despite the different directions of CaM modulation. Our findings provide a unified framework for understanding how CaM controls different Kv7 isoforms and highlight the role of membrane proximal domains for controlling voltage-gated channel function. VIDEO ABSTRACT. Copyright © 2018 Elsevier Inc. All rights reserved.

Italian Exposition

ScienceCinema

None

2017-12-09

Le DG parle dans son allocution à l'occasion de l'exposition (suivi d'une visite)de la contribution du Cern à la création d'une espace de la technologie européenne. Il parle de la manière comment organiser des formes fructueuses de coopération et coordination internationales dans ce domaine. "Afin de renforcer encore notre relation avec l'industrie et intensifier le transfert de la technologie nous proposerons au ministre de recherche de poursuivre dans le cadre du programme EUREKA ensemble avec les industries des programmes concrètes." Le ministre italien prend ensuite la parole.

Coinfection pulmonaire par pneumocystis jirovecii et pseudomonas aeruginosa au cours du SIDA: à propos de deux cas

PubMed Central

Mamoudou, Savadogo; Bellaud, Guillaume; Ana, Canestri; Gilles, Pialoux

2015-01-01

Rapporter deux cas cliniques de coinfections pulmonaires par Pneumocystis jirovecii et par Pseudomonas aeruginosa chez des patients vivant avec le VIH. Les deux patients étaient âgés respectivement de 32 ans et 46 ans. Un patient a été pris en charge à l'hôpital Yalgado Ouédraogo de Ouagadougou au Burkina Faso et l'autre a été pris en charge à l'hôpital Ténon de Paris, en France. Les deux souffraient de pneumopathie confirmée à la radiographie et à la tomodensitométrie. L'un des patients était sévèrement immuno déprimé, contrairement à l'autre. L'examen bactériologique dans les crachats avait permis d'isoler Pseudomonas aeruginosa et Pneumocystis jirovecii chez les deux patients. Sous traitement, l’évolution a été favorable. Les coinfections morbides sont relativement fréquentes chez les patients vivant avec le VIH. Devant une symptomatologie respiratoire du sujet vivant avec le VIH, il faut savoir rechercher en plus du Bacille de Koch, Pneumocystis jirovecii et Pseudomonas aeruginosa par un lavage broncho alvéolaire. PMID:26516396

Modulation of Conformational Equilibria in the S-Adenosylmethionine (SAM) II Riboswitch by SAM, Mg(2+), and Trimethylamine N-Oxide.

PubMed

McPhie, Peter; Brown, Patrick; Chen, Bin; Dayie, Theodore K; Minton, Allen P

2016-09-13

The dependence of the conformation of the S-adenosylmethionine (SAM) II riboswitch on the concentration of added Mg(2+) ions and SAM, individually and in mixtures, was monitored by circular dichroism (CD) spectroscopy and by measurement of the diffusion coefficient. The results are analyzed in the context of two complementary quantitative models, both of which are consistent with a single underlying physical model. Magnesium binding sites in the open state have an affinity on average higher than the affinity of those in the compact state, but formation of the compact state is accompanied by an increase in the number of binding sites. Consequently, at low Mg(2+) concentrations, Mg(2+) binds preferentially to the open state, favoring its formation, but at high concentrations, Mg(2+) binds preferentially to the compact state. The affinity of the riboswitch for SAM increases drastically with an increased level of binding of Mg(2+) to the compact pseudoknot conformation. The effect of increasing concentrations of trimethylamine N-oxide (TMAO), a well-studied molecular crowding agent, on the conformation of the riboswitch and its affinity for SAM were also monitored by CD spectroscopy and measurement of diffusion. In the absence of added Mg(2+), high concentrations of TMAO were found to induce a conformational change compatible with the formation of the pseudoknot form but have only a small effect on the affinity of the RNA for SAM.

Conformation, orientation, and adsorption kinetics of dermaseptin B2 onto synthetic supports at aqueous/solid interface.

PubMed

Noinville, S; Bruston, F; El Amri, C; Baron, D; Nicolas, P

2003-08-01

The antimicrobial activity of cationic amphipathic peptides is due mainly to the adsorption of peptides onto target membranes, which can be modulated by such physicochemical parameters as charge and hydrophobicity. We investigated the structure of dermaseptin B2 (Drs B2) at the aqueous/synthetic solid support interface and its adsorption kinetics using attenuated total reflection Fourier transform infrared spectroscopy and surface plasmon resonance. We determined the conformation and affinity of Drs B2 adsorbed onto negatively charged (silica or dextran) and hydrophobic supports. Synthetic supports of differing hydrophobicity were obtained by modifying silica or gold with omega-functionalized alkylsilanes (bromo, vinyl, phenyl, methyl) or alkylthiols. The peptide molecules adsorbed onto negatively charged supports mostly had a beta-type conformation. In contrast, a monolayer of Drs B2, mainly in the alpha-helical conformation, was adsorbed irreversibly onto the hydrophobic synthetic supports. The conformational changes during formation of the adsorbed monolayer were monitored by two-dimensional Fourier transform infrared spectroscopy correlation; they showed the influence of peptide-peptide interactions on alpha-helix folding on the most hydrophobic support. The orientation of the alpha-helical Drs B2 with respect to the hydrophobic support was determined by polarized attenuated total reflection; it was around 15 +/- 5 degrees. This orientation was confirmed and illustrated by a molecular dynamics study. These combined data demonstrate that specific chemical environments influence the structure of Drs B2, which could explain the many functions of antimicrobial peptides.

Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.

PubMed

Elam, W Austin; Schrank, Travis P; Campagnolo, Andrew J; Hilser, Vincent J

2013-04-01

Intrinsically disordered (ID) proteins function in the absence of a unique stable structure and appear to challenge the classic structure-function paradigm. The extent to which ID proteins take advantage of subtle conformational biases to perform functions, and whether signals for such mechanism can be identified in proteome-wide studies is not well understood. Of particular interest is the polyproline II (PII) conformation, suggested to be highly populated in unfolded proteins. We experimentally determine a complete calorimetric propensity scale for the PII conformation. Projection of the scale into representative eukaryotic proteomes reveals significant PII bias in regions coding for ID proteins. Importantly, enrichment of PII in ID proteins, or protein segments, is also captured by other PII scales, indicating that this enrichment is robustly encoded and universally detectable regardless of the method of PII propensity determination. Gene ontology (GO) terms obtained using our PII scale and other scales demonstrate a consensus for molecular functions performed by high PII proteins across the proteome. Perhaps the most striking result of the GO analysis is conserved enrichment (P < 10(-8) ) of phosphorylation sites in high PII regions found by all PII scales. Subsequent conformational analysis reveals a phosphorylation-dependent modulation of PII, suggestive of a conserved "tunability" within these regions. In summary, the application of an experimentally determined polyproline II (PII) propensity scale to proteome-wide sequence analysis and gene ontology reveals an enrichment of PII bias near disordered phosphorylation sites that is conserved throughout eukaryotes. Copyright © 2013 The Protein Society.

A novel autophagy modulator 6-Bio ameliorates SNCA/α-synuclein toxicity

PubMed Central

Suresh, S. N.; Chavalmane, Aravinda K.; DJ, Vidyadhara; Yarreiphang, Haorei; Rai, Shashank; Paul, Abhik; Clement, James P.; Alladi, Phalguni Anand; Manjithaya, Ravi

2017-01-01

ABSTRACT Parkinson disease (PD) is a life-threatening neurodegenerative movement disorder with unmet therapeutic intervention. We have identified a small molecule autophagy modulator, 6-Bio that shows clearance of toxic SNCA/α-synuclein (a protein implicated in synucleopathies) aggregates in yeast and mammalian cell lines. 6-Bio induces autophagy and dramatically enhances autolysosome formation resulting in SNCA degradation. Importantly, neuroprotective function of 6-Bio as envisaged by immunohistology and behavior analyses in a preclinical model of PD where it induces autophagy in dopaminergic (DAergic) neurons of mice midbrain to clear toxic protein aggregates suggesting that it could be a potential therapeutic candidate for protein conformational disorders. PMID:28350199

Caracterisation environnementale des emissions atmospheriques d'une source fixe et creation d'un outil de gestion dynamique =

NASA Astrophysics Data System (ADS)

Fournier, Marie-Claude

Une caracterisation des emissions atmospheriques provenant des sources fixes en operation, alimentees au gaz et a l'huile legere, a ete conduite aux installations visees des sites no.1 et no.2. La caracterisation et les calculs theoriques des emissions atmospheriques aux installations des sites no.1 et no.2 presentent des resultats qui sont en dessous des valeurs reglementaires pour des conditions d'operation normales en periode hivernale et par consequent, a de plus fortes demandes energetiques. Ainsi, pour une demande energetique plus basse, le taux de contaminants dans les emissions atmospheriques pourrait egalement etre en dessous des reglementations municipales et provinciales en vigueur. Dans la perspective d'une nouvelle reglementation provinciale, dont les termes sont discutes depuis 2005, il serait souhaitable que le proprietaire des infrastructures visees participe aux echanges avec le Ministere du Developpement Durable, de l'Environnement et des Parcs (MDDEP) du Quebec. En effet, meme si le principe de droit acquis permettrait d'eviter d'etre assujetti a la nouvelle reglementation, l'application de ce type de principe ne s'inscrit pas dans ceux d'un developpement durable. L'âge avance des installations etudiees implique la planification d'un entretien rigoureux afin d'assurer les conditions optimales de combustion en fonction du type de combustible. Des tests de combustion sur une base reguliere sont donc recommandes. Afin de supporter le processus de suivi et d'evaluation de la performance environnementale des sources fixes, un outil d'aide a la gestion de l'information environnementale a ete developpe. Dans ce contexte, la poursuite du developpement d'un outil d'aide a la gestion de l'information environnementale faciliterait non seulement le travail des personnes affectees aux inventaires annuels mais egalement le processus de communication entre les differents acteurs concernes tant intra- qu'inter-etablissement. Cet outil serait egalement un bon moyen pour sensibiliser le personnel a leur consommation energetique ainsi qu'a leur role dans la lutte contre les emissions polluantes et les gaz a effets de serre. En outre, ce type d'outil a pour principale fonction de generer des rapports dynamiques pouvant s'adapter a des besoins precis. Le decoupage coherent de l'information associe a un developpement par modules offre la perspective d'application de l'outil pour d'autres types d'activites. Dans ce cas, il s'agit de definir la part commune avec les modules existants et planifier les activites de developpement specifiques selon la meme demarche que celle presentee dans le present document.

Heavy-ion conformal irradiation in the shallow-seated tumor therapy terminal at HIRFL.

PubMed

Li, Qiang; Dai, Zhongying; Yan, Zheng; Jin, Xiaodong; Liu, Xinguo; Xiao, Guoqing

2007-11-01

Basic research related to heavy-ion cancer therapy has been done at the Institute of Modern Physics (IMP), Chinese Academy of Sciences since 1995. Now a plan of clinical trial with heavy ions has been launched at IMP. First, superficially placed tumor treatment with heavy ions is expected in the therapy terminal at the Heavy Ion Research Facility in Lanzhou (HIRFL), where carbon ion beams with energy up to 100 MeV/u can be supplied. The shallow-seated tumor therapy terminal at HIRFL is equipped with a passive beam delivery system including two orthogonal dipole magnets, which continuously scan pencil beams laterally and generate a broad and uniform irradiation field, a motor-driven energy degrader and a multi-leaf collimator. Two different types of range modulator, ripple filter and ridge filter with which Guassian-shaped physical dose and uniform biological effective dose Bragg peaks can be shaped for therapeutic ion beams respectively, have been designed and manufactured. Therefore, two-dimensional and three-dimensional conformal irradiations to tumors can be performed with the passive beam delivery system at the earlier therapy terminal. Both the conformal irradiation methods have been verified experimentally and carbon-ion conformal irradiations to patients with superficially placed tumors have been carried out at HIRFL since November 2006.

Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design

PubMed Central

Rodríguez-Ropero, Francisco; Zanuy, David; Casanovas, Jordi; Nussinov, Ruth; Alemán, Carlos

2009-01-01

Conformationally restricted amino acids are promising candidates to serve as basic pieces in redesigned protein motifs which constitute the basic modules in synthetic nanoconstructs. Here we study the ability of constrained cyclic amino acid 1-aminocyclohexane-1-carboxylic acid (Ac6c) to stabilize highly regular β-helical motifs excised from naturally occurring proteins. Calculations indicate that the conformational flexibility observed in both the ring and the main chain is significantly higher than that detected for other 1-aminocycloalkane-1-carboxylic acid (Acnc, where n refers to the size of the ring) with smaller cycles. Incorporation of Ac6c into the flexible loops of β-helical motifs indicates that the stability of such excised building blocks as well as the nano-assemblies derived from them is significantly enhanced. Thus, the intrinsic Ac6c tendency to adopt folded conformations combined with the low structural strain of the cyclohexane ring confers the ability to both self-adapt to the β-helix motif and to stabilize the overall structure by absorbing part of its conformational fluctuations. Comparison with other Acnc residues indicates that the ability to adapt to the targeted position improves considerably with the ring size, i.e. when the rigidity introduced by the strain of the ring decreases. PMID:18201062

SU-E-T-548: How To Decrease Spine Dose In Patients Who Underwent Sterotactic Spine Radiosurgery?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acar, H; Altinok, A; Kucukmorkoc, E

2014-06-01

Purpose: Stereotactic radiosurgery for spine metastases involves irradiation using a single high dose fraction. The purpose of this study was to dosimetrically compare stereotactic spine radiosurgery(SRS) plans using a recently new volumetric modulated arc therapy(VMAT) technique against fix-field intensity-modulated radiotherapy(IMRT). Plans were evaluated for target conformity and spinal cord sparing. Methods: Fifteen previously treated patients were replanned using the Eclipse 10.1 TPS AAA calculation algorithm. IMRT plans with 7 fields were generated. The arc plans used 2 full arc configurations. Arc and IMRT plans were normalized and prescribed to deliver 16.0 Gy in a single fraction to 90% of themore » planning target volume(PTV). PTVs consisted of the vertebral body expanded by 3mm, excluding the PRV-cord, where the cord was expanded by 2mm.RTOG 0631 recommendations were applied for treatment planning. Partial spinal cord volume was defined as 5mm above and below the radiosurgery target volume. Plans were compared for conformity and gradient index as well as spinal cord sparing. Results: The conformity index values of fifteen patients for two different treatment planning techniques were shown in table 1. Conformity index values for 2 full arc planning (average CI=0.84) were higher than that of IMRT planning (average CI=0.79). The gradient index values of fifteen patients for two different treatment planning techniques were shown in table 2. Gradient index values for 2 full arc planning (average GI=3.58) were higher than that of IMRT planning (average GI=2.82).The spinal cord doses of fifteen patients for two different treatment planning techniques were shown in table 3. D0.35cc, D0.03cc and partial spinal cord D10% values in 2 full arc plannings (average D0.35cc=819.3cGy, D0.03cc=965.4cGy, 10%partial spinal=718.1cGy) were lower than IMRT plannings (average D0.35cc=877.4cGy, D0.03c=1071.4cGy, 10%partial spinal=805.1cGy). Conclusions: The two arc VMAT technique is superior to 7 field IMRT technique in terms of both spinal cord sparing and better conformity and gradient indexes.« less

A planning comparison of 7 irradiation options allowed in RTOG 1005 for early-stage breast cancer.

PubMed

Chen, Guang-Pei; Liu, Feng; White, Julia; Vicini, Frank A; Freedman, Gary M; Arthur, Douglas W; Li, X Allen

2015-01-01

This study compared the 7 treatment plan options in achieving the dose-volume criteria required by the Radiation Therapy Oncology Group (RTOG) 1005 protocol. Dosimetry plans were generated for 15 representative patients with early-stage breast cancer (ESBC) based on the protocol-required dose-volume criteria for each of the following 7 treatment options: 3D conformal radiotherapy (3DCRT), whole-breast irradiation (WBI) plus 3DCRT lumpectomy boost, 3DCRT WBI plus electron boost, 3DCRT WBI plus intensity-modulated radiation therapy (IMRT) boost, IMRT WBI plus 3DCRT boost, IMRT WBI plus electron boost, IMRT WBI plus IMRT boost, and simultaneous integrated boost (SIB) with IMRT. A variety of dose-volume parameters, including target dose conformity and uniformity and normal tissue sparing, were compared for these plans. For the patients studied, all plans met the required acceptable dose-volume criteria, with most of them meeting the ideal criteria. When averaged over patients, most dose-volume goals for all plan options can be achieved with a positive gap of at least a few tenths of standard deviations. The plans for all 7 options are generally comparable. The dose-volume goals required by the protocol can in general be easily achieved. IMRT WBI provides better whole-breast dose uniformity than 3DCRT WBI does, but it causes no significant difference for the dose conformity. All plan options are comparable for lumpectomy dose uniformity and conformity. Patient anatomy is always an important factor when whole-breast dose uniformity and conformity and lumpectomy dose conformity are considered. Copyright © 2015 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.

Effects of solution conditions on methionine oxidation in albinterferon alfa-2b and the role of oxidation in its conformation and aggregation.

PubMed

Chou, Danny K; Krishnamurthy, Rajesh; Manning, Mark Cornell; Randolph, Theodore W; Carpenter, John F

2013-02-01

Physical and chemical degradation of therapeutic proteins can occur simultaneously. In this study, our first objective was to investigate how solution conditions that impact conformational stability of albinterferon alfa-2b, a recombinant fusion protein, modulate rates of methionine (Met) oxidation. Another objective of this work was to determine whether oxidation affects conformation and rate of aggregation of the protein. The protein was subjected to oxidation in solutions of varying pH, ionic strength, and excipients by the addition of 0.02% tertiary-butyl hydroperoxide (TBHP). The rate of formation of Met-sulfoxide species was monitored by reversed-phase high-performance liquid chromatography and compared across solution conditions. Albinterferon alfa-2b exhibited susceptibility to Met oxidation during exposure to TBHP that was highly dependent on solution parameters, but there was not a clear correlation between oxidation rate and protein conformational stability. Met oxidation resulted in significant perturbation of both secondary and tertiary structure of albinterferon alfa-2b as shown by both far-ultraviolet (UV) and near-UV circular dichroism. Moreover, oxidation of the protein caused a noticeable reduction in the protein's resistance to thermal denaturation. Surprisingly, despite its negative effect on solution structure and conformational stability, oxidation actually reduced the protein's aggregation rate during agitation at room temperature as well as during quiescent incubation at 40°C. Oxidation of the protein resulted in improved colloidal stability of the protein, which is manifested by a more positive B(22) value in the oxidized protein. Thus, the reduced aggregation rate after oxidation suggests that increased colloidal stability of oxidized albinterferon alfa-2b counteracted oxidation-induced decreases in conformational stability. Copyright © 2012 Wiley Periodicals, Inc.

Water response to ganglioside GM1 surface remodelling.

PubMed

Brocca, P; Rondelli, V; Mallamace, F; Di Bari, M T; Deriu, A; Lohstroh, W; Del Favero, E; Corti, M; Cantu', L

2017-01-01

Gangliosides are biological glycolipids participating in rafts, structural and functional domains of cell membranes. Their headgroups are able to assume different conformations when packed on the surface of an aggregate, more lying or standing. Switching between different conformations is possible, and is a collective event. Switching can be induced, in model systems, by concentration or temperature increase, then possibly involving ganglioside-water interaction. In the present paper, the effect of GM1 ganglioside headgroup conformation on the water structuring and interactions is addressed. Depolarized Rayleigh Scattering, Raman Scattering, Quasielastic Neutron Scattering and NMR measurements were performed on GM1 ganglioside solutions, focusing on solvent properties. All used techniques agree in evidencing differences in the structure and dynamics of solvent water on different time-and-length scales in the presence of either GM1 headgroup conformations. In general, all results indicate that both the structural properties of solvent water and its interactions with the sugar headgroups of GM1 respond to surface remodelling. The extent of this modification is much higher than expected and, interestingly, ganglioside headgroups seem to turn from cosmotropes to chaotropes upon collective rearrangement from the standing- to the lying-conformation. In a biological perspective, water structure modulation could be one of the physico-chemical elements contributing to the raft strategy, both for rafts formation and persistence and for their functional aspects. In particular, the interaction with approaching bodies could be favoured or inhibited or triggered by complex-sugar-sequence conformational switch. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo. Copyright © 2016 Elsevier B.V. All rights reserved.

Antibody Epitope Analysis to Investigate Folded Structure, Allosteric Conformation, and Evolutionary Lineage of Proteins.

PubMed

Wong, Sienna; Jin, J-P

2017-01-01

Study of folded structure of proteins provides insights into their biological functions, conformational dynamics and molecular evolution. Current methods of elucidating folded structure of proteins are laborious, low-throughput, and constrained by various limitations. Arising from these methods is the need for a sensitive, quantitative, rapid and high-throughput method not only analysing the folded structure of proteins, but also to monitor dynamic changes under physiological or experimental conditions. In this focused review, we outline the foundation and limitations of current protein structure-determination methods prior to discussing the advantages of an emerging antibody epitope analysis for applications in structural, conformational and evolutionary studies of proteins. We discuss the application of this method using representative examples in monitoring allosteric conformation of regulatory proteins and the determination of the evolutionary lineage of related proteins and protein isoforms. The versatility of the method described herein is validated by the ability to modulate a variety of assay parameters to meet the needs of the user in order to monitor protein conformation. Furthermore, the assay has been used to clarify the lineage of troponin isoforms beyond what has been depicted by sequence homology alone, demonstrating the nonlinear evolutionary relationship between primary structure and tertiary structure of proteins. The antibody epitope analysis method is a highly adaptable technique of protein conformation elucidation, which can be easily applied without the need for specialized equipment or technical expertise. When applied in a systematic and strategic manner, this method has the potential to reveal novel and biomedically meaningful information for structure-function relationship and evolutionary lineage of proteins. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Conformational Transition Pathway in the Activation Process of Allosteric Glucokinase

PubMed Central

Shi, Ting; Zhao, Yaxue; Chen, Yingyi; Li, Xiaobai; Liu, Xinyi; Huang, Zhimin; Zhang, Jian

2013-01-01

Glucokinase (GK) is a glycolytic enzyme that plays an important role in regulating blood glucose level, thus acting as a potentially attractive target for drug discovery in the treatment of diabetes of the young type 2 and persistent hyperinsulinemic hypoglycemia of infancy. To characterize the activation mechanism of GK from the super-open state (inactive state) to the closed state (active state), a series of conventional molecular dynamics (MD) and targeted MD (TMD) simulations were performed on this enzyme. Conventional MD simulation showed a specific conformational ensemble of GK when the enzyme is inactive. Seven TMD simulations depicted a reliably conformational transition pathway of GK from the inactive state to the active state, and the components important to the conformational change of GK were identified by analyzing the detailed structures of the TMD trajectories. In combination with the inactivation process, our findings showed that the whole conformational pathway for the activation-inactivation-activation of GK is a one-direction circulation, and the active state is less stable than the inactive state in the circulation. Additionally, glucose was demonstrated to gradually modulate its binding pose with the help of residues in the large domain and connecting region of GK during the activation process. Furthermore, the obtained energy barriers were used to explain the preexisting equilibrium and the slow binding kinetic process of the substrate by GK. The simulated results are in accordance with the recent findings from the mutagenesis experiments and kinetic analyses. Our observations reveal a complicated conformational process in the allosteric protein, resulting in new knowledge about the delicate mechanisms for allosteric biological macromolecules that will be useful in drug design for targeting allosteric proteins. PMID:23409066

Structural investigation of cellobiose dehydrogenase IIA: Insights from small angle scattering into intra- and intermolecular electron transfer mechanisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bodenheimer, Annette M.; O'Dell, William B.; Oliver, Ryan C.

Background: Cellobiose dehydrogenases have gained interest due to their potential applications in sectors from biofuel production to biomedical devices. The CDHIIA variant is comprised of a cytochrome domain (CYT), a dehydrogenase domain (DH), and a carbohydrate-binding module (CBM) that are connected by two flexible linkers. Upon cellobiose oxidation at the DH, intramolecular electron transfer (IaET) occurs from the DH to the CYT. In vivo, CDHIIA CYT subsequently performs intermolecular electron transfer (IeET) to a lytic polysaccharide monooxygenase (LPMO). The relevant solution-state CDH domain conformations for IaET and IeET have not been fully characterized.Methods: Small-angle X-ray and neutron scattering measurements ofmore » oxidized CDHIIA from Myriococcum thermophilum and Neurospora crassa were performed to investigate the structural landscape explored in solution by MtCDHIIA and NcCDHIIA in response to cations, pH, and the presence of an electron acceptor, LPMO9D from N. crassa.Results: The scattering data complemented by modeling show that, under oxidizing conditions, MtCDHIIA undergoes global conformational rearrangement in the presence of Ca2+. Oxidized NcCDHIIA exhibits conformational changes upon pH variation and, in the presence of NcLPMO9D, primarily adopts a compact conformation.Conclusions: These results demonstrate different conformational responses of oxidized MtCDHIIA and NcCDHIIA to changes in environment. The results also reveal a shift in the oxidized NcCDHIIA conformational landscape toward interdomain compaction upon co-incubation with NcLPMO9D.General significance: The present study is the first report on the structural landscapes explored in solution by oxidized cellobiose dehydrogenases under various cation concentrations, pH conditions and in the presence of an electron-accepting LPMO.« less

Structural investigation of cellobiose dehydrogenase IIA: Insights from small angle scattering into intra- and intermolecular electron transfer mechanisms

DOE PAGES

Bodenheimer, Annette M.; O'Dell, William B.; Oliver, Ryan C.; ...

2018-01-31

Background: Cellobiose dehydrogenases have gained interest due to their potential applications in sectors from biofuel production to biomedical devices. The CDHIIA variant is comprised of a cytochrome domain (CYT), a dehydrogenase domain (DH), and a carbohydrate-binding module (CBM) that are connected by two flexible linkers. Upon cellobiose oxidation at the DH, intramolecular electron transfer (IaET) occurs from the DH to the CYT. In vivo, CDHIIA CYT subsequently performs intermolecular electron transfer (IeET) to a lytic polysaccharide monooxygenase (LPMO). The relevant solution-state CDH domain conformations for IaET and IeET have not been fully characterized.Methods: Small-angle X-ray and neutron scattering measurements ofmore » oxidized CDHIIA from Myriococcum thermophilum and Neurospora crassa were performed to investigate the structural landscape explored in solution by MtCDHIIA and NcCDHIIA in response to cations, pH, and the presence of an electron acceptor, LPMO9D from N. crassa.Results: The scattering data complemented by modeling show that, under oxidizing conditions, MtCDHIIA undergoes global conformational rearrangement in the presence of Ca2+. Oxidized NcCDHIIA exhibits conformational changes upon pH variation and, in the presence of NcLPMO9D, primarily adopts a compact conformation.Conclusions: These results demonstrate different conformational responses of oxidized MtCDHIIA and NcCDHIIA to changes in environment. The results also reveal a shift in the oxidized NcCDHIIA conformational landscape toward interdomain compaction upon co-incubation with NcLPMO9D.General significance: The present study is the first report on the structural landscapes explored in solution by oxidized cellobiose dehydrogenases under various cation concentrations, pH conditions and in the presence of an electron-accepting LPMO.« less

Expansion of the octarepeat domain alters the misfolding pathway but not the folding pathway of the prion protein.

PubMed

Leliveld, S Rutger; Stitz, Lothar; Korth, Carsten

2008-06-10

A misfolded conformation of the prion protein (PrP), PrP (Sc), is the essential component of prions, the infectious agents that cause transmissible neurodegenerative diseases. Insertional mutations that lead to an increase in the number of octarepeats (ORs) in PrP are linked to familial human prion disease. In this study, we investigated how expansion of the OR domain causes PrP to favor a prion-like conformation. Therefore, we compared the conformational and aggregation modulating properties of wild-type versus expanded OR domains, either as a fusion construct with the protein G B1 domain (GB1-OR) or as an integral part of full-length mouse PrP (MoPrP). Using circular dichroism spectroscopy, we first demonstrated that ORs are not unfolded but exist as an ensemble of three distinct conformers: polyproline helix-like, beta-turn, and "Trp-related". Domain expansion had little effect on the conformation of GB1-OR fusion proteins. When part of MoPrP however, OR domain expansion changed PrP's folding landscape, not by hampering the production of native alpha-helical monomers but by greatly reducing the propensity to form amyloid and by altering the assembly of misfolded, beta-rich aggregates. These features may relate to subtle pH-dependent conformational differences between wild-type and mutant monomers. In conclusion, we propose that PrP insertional mutations are pathogenic because they enhance specific misfolding pathways of PrP rather than by undermining native folding. This idea was supported by a trial bioassay in transgenic mice overexpressing wild-type MoPrP, where intracerebral injection of recombinant MoPrP with an expanded OR domain but not wild-type MoPrP caused prion disease.

Localized conformational changes trigger the pH-induced fibrillogenesis of an amyloidogenic λ light chain protein.

PubMed

Velázquez-López, Isabel; Valdés-García, Gilberto; Romero Romero, Sergio; Maya Martínez, Roberto; Leal-Cervantes, Ana I; Costas, Miguel; Sánchez-López, Rosana; Amero, Carlos; Pastor, Nina; Fernández Velasco, D Alejandro

2018-07-01

Solvent conditions modulate the expression of the amyloidogenic potential of proteins. In this work the effect of pH on the fibrillogenic behavior and the conformational properties of 6aJL2, a model protein of the highly amyloidogenic variable light chain λ6a gene segment, was examined. Ordered aggregates showing the ultrastructural and spectroscopic properties observed in amyloid fibrils were formed in the 2.0-8.0 pH range. At pH <3.0 a drastic decrease in lag time and an increase in fibril formation rate were found. In the 4.0-8.0 pH range there was no spectroscopic evidence for significant conformational changes in the native state. Likewise, heat capacity measurements showed no evidence for residual structure in the unfolded state. However, at pH <3.0 stability is severely decreased and the protein suffers conformational changes as detected by circular dichroism, tryptophan and ANS fluorescence, as well as by NMR spectroscopy. Molecular dynamics simulations indicate that acid-induced conformational changes involve the exposure of the loop connecting strands E and F. These results are compatible with pH-induced changes in the NMR spectra. Overall, the results indicate that the mechanism involved in the acid-induced increase in the fibrillogenic potential of 6aJL2 is profoundly different to that observed in κ light chains, and is promoted by localized conformational changes in a region of the protein that was previously not known to be involved in acid-induced light chain fibril formation. The identification of this region opens the potential for the design of specific inhibitors. Copyright © 2018 Elsevier B.V. All rights reserved.

Comparison of the helical tomotherapy against the multileaf collimator-based intensity-modulated radiotherapy and 3D conformal radiation modalities in lung cancer radiotherapy

PubMed Central

Mavroidis, P; Shi, C; Plataniotis, G A; Delichas, M G; Costa Ferreira, B; Rodriguez, S; Lind, B K; Papanikolaou, N

2011-01-01

Objectives The aim of this study was to compare three-dimensional (3D) conformal radiotherapy and the two different forms of IMRT in lung cancer radiotherapy. Methods Cases of four lung cancer patients were investigated by developing a 3D conformal treatment plan, a linac MLC-based step-and-shoot IMRT plan and an HT plan for each case. With the use of the complication-free tumour control probability (P+) index and the uniform dose concept as the common prescription point of the plans, the different treatment plans were compared based on radiobiological measures. Results The applied plan evaluation method shows the MLC-based IMRT and the HT treatment plans are almost equivalent over the clinically useful dose prescription range; however, the 3D conformal plan inferior. At the optimal dose levels, the 3D conformal treatment plans give an average P+ of 48.1% for a effective uniform dose to the internal target volume (ITV) of 62.4 Gy, whereas the corresponding MLC-based IMRT treatment plans are more effective by an average ΔP+ of 27.0% for a Δ effective uniform dose of 16.3 Gy. Similarly, the HT treatment plans are more effective than the 3D-conformal plans by an average ΔP+ of 23.8% for a Δ effective uniform dose of 11.6 Gy. Conclusion A radiobiological treatment plan evaluation can provide a closer association of the delivered treatment with the clinical outcome by taking into account the dose–response relations of the irradiated tumours and normal tissues. The use of P – effective uniform dose diagrams can complement the traditional tools of evaluation to compare and effectively evaluate different treatment plans. PMID:20858664

Effect of Inactivating Mutations on Peptide Conformational Ensembles: The Plant Polypeptide Hormone Systemin.

PubMed

Chowdhury, Saikat Dutta; Sarkar, Aditya K; Lahiri, Ansuman

2016-07-25

As part of their basal immune mechanism against insect/herbivore attacks, plants have evolved systemic response mechanisms. Such a systemic wound response in tomato was found to involve an 18 amino acid polypeptide called systemin, the first polypeptide hormone to be discovered in plants. Systematic alanine scanning and deletion studies showed differential modulation in its activity, particularly a major loss of function due to alanine substitution at positions 13 and 17 and less extentive loss of function due to substitution at position 12. We have studied the conformational ensembles of wild-type systemin along with its 17 variants by carrying out a total of 5.76 μs of replica-exchange molecular dynamics simulation in an implicit solvent environment. In our simulations, wild-type systemin showed a lack of α-helical and β-sheet structures, in conformity with earlier circular dichroism and NMR data. On the other hand, two regions containing diproline segments showed a tendency to adopt polyproline II structures. Examination of conformational ensembles of the 17 variants revealed a change in the population distributions, suggesting a less flexible structure for alanine substitutions at positions 12 and 13 but not for position 17. Combined with the experimental observations that positions 1-14 of systemin are important for the formation of the peptide-receptor complex, this leads to the hypothesis that loss of conformational flexibility may play a role in the loss of activity of systemin due to the P12A and P13A substitutions, while T17A deactivation probably occurs for a different reason, most likely the loss of the threonine phosphorylation site. We also indicate possible structural reasons why the substitution of the prolines at positions 12 and 13 leads to a loss of conformational freedom in the peptide.

Long-term modulation of cosmic rays during solar cycle 21

NASA Technical Reports Server (NTRS)

Fenton, A. G.; Fenton, K. B.; Humble, J. E.

1985-01-01

A preliminary result concerning the rigidity dependence of the longer-term solar cycle modulation is reported. The long-term modulation, using monthly mean intensities and referred to November 1977 as a normalizing level, appear to be in accordance with the exponent gamma = 1, provided only Brisbane and Hobart data are used. Darwin data do not conform to this pattern except perhaps during the early years of the cycle until about the end of 1980, since when the Darwin long-term intensity has been largely steady, apart from Forbush-type decreases and the as yet unidentified vector from the observed SI vector. The true SI vector of galactic origin can be obtained. The resultant vector has the amplitude of 0.031% and the phase of 2.3h. The present result seems to be consistent with those so far reported.

Coupling of conformational transitions in the N-terminal domain of the 51-kDa FK506-binding protein (FKBP51) near its site of interaction with the steroid receptor proteins

DOE PAGES

LeMaster, David M.; Mustafi, Sourajit M.; Brecher, Matthew; ...

2015-05-07

Interchanging Leu-119 for Pro-119 at the tip of the β 4-β 5 loop in the first FK506 binding domain (FK1) of the FKBP51 and FKBP52 proteins, respectively, has been reported to largely reverse the inhibitory (FKBP51) or stimulatory (FKBP52) effects of these co-chaperones on the transcriptional activity of glucocorticoid and androgen receptor-protein complexes. Previous NMR relaxation studies have identified exchange line broadening, indicative of submillisecond conformational motion, throughout the β 4-β 5 loop in the FK1 domain of FKBP51, which are suppressed by the FKBP52-like L119P substitution. This substitution also attenuates exchange line broadening in the underlying β 2 andmore » β 3a strands that is centered near a bifurcated main chain hydrogen bond interaction between these two strands. The present study demonstrates that these exchange line broadening effects arise from two distinct coupled conformational transitions, and the transition within the β 2 and β 3a strands samples a transient conformation that resembles the crystal structures of the selectively inhibited FK1 domain of FKBP51 recently reported. Although the crystal structures for their series of inhibitors were interpreted as evidence for an induced fit mechanism of association, the presence of a similar conformation being significantly populated in the unliganded FKBP51 domain is more consistent with a conformational selection binding process. As a result, the contrastingly reduced conformational plasticity of the corresponding FK1 domain of FKBP52 is consistent with the current model in which FKBP51 binds to both the apo- and hormone-bound forms of the steroid receptor to modulate its affinity for ligand, whereas FKBP52 binds selectively to the latter state.« less

Uncoupling of Protease trans-Cleavage and Helicase Activities in Pestivirus NS3

PubMed Central

Zheng, Fengwei; Lu, Guoliang; Li, Ling

2017-01-01

ABSTRACT The nonstructural protein NS3 from the Flaviviridae family is a multifunctional protein that contains an N-terminal protease and a C-terminal helicase, playing essential roles in viral polyprotein processing and genome replication. Here we report a full-length crystal structure of the classical swine fever virus (CSFV) NS3 in complex with its NS4A protease cofactor segment (PCS) at a 2.35-Å resolution. The structure reveals a previously unidentified ∼2,200-Å2 intramolecular protease-helicase interface comprising three clusters of interactions, representing a “closed” global conformation related to the NS3-NS4A cis-cleavage event. Although this conformation is incompatible with protease trans-cleavage, it appears to be functionally important and beneficial to the helicase activity, as the mutations designed to perturb this conformation impaired both the helicase activities in vitro and virus production in vivo. Our work reveals important features of protease-helicase coordination in pestivirus NS3 and provides a key basis for how different conformational states may explicitly contribute to certain functions of this natural protease-helicase fusion protein. IMPORTANCE Many RNA viruses encode helicases to aid their RNA genome replication and transcription by unwinding structured RNA. Being naturally fused to a protease participating in viral polyprotein processing, the NS3 helicases encoded by the Flaviviridae family viruses are unique. Therefore, how these two enzyme modules coordinate in a single polypeptide is of particular interest. Here we report a previously unidentified conformation of pestivirus NS3 in complex with its NS4A protease cofactor segment (PCS). This conformational state is related to the protease cis-cleavage event and is optimal for the function of helicase. This work provides an important basis to understand how different enzymatic activities of NS3 may be achieved by the coordination between the protease and helicase through different conformational states. PMID:28835495

Initial Results from the Royal College of Radiologists' UK National Audit of Anal Cancer Radiotherapy 2015.

PubMed

Muirhead, R; Drinkwater, K; O'Cathail, S M; Adams, R; Glynne-Jones, R; Harrison, M; Hawkins, M A; Sebag-Montefiore, D; Gilbert, D C

2017-03-01

UK guidance was recently developed for the treatment of anal cancer using intensity-modulated radiotherapy (IMRT). We audited the current use of radiotherapy in UK cancer centres for the treatment of anal cancer against such guidance. We describe the acute toxicity of IMRT in comparison with patient population in the audit treated with two-phase conformal radiotherapy and the previous published data from two-phase conformal radiotherapy, in the UK ACT2 trial. A Royal College of Radiologists' prospective national audit of patients treated with radiotherapy in UK cancer centres was carried out over a 6 month period between February and July 2015. Two hundred and forty-two cases were received from 40/56 cancer centres (71%). In total, 231 (95%) underwent full dose radiotherapy with prophylactic nodal irradiation. Of these, 180 (78%) received IMRT or equivalent, 52 (22%) two-phase conformal (ACT2) technique. The number of interruptions in radiotherapy treatment in the ACT2 trial was 15%. Interruptions were noted in 7% (95% confidence interval 0-14%) of courses receiving two-phase conformal and 4% (95% confidence interval 1-7%) of those receiving IMRT. The percentage of patients completing the planned radiotherapy dose, irrelevant of gaps, was 90% (95% confidence interval 82-98%) and 96% (95% confidence interval 93-99%), in two-phase conformal and IMRT respectively. The toxicity reported in the ACT2 trial, in patients receiving two-phase conformal in the audit and in patients receiving IMRT in the audit was: any toxic effect 71%, 54%, 48%, non-haematological 62%, 49%, 40% and haematological 26%, 13%, 18%, respectively. IMRT implementation for anal cancer is well underway in the UK with most patients receiving IMRT delivery, although its usage is not yet universal. This audit confirms that IMRT results in reduced acute toxicity and minimised treatment interruptions in comparison with previous two-phase conformal techniques. Copyright © 2016 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Surveying the Hydrogen Bonding Landscape of AN Achiral, α-AMINO Acid: Conformation Specific IR and UV Spectroscopy of 2-AMINOISOBUTYRIC Acid

NASA Astrophysics Data System (ADS)

Gord, Joseph R.; Hewett, Daniel M.; Kubasik, Matthew A.; Zwier, Timothy S.

2014-06-01

2-Aminoisobutyric acid (Aib) is an achiral, α-amino acid having two equivalent methyl groups attached to Cα. Extended Aib oligomers are known to preferentially adopt a 310-helical structure in the condensed phase. Here, we take a simplifying step and focus on the intrinsic folding propensities of Aib by looking at a single, capped Aib structure and then extending to longer oligomers in the gas phase, free from the influence of solvent molecules and cooled in a supersonic expansion. Resonant two-photon ionization and IR-UV holeburning will be used to record single-conformation UV spectra using the Z-cap as UV chromophore. Resonant ion-dip infrared (RIDIR) spectroscopy provides single-conformation IR spectra in the OH stretch, NH stretch, amide I and amide II regions. Two conformational isomers have been identified for the smallest unit in the study, Z-Aib-OH, and four conformational isomers were seen for Z-Aib-Aib-OH, with widely-varying IR spectral patterns. In addition to investigating the conformational dependence on oligomer length, this work also studies the steric and electrostatic impact of different capping groups, R-X where X = -OH, -OMethyl, and -OtButyl. These caps are considered here for the case of Z-Aib-Aib-X. Extension to larger Z-(Aib)n-X oligomers will shed light on the extent to which the solution phase preference for 310-helix formation is retained in the gas phase, and when its onset first appears. When possible 13C isotopomers will be used to assist with the assignments and modulate the coupling between amide I fundamentals. Toniolo, C.; Bonora, G. M.; Barone, V.; Bavoso, A.; Benedetti, E.; Di Blasio, B.; Grimaldi, P.; Lelj, F.; Pavone, V.; Padone, C., Conformation of Pleionomers of α-Aminoisobutyric Acid. Macromolecules 1985, 18, 895-902.

Travelling for treatment; does distance and deprivation affect travel for intensity-modulated radiotherapy in the rural setting for head and neck cancer?

PubMed

Cosway, B; Douglas, L; Armstrong, N; Robson, A

2017-06-01

NHS England has commissioned intensity-modulated radiotherapy for head and neck cancers from Newcastle hospitals for patients in North Cumbria. This study assessed whether travel distances affected the decision to travel to Newcastle (to receive intensity-modulated radiotherapy) or Carlisle (to receive conformal radiotherapy). All patients for whom the multidisciplinary team recommended intensity-modulated radiotherapy between December 2013 and January 2016 were included. Index of multiple deprivation scores and travel distances were calculated. Patients were also asked why they chose their treating centre. Sixty-nine patients were included in this study. There were no significant differences in travel distance (p = 0.53) or index of multiple deprivation scores (p = 0.47) between patients opting for treatment in Carlisle or Newcastle. However, 29 of the 33 patients gave travel distance as their main reason for not travelling for treatment. Quantitatively, travel distance and deprivation does not impact on whether patients accept intensity-modulated radiotherapy. However, patients say distance is a major barrier for access. Future research should explore how to reduce this.

Intensity modulated neutron radiotherapy optimization by photon proxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Snyder, Michael; Hammoud, Ahmad; Bossenberger, Todd

2012-08-15

Purpose: Introducing intensity modulation into neutron radiotherapy (IMNRT) planning has the potential to mitigate some normal tissue complications seen in past neutron trials. While the hardware to deliver IMNRT plans has been in use for several years, until recently the IMNRT planning process has been cumbersome and of lower fidelity than conventional photon plans. Our in-house planning system used to calculate neutron therapy plans allows beam weight optimization of forward planned segments, but does not provide inverse optimization capabilities. Commercial treatment planning systems provide inverse optimization capabilities, but currently cannot model our neutron beam. Methods: We have developed a methodologymore » and software suite to make use of the robust optimization in our commercial planning system while still using our in-house planning system to calculate final neutron dose distributions. Optimized multileaf collimator (MLC) leaf positions for segments designed in the commercial system using a 4 MV photon proxy beam are translated into static neutron ports that can be represented within our in-house treatment planning system. The true neutron dose distribution is calculated in the in-house system and then exported back through the MATLAB software into the commercial treatment planning system for evaluation. Results: The planning process produces optimized IMNRT plans that reduce dose to normal tissue structures as compared to 3D conformal plans using static MLC apertures. The process involves standard planning techniques using a commercially available treatment planning system, and is not significantly more complex than conventional IMRT planning. Using a photon proxy in a commercial optimization algorithm produces IMNRT plans that are more conformal than those previously designed at our center and take much less time to create. Conclusions: The planning process presented here allows for the optimization of IMNRT plans by a commercial treatment planning optimization algorithm, potentially allowing IMNRT to achieve similar conformality in treatment as photon IMRT. The only remaining requirements for the delivery of very highly modulated neutron treatments are incremental improvements upon already implemented hardware systems that should be readily achievable.« less

Nitric oxide/cGMP pathway signaling actively down-regulates α4β1-integrin affinity: an unexpected mechanism for inducing cell de-adhesion.

PubMed

Chigaev, Alexandre; Smagley, Yelena; Sklar, Larry A

2011-05-17

Integrin activation in response to inside-out signaling serves as the basis for rapid leukocyte arrest on endothelium, migration, and mobilization of immune cells. Integrin-dependent adhesion is controlled by the conformational state of the molecule, which is regulated by seven-transmembrane Guanine nucleotide binding Protein-Coupled Receptors (GPCRs). α4β1-integrin (CD49d/CD29, Very Late Antigen-4, VLA-4) is expressed on leukocytes, hematopoietic progenitors, stem cells, hematopoietic cancer cells, and others. VLA-4 conformation is rapidly up-regulated by inside-out signaling through Gαi-coupled GPCRs and down-regulated by Gαs-coupled GPCRs. However, other signaling pathways, which include nitric oxide-dependent signaling, have been implicated in the regulation of cell adhesion. The goal of the current report was to study the effect of nitric oxide/cGMP signaling pathway on VLA-4 conformational regulation. Using fluorescent ligand binding to evaluate the integrin activation state on live cells in real-time, we show that several small molecules, which specifically modulate nitric oxide/cGMP signaling pathway, as well as a cell permeable cGMP analog, can rapidly down-modulate binding of a VLA-4 specific ligand on cells pre-activated through three Gαi-coupled receptors: wild type CXCR4, CXCR2 (IL-8RB), and a non-desensitizing mutant of formyl peptide receptor (FPR ΔST). Upon signaling, we detected rapid changes in the ligand dissociation rate. The dissociation rate after inside-out integrin de-activation was similar to the rate for resting cells. In a VLA-4/VCAM-1-specific myeloid cell adhesion system, inhibition of the VLA-4 affinity change by nitric oxide had a statistically significant effect on real-time cell aggregation. We conclude that nitric oxide/cGMP signaling pathway can rapidly down-modulate the affinity state of the VLA-4 binding pocket, especially under the condition of sustained Gαi-coupled GPCR signaling, generated by a non-desensitizing receptor mutant. This suggests a fundamental role of this pathway in de-activation of integrin-dependent cell adhesion.

The dosimetric effects of photon energy on the quality of prostate volumetric modulated arc therapy.

PubMed

Mattes, Malcolm D; Tai, Cyril; Lee, Alvin; Ashamalla, Hani; Ikoro, N C

2014-01-01

Studies comparing the dosimetric effects of high- and low-energy photons to treat prostate cancer using 3-dimensional conformal and intensity modulated radiation therapy have yielded mixed results. With the advent of newer radiation delivery systems like volumetric modulated arc therapy (VMAT), the impact of changing photon energy is readdressed. Sixty-five patients treated for prostate cancer at our institution from 2011 to 2012 underwent CT simulation. A target volume encompassing the prostate and entire seminal vesicles was treated to 50.4 Gy, followed by a boost to the prostate and proximal seminal vesicles to a total dose of 81 Gy. The VMAT plans were generated for 6-MV and 10-MV photons under identical optimization conditions using the Eclipse system version 8.6 (Varian Medical Systems, Palo Alto, CA). The analytical anisotropic algorithm was used for all dose calculations. Plans were normalized such that 98% of the planning target volume (PTV) received 100% of the prescribed dose. Dose-volumetric data from the treatment planning system was recorded for both 6-MV and 10-MV plans, which were compared for both the entire cohort and subsets of patients stratified according to the anterior-posterior separation. Plans using 10-MV photons had statistically significantly lower relative integral dose (4.1%), gradient measure (4.1%), skin Dmax (16.9%), monitor units (13.0%), and bladder V(30) (3.1%) than plans using 6-MV photons (P < .05). There was no difference in rectal dose, high-dose-region bladder dose, PTV coverage, or conformity index. The benefit of 10-MV photons was more pronounced for thicker patients (anterior-posterior separation >21 cm) for most parameters, with statistically significant differences in bladder V(30), bladder V(65), integral dose, conformity index, and monitor units. The main dosimetric benefits of 10-MV as compared with 6-MV photons are seen in thicker patients, though for the entire cohort 10-MV plans resulted in a lower integral dose, gradient measure, skin Dmax, monitor units, and bladder V(30), possibly at the expense of higher rectum V(81). Copyright © 2014 American Society for Radiation Oncology. Published by Elsevier Inc. All rights reserved.

Dosimetric impact of different CT datasets for stereotactic treatment planning using 3D conformal radiotherapy or volumetric modulated arc therapy.

PubMed

Oechsner, Markus; Odersky, Leonhard; Berndt, Johannes; Combs, Stephanie Elisabeth; Wilkens, Jan Jakob; Duma, Marciana Nona

2015-12-01

The purpose of this study was to assess the impact on dose to the planning target volume (PTV) and organs at risk (OAR) by using four differently generated CT datasets for dose calculation in stereotactic body radiotherapy (SBRT) of lung and liver tumors. Additionally, dose differences between 3D conformal radiotherapy and volumetric modulated arc therapy (VMAT) plans calculated on these CT datasets were determined. Twenty SBRT patients, ten lung cases and ten liver cases, were retrospectively selected for this study. Treatment plans were optimized on average intensity projection (AIP) CTs using 3D conformal radiotherapy (3D-CRT) and volumetric modulated arc therapy (VMAT). Afterwards, the plans were copied to the planning CTs (PCT), maximum intensity projection (MIP) and mid-ventilation (MidV) CT datasets and dose was recalculated keeping all beam parameters and monitor units unchanged. Ipsilateral lung and liver volumes and dosimetric parameters for PTV (Dmean, D2, D98, D95), ipsilateral lung and liver (Dmean, V30, V20, V10) were determined and statistically analysed using Wilcoxon test. Significant but small mean differences were found for PTV dose between the CTs (lung SBRT: ≤2.5 %; liver SBRT: ≤1.6 %). MIPs achieved the smallest lung and the largest liver volumes. OAR mean doses in MIP plans were distinctly smaller than in the other CT datasets. Furthermore, overlapping of tumors with the diaphragm results in underestimated ipsilateral lung dose in MIP plans. Best agreement was found between AIP and MidV (lung SBRT). Overall, differences in liver SBRT were smaller than in lung SBRT and VMAT plans achieved slightly smaller differences than 3D-CRT plans. Only small differences were found for PTV parameters between the four CT datasets. Larger differences occurred for the doses to organs at risk (ipsilateral lung, liver) especially for MIP plans. No relevant differences were observed between 3D-CRT or VMAT plans. MIP CTs are not appropriate for OAR dose assessment. PCT, AIP and MidV resulted in similar doses. If a 4DCT is acquired PCT can be omitted using AIP or MidV for treatment planning.

SU-F-T-87: Comparison of Advanced Radiotherapy Techniques for Post- Mastectomy Breast Cancer Patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heins, D; Zhang, R; Hogstrom, K

2016-06-15

Purpose: To determine if bolus electron conformal therapy (Bolus-ECT) combined with intensity modulated x-ray therapy (IMXT) and flattening filter free volumetric modulated arc therapy (FFF-VMAT (6x and 10x)) can maintain equal or better dose coverage than standard volumetric modulated arc therapy (Std-VMAT) while reducing doses to organs at risk (OARs). Methods: Bolus-ECT with IMXT, FFF-VMAT, and Std-VMAT treatment plans were produced for ten post-mastectomy radiotherapy (PMRT) patients previously treated at our clinic. The treatment plans were created on commercially available treatment planning system (TPS) and all completed treatment plans were reviewed and approved by a radiation oncologist. The plans weremore » evaluated based on planning target volume (PTV) coverage, tumor control probability (TCP), dose homogeneity index (DHI), conformity index (CI), and dose to organs at risk (OAR). Results: All techniques produced clinically acceptable PMRT plans. Overall, Bolus-ECT with IMXT exhibited higher maximum dose compared to all VMAT techniques. Bolus-ECT with IMXT and FFF-VMAT10x had slightly improved TCP over FFF-VMAT6x and Std-VMAT. However, all VMAT techniques showed improved CI and DHI over Bolus-ECT with IMXT. All techniques showed very similar mean lung dose. Bolus-ECT with IMXT exhibited a reduced mean heart dose over Std-VMAT. Both FFF-VMAT techniques had higher mean heart dose compared to Std-VMAT. In addition, Bolus-ECT with IMXT was able to reduce mean dose to the contralateral breast compared to Std-VMAT and both FFF-VMAT techniques had comparable but slightly reduced dose compared to Std-VMAT. Conclusion: This work has shown that Bolus-ECT with IMXT produces clinically acceptable plans while reducing OAR doses. Both FFF-VMAT techniques are comparable to Std-VMAT with slight improvements. Even though all VMAT techniques produce more homogenous and conformal dose distributions, Bolus-ECT with IMXT is a viable option for treating post-mastectomy patients possibly leading to reduced risks of normal tissue complications.« less

TH-AB-BRB-01: Trajectory Modulated Arc Therapy: Application to Partial Breast Irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hristov, D.

2016-06-15

Current state-of-the art digital C-arm medical linear accelerators are capable of delivering radiation treatments with high level of automation, which affords coordinated motions of gantry, couch, and multileaf collimator (MLC) with dose rate modulations. The new machine capacity has shown the potential to bring substantially improved radiation dosimetry and/or delivery efficiency to many challenging diseases. Combining an integrated beam orientation optimization algorithm with automated machine navigation, markedly improved dose conformity has been achieved using 4ρ therapy. Trajectory modulated radiation therapy (TMAT) can be used to deliver highly conformal dose to partial breast or to carve complex dose distribution for therapymore » involving extended volumes such as total marrow and total lymph node treatment. Dynamic electron arc radiotherapy (DEAR) not only overcomes the deficiencies of conventional electron therapy in dose conformity and homogeneity but also achieves so without patient-specific shields. The combination of MLC and couch tracking provides improved motion management of thoracic and abdominal tumors. A substantial body of work has been done in these technological advances for clinical translation. The proposed symposium will provide a timely review of these exciting opportunities. Learning Objectives: Recognize the potential of using digitally controlled linacs for clinically significant improvements in delivered dose distributions for various treatment sites. Identify existing approaches to treatment planning, optimization and delivery for treatment techniques utilizing the advanced functions of digital linacs and venues for further development and improvement. Understand methods for testing and validating delivery system performance. Identify tools available on current delivery systems for implementation and control for such treatments. Obtain the update in clinical applications, trials and regulatory approval. K. Sheng, NIH U19AI067769, NIH R43CA183390, NIH R01CA188300, Varian Medical Systems V. Yu, Varian Medical Systems, AAPM Summer Undergraduate Fellowship, NSF graduate fellowship S. Nill, Elekta AB. Cancer Research UK under Programme C33589/A19727, NIHR Biomedical Research Centre at The Royal Marsden and The Institute of Cancer Research.« less

Comparison of anatomy-based, fluence-based and aperture-based treatment planning approaches for VMAT

NASA Astrophysics Data System (ADS)

Rao, Min; Cao, Daliang; Chen, Fan; Ye, Jinsong; Mehta, Vivek; Wong, Tony; Shepard, David

2010-11-01

Volumetric modulated arc therapy (VMAT) has the potential to reduce treatment times while producing comparable or improved dose distributions relative to fixed-field intensity-modulated radiation therapy. In order to take full advantage of the VMAT delivery technique, one must select a robust inverse planning tool. The purpose of this study was to evaluate the effectiveness and efficiency of VMAT planning techniques of three categories: anatomy-based, fluence-based and aperture-based inverse planning. We have compared these techniques in terms of the plan quality, planning efficiency and delivery efficiency. Fourteen patients were selected for this study including six head-and-neck (HN) cases, and two cases each of prostate, pancreas, lung and partial brain. For each case, three VMAT plans were created. The first VMAT plan was generated based on the anatomical geometry. In the Elekta ERGO++ treatment planning system (TPS), segments were generated based on the beam's eye view (BEV) of the target and the organs at risk. The segment shapes were then exported to Pinnacle3 TPS followed by segment weight optimization and final dose calculation. The second VMAT plan was generated by converting optimized fluence maps (calculated by the Pinnacle3 TPS) into deliverable arcs using an in-house arc sequencer. The third VMAT plan was generated using the Pinnacle3 SmartArc IMRT module which is an aperture-based optimization method. All VMAT plans were delivered using an Elekta Synergy linear accelerator and the plan comparisons were made in terms of plan quality and delivery efficiency. The results show that for cases of little or modest complexity such as prostate, pancreas, lung and brain, the anatomy-based approach provides similar target coverage and critical structure sparing, but less conformal dose distributions as compared to the other two approaches. For more complex HN cases, the anatomy-based approach is not able to provide clinically acceptable VMAT plans while highly conformal dose distributions were obtained using both aperture-based and fluence-based inverse planning techniques. The aperture-based approach provides improved dose conformity than the fluence-based technique in complex cases.

Material conformity and bactericidal properties of high-frequency-pulse-modulated and low-frequency-pulse-excited plasmas

NASA Astrophysics Data System (ADS)

Okawa, H.; Akitsu, T.

2018-05-01

Plasma sterilization attracts an increasing attention as an alternative method for chemical sterilization. In this study, we investigate plasma sterilization for practical applications, particularly in dentistry and oral surgery [1]. Helium-diluted oxygen was excited by a dielectric barrier electrode at normal atmospheric pressure. Control of the neutral gas temperature was performed under the plasma sterilization. The relation between the intensity of the spectral emission from the excited oxygen atoms and bactericidal effect was investigated using Bacillus stearothermophilus and opportunistic infection bacterium. A comparison is performed with a low-frequency wide-gap discharge. Degradation and material conformity were investigated using the Tyvek unwoven fabric for the sterile package and soft-silicone resin, methyl-methacrylate powder filler used in the dental surgery.

Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin.

PubMed

Pozzi, Nicola; Zerbetto, Mirco; Acquasaliente, Laura; Tescari, Simone; Frezzato, Diego; Polimeno, Antonino; Gohara, David W; Di Cera, Enrico; De Filippis, Vincenzo

2016-07-19

Thrombin exists as an ensemble of active (E) and inactive (E*) conformations that differ in their accessibility to the active site. Here we show that redistribution of the E*-E equilibrium can be achieved by perturbing the electrostatic properties of the enzyme. Removal of the negative charge of the catalytic Asp102 or Asp189 in the primary specificity site destabilizes the E form and causes a shift in the 215-217 segment that compromises substrate entrance. Solution studies and existing structures of D102N document stabilization of the E* form. A new high-resolution structure of D189A also reveals the mutant in the collapsed E* form. These findings establish a new paradigm for the control of the E*-E equilibrium in the trypsin fold.

Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site.

PubMed

Fuchs, Gabriele; Petrov, Alexey N; Marceau, Caleb D; Popov, Lauren M; Chen, Jin; O'Leary, Seán E; Wang, Richard; Carette, Jan E; Sarnow, Peter; Puglisi, Joseph D

2015-01-13

Translation initiation can occur by multiple pathways. To delineate these pathways by single-molecule methods, fluorescently labeled ribosomal subunits are required. Here, we labeled human 40S ribosomal subunits with a fluorescent SNAP-tag at ribosomal protein eS25 (RPS25). The resulting ribosomal subunits could be specifically labeled in living cells and in vitro. Using single-molecule Förster resonance energy transfer (FRET) between RPS25 and domain II of the hepatitis C virus (HCV) internal ribosome entry site (IRES), we measured the rates of 40S subunit arrival to the HCV IRES. Our data support a single-step model of HCV IRES recruitment to 40S subunits, irreversible on the initiation time scale. We furthermore demonstrated that after binding, the 40S:HCV IRES complex is conformationally dynamic, undergoing slow large-scale rearrangements. Addition of translation extracts suppresses these fluctuations, funneling the complex into a single conformation on the 80S assembly pathway. These findings show that 40S:HCV IRES complex formation is accompanied by dynamic conformational rearrangements that may be modulated by initiation factors.

Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy.

PubMed

Gupta, Sebanti; Bhattacharjya, Surajit

2014-11-01

The sterile alpha motif or SAM domain is one of the most frequently present protein interaction modules with diverse functional attributions. SAM domain of the Ste11 protein of budding yeast plays important roles in mitogen-activated protein kinase cascades. In the current study, urea-induced, at subdenaturing concentrations, structural, and dynamical changes in the Ste11 SAM domain have been investigated by nuclear magnetic resonance spectroscopy. Our study revealed that a number of residues from Helix 1 and Helix 5 of the Ste11 SAM domain display plausible alternate conformational states and largest chemical shift perturbations at low urea concentrations. Amide proton (H/D) exchange experiments indicated that Helix 1, loop, and Helix 5 become more susceptible to solvent exchange with increased concentrations of urea. Notably, Helix 1 and Helix 5 are directly involved in binding interactions of the Ste11 SAM domain. Our data further demonstrate that the existence of alternate conformational states around the regions involved in dimeric interactions in native or near native conditions. © 2014 Wiley Periodicals, Inc.

Bacterial protease uses distinct thermodynamic signatures for substrate recognition.

PubMed

Bezerra, Gustavo Arruda; Ohara-Nemoto, Yuko; Cornaciu, Irina; Fedosyuk, Sofiya; Hoffmann, Guillaume; Round, Adam; Márquez, José A; Nemoto, Takayuki K; Djinović-Carugo, Kristina

2017-06-06

Porphyromonas gingivalis and Porphyromonas endodontalis are important bacteria related to periodontitis, the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable interest. Surprisingly, these two microorganisms do not ferment carbohydrates; rather they use proteinaceous substrates as carbon and energy sources. However, the underlying biochemical mechanisms of their energy metabolism remain unknown. Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. It binds substrates through an entropy-driven process and end products in an enthalpy-driven fashion. We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme ("entropy reservoirs"). The relationship between our structural and thermodynamics data yields a distinct model for protein-protein interactions where protein conformational entropy modulates the binding free-energy. Further, our findings provide a framework for the structure-based design of specific DPP11 inhibitors.

LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome

PubMed Central

Ariel, Federico; Latrasse, David; Mariappan, Kiruthiga Gayathri; Kim, Soon-Kap; Crespi, Martin; Hirt, Heribert; Bergounioux, Catherine; Raynaud, Cécile; Benhamed, Moussa

2016-01-01

Precise expression patterns of genes in time and space are essential for proper development of multicellular organisms. Dynamic chromatin conformation and spatial organization of the genome constitute a major step in this regulation to modulate developmental outputs. Polycomb repressive complexes (PRCs) mediate stable or flexible gene repression in response to internal and environmental cues. In Arabidopsis thaliana, LHP1 co-localizes with H3K27me3 epigenetic marks throughout the genome and interacts with PRC1 and PRC2 members as well as with a long noncoding RNA. Here, we show that LHP1 is responsible for the spreading of H3K27me3 towards the 3’ end of the gene body. We also identified a subset of LHP1-activated genes and demonstrated that LHP1 shapes local chromatin topology in order to control transcriptional co-regulation. Our work reveals a general role of LHP1 from local to higher conformation levels of chromatin configuration to determine its accessibility to define gene expression patterns. PMID:27410265

Conformational Response of 30S-bound IF3 to A-Site Binders Streptomycin and Kanamycin

PubMed Central

Chulluncuy, Roberto; Espiche, Carlos; Nakamoto, Jose Alberto; Fabbretti, Attilio; Milón, Pohl

2016-01-01

Aminoglycoside antibiotics are widely used to treat infectious diseases. Among them, streptomycin and kanamycin (and derivatives) are of importance to battle multidrug-resistant (MDR) Mycobacterium tuberculosis. Both drugs bind the small ribosomal subunit (30S) and inhibit protein synthesis. Genetic, structural, and biochemical studies indicate that local and long-range conformational rearrangements of the 30S subunit account for this inhibition. Here, we use intramolecular FRET between the C- and N-terminus domains of the flexible IF3 to monitor real-time perturbations of their binding sites on the 30S platform. Steady and pre-steady state binding experiments show that both aminoglycosides bring IF3 domains apart, promoting an elongated state of the factor. Binding of Initiation Factor IF1 triggers closure of IF3 bound to the 30S complex, while both aminoglycosides revert the IF1-dependent conformation. Our results uncover dynamic perturbations across the 30S subunit, from the A-site to the platform, and suggest that both aminoglycosides could interfere with prokaryotic translation initiation by modulating the interaction between IF3 domains with the 30S platform. PMID:27983590

Mechanism of UCH-L5 Activation and Inhibition by DEUBAD Domains in RPN13 and INO80G

PubMed Central

Sahtoe, Danny D.; van Dijk, Willem J.; El Oualid, Farid; Ekkebus, Reggy; Ovaa, Huib; Sixma, Titia K.

2015-01-01

Summary Deubiquitinating enzymes (DUBs) control vital processes in eukaryotes by hydrolyzing ubiquitin adducts. Their activities are tightly regulated, but the mechanisms remain elusive. In particular, the DUB UCH-L5 can be either activated or inhibited by conserved regulatory proteins RPN13 and INO80G, respectively. Here we show how the DEUBAD domain in RPN13 activates UCH-L5 by positioning its C-terminal ULD domain and crossover loop to promote substrate binding and catalysis. The related DEUBAD domain in INO80G inhibits UCH-L5 by exploiting similar structural elements in UCH-L5 to promote a radically different conformation, and employs molecular mimicry to block ubiquitin docking. In this process, large conformational changes create small but highly specific interfaces that mediate activity modulation of UCH-L5 by altering the affinity for substrates. Our results establish how related domains can exploit enzyme conformational plasticity to allosterically regulate DUB activity. These allosteric sites may present novel insights for pharmaceutical intervention in DUB activity. PMID:25702870

Software Assists in Extensive Environmental Auditing

NASA Technical Reports Server (NTRS)

Callac, Christopher; Matherne, Charlie

2002-01-01

The Base Enivronmental Management System (BEMS) is a Web-based application program for managing and tracking audits by the Environmental Office of Stennis Space Center in conformity with standard 14001 of the International Organization for Standardization (ISO 14001). (This standard specifies requirements for an environmental-management system.) BEMS saves time by partly automating what were previously manual processes for creating audit checklists; recording and tracking audit results; issuing, tracking, and implementing corrective-action requests (CARs); tracking continuous improvements (CIs); and tracking audit results and statistics. BEMS consists on an administration module and an auditor module. As its name suggests, the administration module is used to administer the audit. It helps administrators to edit the list of audit questions; edit the list of audit locations; assign manditory questions to locations; track, approve, and edit CARs; and edit completed audits. The auditor module is used by auditors to perform audits and record audit results: It helps the auditors to create audit checklists, complete audits, view completed audits, create CARs, record and acknowledge CIs, and generate reports from audit results.

Software Assists in Extensive Environmental Auditing

NASA Technical Reports Server (NTRS)

Callac, Christopher; Matherne, Charlie

2003-01-01

The Base Environmental Management System (BEMS) is a Web-based application program for managing and tracking audits by the Environmental Office of Stennis Space Center in conformity with standard 14001 of the International Organization for Standardization (ISO 14001). (This standard specifies requirements for an environmental-management system.) BEMS saves time by partly automating what were previously manual processes for creating audit checklists; recording and tracking audit results; issuing, tracking, and implementing corrective-action requests (CARs); tracking continuous improvements (CIs); and tracking audit results and statistics. BEMS consists of an administration module and an auditor module. As its name suggests, the administration module is used to administer the audit. It helps administrators to edit the list of audit questions; edit the list of audit locations; assign mandatory questions to locations; track, approve, and edit CARs; and edit completed audits. The auditor module is used by auditors to perform audits and record audit results: it helps the auditors to create audit checklists, complete audits, view completed audits, create CARs, record and acknowledge CIs, and generate reports from audit results.

Software Assists in Extensive Environmental Auditing

NASA Technical Reports Server (NTRS)

Callac, Christopher; Matherne, Charlie; Selinsky, T.

2002-01-01

The Base Environmental Management System (BEMS) is a Web-based application program for managing and tracking audits by the Environmental Office of Stennis Space Center in conformity with standard 14001 of the International Organization for Standardization (ISO 14001). (This standard specifies requirements for an environmental-management system.) BEMS saves time by partly automating what were previously manual processes for creating audit checklists; recording and tracking audit results; issuing, tracking, and implementing corrective-action requests (CARs); tracking continuous improvements (CIs); and tracking audit results and statistics. BEMS consists of an administration module and an auditor module. As its name suggests, the administration module is used to administer the audit. It helps administrators to edit the list of audit questions; edit the list of audit locations; assign mandatory questions to locations; track, approve, and edit CARs; and edit completed audits. The auditor module is used by auditors to perform audits and record audit results: it helps the auditors to create audit checklists, complete audits, view completed audits, create CARs, record and acknowledge CIs, and generate reports from audit results.

Architecture of the RNA polymerase II-Mediator core initiation complex.

PubMed

Plaschka, C; Larivière, L; Wenzeck, L; Seizl, M; Hemann, M; Tegunov, D; Petrotchenko, E V; Borchers, C H; Baumeister, W; Herzog, F; Villa, E; Cramer, P

2015-02-19

The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 Å resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation.

Fluorine Substitution in Neurotransmitters: Microwave Spectroscopy and Modelling of the Conformational Space and Non Bonding Interactions

NASA Astrophysics Data System (ADS)

Melandri, S.; Maris, A.; Merloni, A.

2011-06-01

Fluorine substitution in molecules is a common practice in bio-organic chemistry in order to modulate physicochemical properties and biological activity of molecules and an increasing number of drugs on the market contain fluorine, the presence of which is often of major importance to modify pharmacokinetics properties and molecular activity. The rationale for such a strategy is that fluorine is generally a stronger electron acceptor than the other halogen atoms and its size is intermediate between that of hydrogen and oxygen. We have studied two fluorinated analogs of 2-phenylethylamine (PEA), the prototype molecule for adrenergic neurotransmitters, namely: 4-Fluoro (4FPEA) and 2-Fluoro-2-phenylethylamine (2FPEA) by Molecular Beam Fourier Transform Microwave Spectroscopy in the frequency range 6-18 GHz and ab initio calculations at the MP2/6311++G** level. The aim is to obtain information on the spatial arrangement of the ethylamine side chain and the effects of fluorination on the energy landscape. The conformational space is dominated by low energy gauche conformations stabilized by weak interactions between the aminic hydrogens and the electron cloud of the benzene ring and anti conformations higher in energy. In 2FPEA the presence of the fluorine atom almost duplicate the number of possible conformation with respect to 4FPEA. We observed two conformers of 4FPEA and five conformers of 2FPEA which have been classified with the guide provided by accurate ab initio calculations. The identification of the conformational species was helped by the analysis of the quadrupole hyperfine pattern which is greatly influenced by the orientation of the amino group and acts as a fingerprint for each conformation. The orientation of the dipole moment within the principal axis frame and the order of stability of the different conformations are other independent pieces of evidence for the unambiguous assignment and identification of the conformers. The order of stability was found to be altered in both molecules with respect to the prototype PEA molecule, especially in the case of 2FPEA where we observe a stabilization of some of the anti forms and great destabilization of some of the gauche forms. These observations are in agreement with the results of the theoretical calculation and can be rationalized in terms of the effect of the fluorine atom on the electron density of the molecule and in particular on the electron cloud on the benzene ring.

The arrestin-1 finger loop interacts with two distinct conformations of active rhodopsin.

PubMed

Elgeti, Matthias; Kazmin, Roman; Rose, Alexander S; Szczepek, Michal; Hildebrand, Peter W; Bartl, Franz J; Scheerer, Patrick; Hofmann, Klaus Peter

2018-03-23

Signaling of the prototypical G protein-coupled receptor (GPCR) rhodopsin through its cognate G protein transducin (G t ) is quenched when arrestin binds to the activated receptor. Although the overall architecture of the rhodopsin/arrestin complex is known, many questions regarding its specificity remain unresolved. Here, using FTIR difference spectroscopy and a dual pH/peptide titration assay, we show that rhodopsin maintains certain flexibility upon binding the "finger loop" of visual arrestin (prepared as synthetic peptide ArrFL-1). We found that two distinct complexes can be stabilized depending on the protonation state of E3.49 in the conserved (D)ERY motif. Both complexes exhibit different interaction modes and affinities of ArrFL-1 binding. The plasticity of the receptor within the rhodopsin/ArrFL-1 complex stands in contrast to the complex with the C terminus of the G t α-subunit (GαCT), which stabilizes only one specific substate out of the conformational ensemble. However, G t α-subunit binding and both ArrFL-1-binding modes involve a direct interaction to conserved R3.50, as determined by site-directed mutagenesis. Our findings highlight the importance of receptor conformational flexibility and cytoplasmic proton uptake for modulation of rhodopsin signaling and thereby extend the picture provided by crystal structures of the rhodopsin/arrestin and rhodopsin/ArrFL-1 complexes. Furthermore, the two binding modes of ArrFL-1 identified here involve motifs of conserved amino acids, which indicates that our results may have elucidated a common modulation mechanism of class A GPCR-G protein/-arrestin signaling. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Direct Binding of the Corrector VX-809 to Human CFTR NBD1: Evidence of an Allosteric Coupling between the Binding Site and the NBD1:CL4 Interface.

PubMed

Hudson, Rhea P; Dawson, Jennifer E; Chong, P Andrew; Yang, Zhengrong; Millen, Linda; Thomas, Philip J; Brouillette, Christie G; Forman-Kay, Julie D

2017-08-01

Understanding the mechanism of action of modulator compounds for the cystic fibrosis transmembrane conductance regulator (CFTR) is key for the optimization of therapeutics as well as obtaining insights into the molecular mechanisms of CFTR function. We demonstrate the direct binding of VX-809 to the first nucleotide-binding domain (NBD1) of human CFTR. Disruption of the interaction between C-terminal helices and the NBD1 core upon VX-809 binding is observed from chemical shift changes in the NMR spectra of residues in the helices and on the surface of β -strands S3, S9, and S10. Binding to VX-809 leads to a significant negative shift in NBD1 thermal melting temperature (T m ), pointing to direct VX-809 interaction shifting the NBD1 conformational equilibrium. An inter-residue correlation analysis of the chemical shift changes provides evidence of allosteric coupling between the direct binding site and the NBD1:CL4 interface, thus enabling effects on the interface in the absence of direct binding in that location. These NMR binding data and the negative T m shifts are very similar to those previously reported by us for binding of the dual corrector-potentiator CFFT-001 to NBD1 (Hudson et al., 2012), suggesting that the two compounds may share some aspects of their mechanisms of action. Although previous studies have shown an important role for VX-809 in modulating the conformation of the first membrane spanning domain (Aleksandrov et al., 2012; Ren et al., 2013), this additional mode of VX-809 binding provides insight into conformational dynamics and allostery within CFTR. Copyright © 2017 by The Author(s).

SU-E-T-621: Planning Methodologies for Cancer of the Anal Canal: Comparing IMRT, Rapid Arc, and Pencil Beam Scanning Proton Beam

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGlade, J; Kassaee, A

2015-06-15

Purpose: To evaluate planning methods for anal canal cancer and compare the results of 9-field Intensity Modulated Radiotherapy (IMRT), Volumetric Modulated Arc Therapy (Varian, RapidArc), and Proton Pencil Beam Scanning (PBS). Methods: We generated plans with IMRT, RapidArc (RA) and PBS for twenty patients for both initial phase including nodes and cone down phase of treatment using Eclipe (Varian). We evaluated the advantage of each technique for each phase. RA plans used 2 to 4 arcs and various collimator orientations. PBS used two posterior oblique fields. We evaluated the plans comparing dose volume histogram (DVH), locations of hot spots, andmore » PTV dose conformity. Results: Due to complex shape of target, for RA plans, multiple arcs (>2) are required to achieve optimal PTV conformity. When the PTV exceeds 15 cm in the superior-inferior direction, limitations of deliverability start to dominate. The PTV should be divided into a superior and an inferior structure. The optimization is performed with fixed jaws for each structure and collimator set to 90 degrees for the inferior PTV. Proton PBS plans show little advantage in small bowel sparing when treating the nodes. However, PBS plan reduces volumetric dose to the bladder at the cost of higher doses to the perineal skin. IMRT plans provide good target conformity, but they generate hot spots outside of the target volume. Conclusion: When using one planning technique for entire course of treatment, Multiple arc (>2) RA plans are better as compared to IMRT and PBS plans. When combining techniques, RA for the initial phase in combination with PBS for the cone down phase results in the most optimal plans.« less

Evaluation of radiotherapy techniques for radical treatment of lateralised oropharyngeal cancers : Dosimetry and NTCP.

PubMed

McQuaid, D; Dunlop, A; Nill, S; Franzese, C; Nutting, C M; Harrington, K J; Newbold, K L; Bhide, S A

2016-08-01

The aim of this study was to investigate potential advantages and disadvantages of three-dimensional conformal radiotherapy (3DCRT), multiple fixed-field intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc therapy (VMAT) in terms of dose to the planning target volume (PTV), organs at risk (OARs) and normal tissue complication probability (NTCP) for delivering ipsilateral radiotherapy. 3DCRT, IMRT and VMAT were compared in patients with well-lateralised primary tonsillar cancers who underwent primary radical ipsilateral radiotherapy. The following parameters were compared: conformity index (CI); homogeneity index (HI); dose-volume histograms (DVHs) of PTVs and OARs; NTCP, risk of radiation-induced cancer and dose accumulation during treatment. IMRT and VMAT were superior to 3DCRT in terms of CI, HI and dose to the target volumes, as well as mandible and dose accumulation robustness. The techniques were equivalent in terms of dose and NTCP for the contralateral oral cavity, contralateral submandibular gland and mandible, when specific dose constraint objectives were used on the oral cavity volume. Although the volume of normal tissue exposed to low-dose radiation was significantly higher with IMRT and VMAT, the risk of radiation-induced secondary malignancy was dependant on the mathematical model used. This study demonstrates the superiority of IMRT/VMAT techniques over 3DCRT in terms of dose homogeneity, conformity and consistent dose delivery to the PTV throughout the course of treatment in patients with lateralised oropharyngeal cancers. Dosimetry and NTCP calculations show that these techniques are equivalent to 3DCRT with regard to the risk of acute mucositis when specific dose constraint objectives were used on the contralateral oral cavity OAR.

Determinants of the heme-CO vibrational modes in the H-NOX family.

PubMed

Tran, Rosalie; Weinert, Emily E; Boon, Elizabeth M; Mathies, Richard A; Marletta, Michael A

2011-08-02

The Heme Nitric oxide/OXygen binding (H-NOX) family of proteins have important functions in gaseous ligand signaling in organisms from bacteria to humans, including nitric oxide (NO) sensing in mammals, and provide a model system for probing ligand selectivity in hemoproteins. A unique vibrational feature that is ubiquitous throughout the H-NOX family is the presence of a high C-O stretching frequency. To investigate the cause of this spectroscopic characteristic, the Fe-CO and C-O stretching frequencies were probed in the H-NOX domain from Thermoanaerobacter tengcongensis (Tt H-NOX) using resonance Raman (RR) spectroscopy. Four classes of heme pocket mutants were generated to assess the changes in stretching frequency: (i) the distal H-bonding network, (ii) the proximal histidine ligand, (iii) modulation of the heme conformation via Ile-5 and Pro-115, and (iv) the conserved Tyr-Ser-Arg (YxSxR) motif. These mutations revealed important electrostatic interactions that dampen the back-donation of the Fe(II) d(π) electrons into the CO π* orbitals. The most significant change occurred upon disruption of the H-bonds between the strictly conserved YxSxR motif and the heme propionate groups, producing two dominant CO-bound heme conformations. One conformer was structurally similar to Tt H-NOX WT, whereas the other displayed a decrease in ν(C-O) of up to ∼70 cm(-1) relative to the WT protein, with minimal changes in ν(Fe-CO). Taken together, these results show that the electrostatic interactions in the Tt H-NOX binding pocket are primarily responsible for the high ν(C-O) by decreasing the Fe d(π) → CO π* back-donation and suggest that the dominant mechanism by which this family modulates the Fe(II)-CO bond likely involves the YxSxR motif.

Technique for comprehensive head and neck irradiation using 3-dimensional conformal proton therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

McDonald, Mark W., E-mail: markmcdonaldmd@gmail.com; Indiana University Health Proton Therapy Center, Bloomington, IN; Walter, Alexander S.

2015-01-01

Owing to the technical and logistical complexities of matching photon and proton treatment modalities, we developed and implemented a technique of comprehensive head and neck radiation using 3-dimensional (3D) conformal proton therapy. A monoisocentric technique was used with a 30-cm snout. Cervical lymphatics were treated with 3 fields: a posterior-anterior field with a midline block and a right and a left posterior oblique field. The matchline of the 3 cervical nodal fields with the primary tumor site fields was staggered by 0.5 cm. Comparative intensity-modulated photon plans were later developed for 12 previously treated patients to provide equivalent target coverage,more » while matching or improving on the proton plans' sparing of organs at risk (OARs). Dosimetry to OARs was evaluated and compared by treatment modality. Comprehensive head and neck irradiation using proton therapy yielded treatment plans with significant dose avoidance of the oral cavity and midline neck structures. When compared with the generated intensity-modulated radiation therapy (IMRT) plans, the proton treatment plans yielded statistically significant reductions in the mean and integral radiation dose to the oral cavity, larynx, esophagus, and the maximally spared parotid gland. There was no significant difference in mean dose to the lesser-spared parotid gland by treatment modality or in mean or integral dose to the spared submandibular glands. A technique for cervical nodal irradiation using 3D conformal proton therapy with uniform scanning was developed and clinically implemented. Use of proton therapy for cervical nodal irradiation resulted in large volume of dose avoidance to the oral cavity and low dose exposure to midline structures of the larynx and the esophagus, with lower mean and integral dose to assessed OARs when compared with competing IMRT plans.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acar, H; Cebe, M; Mabhouti, H

Purpose: Stereotactic body radiosurgery (SBRT) for spine metastases involves irradiation using a single high dose fraction. The purpose of this study was to investigate a Hybrid VMAT/IMRT technique which combines volumetric modulated arc therapy (VMAT) and intensity modulated radiation therapy (IMRT) for spine SBRT in terms of its dosimetric quality and treatment efficiency using Radiation Therapy Oncology Group (RTOG) 0631 guidelines. Methods: 7 fields IMRT, 2 full arcs VMAT and Hybrid VMAT/IMRT were created for ten previously treated patients. The Hybrid VMAT/IMRT technique consisted of 1 full VMAT arc and 5 IMRT fields. Hybrid VMAT/IMRT plans were compared with IMRTmore » and VMAT plans in terms of the dose distribution, spinal cord sparing, homogeneity, conformity and gradient indexies, monitor unit (MU) and beam on time (BOT). RTOG 0631 recommendations were applied for treatment planning. All plans were normalized and prescribed to deliver 18.0 Gy in a single fraction to 90% of the target volume. Results: The Hybrid VMAT/IMRT technique significantly improved target dose homogeneity and conformity compared with IMRT and VMAT techniques. Providing sharp dose gradient Hybrid VMAT/IMRT plans spare the spinal cord and healthy tissue more effectively. Although, both MU and BOT slightly increased in Hybrid VMAT/IMRT plans there is no statistically meaningful difference between VMAT and Hybrid VMAT/IMRT plans. Conclusion: In IMRT, a smaller volume of healthy tissue can be irradiated in the low dose region, VMAT plans provide better target volume coverage, favorable dose gradient, conformity and better OAR sparing and also they require a much smaller number of MUs and thus a shorter treatment time than IMRT plans. Hybrid plan offers a sinergy through combination of these two techniques with slightly increased number of MU and thus more treatment time.« less

Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation.

PubMed

Hu, Haidai; Nemecz, Ákos; Van Renterghem, Catherine; Fourati, Zaineb; Sauguet, Ludovic; Corringer, Pierre-Jean; Delarue, Marc

2018-04-24

Pentameric ligand-gated ion channels (pLGICs) constitute a widespread class of ion channels, present in archaea, bacteria, and eukaryotes. Upon binding of their agonists in the extracellular domain, the transmembrane pore opens, allowing ions to go through, via a gating mechanism that can be modulated by a number of drugs. Even though high-resolution structural information on pLGICs has increased in a spectacular way in recent years, both in bacterial and in eukaryotic systems, the structure of the open channel conformation of some intensively studied receptors whose structures are known in a nonactive (closed) form, such as Erwinia chrysanthemi pLGIC (ELIC), is still lacking. Here we describe a gammaproteobacterial pLGIC from an endo-symbiont of Tevnia jerichonana (sTeLIC), whose sequence is closely related to the pLGIC from ELIC with 28% identity. We provide an X-ray crystallographic structure at 2.3 Å in an active conformation, where the pore is found to be more open than any current conformation found for pLGICs. In addition, two charged restriction rings are present in the vestibule. Functional characterization shows sTeLIC to be a cationic channel activated at alkaline pH. It is inhibited by divalent cations, but not by quaternary ammonium ions, such as tetramethylammonium. Additionally, we found that sTeLIC is allosterically potentiated by aromatic amino acids Phe and Trp, as well as their derivatives, such as 4-bromo-cinnamate, whose cocrystal structure reveals a vestibular binding site equivalent to, but more deeply buried than, the one already described for benzodiazepines in ELIC.

Mechanism of Transport Modulation by an Extracellular Loop in an Archaeal Excitatory Amino Acid Transporter (EAAT) Homolog*

PubMed Central

Mulligan, Christopher; Mindell, Joseph A.

2013-01-01

Secondary transporters in the excitatory amino acid transporter family terminate glutamatergic synaptic transmission by catalyzing Na+-dependent removal of glutamate from the synaptic cleft. Recent structural studies of the aspartate-specific archaeal homolog, GltPh, suggest that transport is achieved by a rigid body, piston-like movement of the transport domain, which houses the substrate-binding site, between the extracellular and cytoplasmic sides of the membrane. This transport domain is connected to an immobile scaffold by three loops, one of which, the 3–4 loop (3L4), undergoes substrate-sensitive conformational change. Proteolytic cleavage of the 3L4 was found to abolish transport activity indicating an essential function for this loop in the transport mechanism. Here, we demonstrate that despite the presence of fully cleaved 3L4, GltPh is still able to sample conformations relevant for transport. Optimized reconstitution conditions reveal that fully cleaved GltPh retains some transport activity. Analysis of the kinetics and temperature dependence of transport accompanied by direct measurements of substrate binding reveal that this decreased transport activity is not due to alteration of the substrate binding characteristics but is caused by the significantly reduced turnover rate. By measuring solute counterflow activity and cross-link formation rates, we demonstrate that cleaving 3L4 severely and specifically compromises one or more steps contributing to the movement of the substrate-loaded transport domain between the outward- and inward-facing conformational states, sparing the equivalent step(s) during the movement of the empty transport domain. These results reveal a hitherto unknown role for the 3L4 in modulating an essential step in the transport process. PMID:24155238

Modulation of calmodulin plasticity by the effect of macromolecular crowding.

PubMed

Homouz, Dirar; Sanabria, Hugo; Waxham, M Neal; Cheung, Margaret S

2009-09-04

In vitro biochemical reactions are most often studied in dilute solution, a poor mimic of the intracellular space of eukaryotic cells, which are crowded with mobile and immobile macromolecules. Such crowded conditions exert volume exclusion and other entropic forces that have the potential to impact chemical equilibria and reaction rates. In this article, we used the well-characterized and ubiquitous molecule calmodulin (CaM) and a combination of theoretical and experimental approaches to address how crowding impacts CaM's conformational plasticity. CaM is a dumbbell-shaped molecule that contains four EF hands (two in the N-lobe and two in the C-lobe) that each could bind Ca(2+), leading to stabilization of certain substates that favor interactions with other target proteins. Using coarse-grained molecular simulations, we explored the distribution of CaM conformations in the presence of crowding agents. These predictions, in which crowding effects enhance the population of compact structures, were then confirmed in experimental measurements using fluorescence resonance energy transfer techniques of donor- and acceptor-labeled CaM under normal and crowded conditions. Using protein reconstruction methods, we further explored the folding-energy landscape and examined the structural characteristics of CaM at free-energy basins. We discovered that crowding stabilizes several different compact conformations, which reflects the inherent plasticity in CaM's structure. From these results, we suggest that the EF hands in the C-lobe are flexible and can be thought of as a switch, while those in the N-lobe are stiff, analogous to a rheostat. New combinatorial signaling properties may arise from the product of the differential plasticity of the two distinct lobes of CaM in the presence of crowding. We discuss the implications of these results for modulating CaM's ability to bind Ca(2+) and target proteins.

Quality of Intensity Modulated Radiation Therapy Treatment Plans Using a ⁶⁰Co Magnetic Resonance Image Guidance Radiation Therapy System.

PubMed

Wooten, H Omar; Green, Olga; Yang, Min; DeWees, Todd; Kashani, Rojano; Olsen, Jeff; Michalski, Jeff; Yang, Deshan; Tanderup, Kari; Hu, Yanle; Li, H Harold; Mutic, Sasa

2015-07-15

This work describes a commercial treatment planning system, its technical features, and its capabilities for creating (60)Co intensity modulated radiation therapy (IMRT) treatment plans for a magnetic resonance image guidance radiation therapy (MR-IGRT) system. The ViewRay treatment planning system (Oakwood Village, OH) was used to create (60)Co IMRT treatment plans for 33 cancer patients with disease in the abdominal, pelvic, thorax, and head and neck regions using physician-specified patient-specific target coverage and organ at risk (OAR) objectives. Backup plans using a third-party linear accelerator (linac)-based planning system were also created. Plans were evaluated by attending physicians and approved for treatment. The (60)Co and linac plans were compared by evaluating conformity numbers (CN) with 100% and 95% of prescription reference doses and heterogeneity indices (HI) for planning target volumes (PTVs) and maximum, mean, and dose-volume histogram (DVH) values for OARs. All (60)Co IMRT plans achieved PTV coverage and OAR sparing that were similar to linac plans. PTV conformity for (60)Co was within <1% and 3% of linac plans for 100% and 95% prescription reference isodoses, respectively, and heterogeneity was on average 4% greater. Comparisons of OAR mean dose showed generally better sparing with linac plans in the low-dose range <20 Gy, but comparable sparing for organs with mean doses >20 Gy. The mean doses for all (60)Co plan OARs were within clinical tolerances. A commercial (60)Co MR-IGRT device can produce highly conformal IMRT treatment plans similar in quality to linac IMRT for a variety of disease sites. Additional work is in progress to evaluate the clinical benefit of other novel features of this MR-IGRT system. Copyright © 2015 Elsevier Inc. All rights reserved.

Structural control of caspase-generated glutamyl-tRNA synthetase by appended noncatalytic WHEP domains.

PubMed

Halawani, Dalia; Gogonea, Valentin; DiDonato, Joseph A; Pipich, Vitaliy; Yao, Peng; China, Arnab; Topbas, Celalettin; Vasu, Kommireddy; Arif, Abul; Hazen, Stanley L; Fox, Paul L

2018-06-08

Aminoacyl-tRNA synthetases are ubiquitous, evolutionarily conserved enzymes catalyzing the conjugation of amino acids onto cognate tRNAs. During eukaryotic evolution, tRNA synthetases have been the targets of persistent structural modifications. These modifications can be additive, as in the evolutionary acquisition of noncatalytic domains, or subtractive, as in the generation of truncated variants through regulated mechanisms such as proteolytic processing, alternative splicing, or coding region polyadenylation. A unique variant is the human glutamyl-prolyl-tRNA synthetase (EPRS) consisting of two fused synthetases joined by a linker containing three copies of the WHEP domain (termed by its presence in tryptophanyl-, histidyl-, and glutamyl-prolyl-tRNA synthetases). Here, we identify site-selective proteolysis as a mechanism that severs the linkage between the EPRS synthetases in vitro and in vivo Caspase action targeted Asp-929 in the third WHEP domain, thereby separating the two synthetases. Using a neoepitope antibody directed against the newly exposed C terminus, we demonstrate EPRS cleavage at Asp-929 in vitro and in vivo Biochemical and biophysical characterizations of the N-terminally generated EPRS proteoform containing the glutamyl-tRNA synthetase and most of the linker, including two WHEP domains, combined with structural analysis by small-angle neutron scattering, revealed a role for the WHEP domains in modulating conformations of the catalytic core and GSH- S -transferase-C-terminal-like (GST-C) domain. WHEP-driven conformational rearrangement altered GST-C domain interactions and conferred distinct oligomeric states in solution. Collectively, our results reveal long-range conformational changes imposed by the WHEP domains and illustrate how noncatalytic domains can modulate the global structure of tRNA synthetases in complex eukaryotic systems. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

The Minimal Pharmacophore for Silent Agonism of the α7 Nicotinic Acetylcholine Receptor

PubMed Central

Chojnacka, Kinga; Horenstein, Nicole A.

2014-01-01

The minimum pharmacophore for activation of the human α7 nicotinic acetylcholine receptor (nAChR) is the tetramethylammonium cation. Previous work demonstrated that larger quaternary ammonium compounds, such as diethyldimethylammonium or 1-methyl quinuclidine, were α7-selective partial agonists, but additional increase in the size of the ammonium cation or the quinuclidine N-alkyl group by a single carbon to an N-ethyl group led to a loss of efficacy for ion channel activation. We report that although such compounds are ineffective at inducing the normal channel open state, they nonetheless regulate the induction of specific conformational states normally considered downstream of channel activation. We synthesized several panels of quaternary ammonium nAChR ligands that systematically varied the size of the substituents bonded to the central positively charged nitrogen atom. In these molecular series, we found a correlation between the molecular volume of the ligand and/or charge density, and the receptor’s preferred distribution among conformational states including the closed state, the active state, a nonconducting state that could be converted to an activated state by a positive allosteric modulator (PAM), and a PAM-insensitive nonconducting state. We hypothesize that the changes of molecular volume of an agonist’s cationic core subtly impact interactions at the subunit interface constituting the orthosteric binding site in such a way as to regulate the probability of conversions among the conformational states. We define a new minimal pharmacophore for the class of compounds we have termed “silent agonists,” which are able to induce allosteric modulator-dependent activation but not the normal activated state. PMID:24990939

Supporting Uncertainty Reasoning in SIMulated Operators for Networks (SIMON) (Le support du raisonnement dans l’incertitude pour des operateurs simules dans un reseau)

DTIC Science & Technology

2005-12-01

moteur de simulation de l’Environnement Intégré de Modélisation de la Performance est utilisé de pair avec l’approche pour démontrer comment des...d’être utilisé dans les forces générées par ordinateur. Le travail ultérieur inclura plus d’essais, l’intégration avec les moteurs de simulateurs et...Aspects are reasoning units relevant to simulated tasks. Each Aspect schema is a 4-tuple: AspectSchema = <MA, WM, LM, CL>, where MA refers to meta

The Crystal Structure of a Cardiovirus RNA-Dependent RNA Polymerase Reveals an Unusual Conformation of the Polymerase Active Site

PubMed Central

Vives-Adrian, Laia; Lujan, Celia; Oliva, Baldo; van der Linden, Lonneke; Selisko, Barbara; Coutard, Bruno; Canard, Bruno; van Kuppeveld, Frank J. M.

2014-01-01

ABSTRACT Encephalomyocarditis virus (EMCV) is a member of the Cardiovirus genus within the large Picornaviridae family, which includes a number of important human and animal pathogens. The RNA-dependent RNA polymerase (RdRp) 3Dpol is a key enzyme for viral genome replication. In this study, we report the X-ray structures of two different crystal forms of the EMCV RdRp determined at 2.8- and 2.15-Å resolution. The in vitro elongation and VPg uridylylation activities of the purified enzyme have also been demonstrated. Although the overall structure of EMCV 3Dpol is shown to be similar to that of the known RdRps of other members of the Picornaviridae family, structural comparisons show a large reorganization of the active-site cavity in one of the crystal forms. The rearrangement affects mainly motif A, where the conserved residue Asp240, involved in ribonucleoside triphosphate (rNTP) selection, and its neighbor residue, Phe239, move about 10 Å from their expected positions within the ribose binding pocket toward the entrance of the rNTP tunnel. This altered conformation of motif A is stabilized by a cation-π interaction established between the aromatic ring of Phe239 and the side chain of Lys56 within the finger domain. Other contacts, involving Phe239 and different residues of motif F, are also observed. The movement of motif A is connected with important conformational changes in the finger region flanked by residues 54 to 63, harboring Lys56, and in the polymerase N terminus. The structures determined in this work provide essential information for studies on the cardiovirus RNA replication process and may have important implications for the development of new antivirals targeting the altered conformation of motif A. IMPORTANCE The Picornaviridae family is one of the largest virus families known, including many important human and animal pathogens. The RNA-dependent RNA polymerase (RdRp) 3Dpol is a key enzyme for picornavirus genome replication and a validated target for the development of antiviral therapies. Solving the X-ray structure of the first cardiovirus RdRp, EMCV 3Dpol, we captured an altered conformation of a conserved motif in the polymerase active site (motif A) containing the aspartic acid residue involved in rNTP selection and binding. This altered conformation of motif A, which interferes with the correct positioning of the rNTP substrate in the active site, is stabilized by a number of residues strictly conserved among picornaviruses. The rearrangements observed suggest that this motif A segment is a dynamic element that can be modulated by external effectors, either activating or inhibiting enzyme activity, and this type of modulation appears to be general to all picornaviruses. PMID:24600002

The crystal structure of a cardiovirus RNA-dependent RNA polymerase reveals an unusual conformation of the polymerase active site.

PubMed

Vives-Adrian, Laia; Lujan, Celia; Oliva, Baldo; van der Linden, Lonneke; Selisko, Barbara; Coutard, Bruno; Canard, Bruno; van Kuppeveld, Frank J M; Ferrer-Orta, Cristina; Verdaguer, Núria

2014-05-01

Encephalomyocarditis virus (EMCV) is a member of the Cardiovirus genus within the large Picornaviridae family, which includes a number of important human and animal pathogens. The RNA-dependent RNA polymerase (RdRp) 3Dpol is a key enzyme for viral genome replication. In this study, we report the X-ray structures of two different crystal forms of the EMCV RdRp determined at 2.8- and 2.15-Å resolution. The in vitro elongation and VPg uridylylation activities of the purified enzyme have also been demonstrated. Although the overall structure of EMCV 3Dpol is shown to be similar to that of the known RdRps of other members of the Picornaviridae family, structural comparisons show a large reorganization of the active-site cavity in one of the crystal forms. The rearrangement affects mainly motif A, where the conserved residue Asp240, involved in ribonucleoside triphosphate (rNTP) selection, and its neighbor residue, Phe239, move about 10 Å from their expected positions within the ribose binding pocket toward the entrance of the rNTP tunnel. This altered conformation of motif A is stabilized by a cation-π interaction established between the aromatic ring of Phe239 and the side chain of Lys56 within the finger domain. Other contacts, involving Phe239 and different residues of motif F, are also observed. The movement of motif A is connected with important conformational changes in the finger region flanked by residues 54 to 63, harboring Lys56, and in the polymerase N terminus. The structures determined in this work provide essential information for studies on the cardiovirus RNA replication process and may have important implications for the development of new antivirals targeting the altered conformation of motif A. The Picornaviridae family is one of the largest virus families known, including many important human and animal pathogens. The RNA-dependent RNA polymerase (RdRp) 3Dpol is a key enzyme for picornavirus genome replication and a validated target for the development of antiviral therapies. Solving the X-ray structure of the first cardiovirus RdRp, EMCV 3Dpol, we captured an altered conformation of a conserved motif in the polymerase active site (motif A) containing the aspartic acid residue involved in rNTP selection and binding. This altered conformation of motif A, which interferes with the correct positioning of the rNTP substrate in the active site, is stabilized by a number of residues strictly conserved among picornaviruses. The rearrangements observed suggest that this motif A segment is a dynamic element that can be modulated by external effectors, either activating or inhibiting enzyme activity, and this type of modulation appears to be general to all picornaviruses.

Post-Translational Phosphorylation of Serine 74 of Human Deoxycytidine Kinase Favors the Enzyme Adopting the Open Conformation Making It Competent for Nucleoside Binding and Release

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hazra, Saugata; Szewczak, Andrzej; Ort, Stephan

2012-03-26

Deoxycytidine kinase (dCK) uses either ATP or UTP as a phosphoryl donor to catalyze the phosphorylation of nucleoside acceptors. The kinetic properties of human dCK are modulated in vivo by phosphorylation of serine 74. This residue is a part of the insert region and is distant from the active site. Replacing the serine with a glutamic acid (S74E variant) can mimic phosphorylation of Ser74. To understand how phosphorylation affects the catalytic properties of dCK, we examined the S74E variant of dCK both structurally and kinetically. We observe that the presence of a glutamic acid at position 74 favors the adoptionmore » by the enzyme of the open conformation. Glu74 stabilizes the open conformation by directly interacting with the indole side chain of Trp58, a residue that is in the proximity of the base of the nucleoside substrate. The open dCK conformation is competent for the binding of nucleoside but not for phosphoryl transfer. In contrast, the closed conformation is competent for phosphoryl transfer but not for product release. Thus, dCK must make the transition between the open and closed states during the catalytic cycle. We propose a reaction scheme for dCK that incorporates the transition between the open and closed states, and this serves to rationalize the observed kinetic differences between wild-type dCK and the S74E variant.« less

The shape of the electronic circular dichroism spectrum of (2,6-dimethylphenyl)(phenyl)methanol: interplay between conformational equilibria and vibronic effects.

PubMed

Padula, Daniele; Cerezo, Javier; Pescitelli, Gennaro; Santoro, Fabrizio

2017-12-13

Comparison between chiroptical spectra and theoretical predictions is the method of choice for the assignment of the absolute configuration of chiral compounds in solution. Here we report the case of an apparently simple biarylcarbinol, whose electronic circular dichroism (ECD) in the 1 L b region exhibits a peculiar alternation of negative and positive bands. Adopting Density Functional Theory, and describing solvent effects with implicit methods, we found three stable conformers in ethanol, each of them with two close lying states corresponding to similar local 1 L b excitations on the two phenyls. We computed the corresponding vibronic ECD spectra in harmonic approximation, including Duschinsky mixings as well as both Franck Condon (FC) and Herzberg Teller (HT) effects. Exploiting a recently developed mixed quantum/classical method, we further investigated the contribution of the vibronic spectra of out-of-equilibrium structures along the interconversion path connecting the different conformers. In this way, we achieved a reasonable agreement with experiment and attributed the alternating signs of the bands to the existence of different conformers. The remaining discrepancies with experiment indicate that specific solute-solvent interactions modulate the relative conformers' stabilities, calling for new methods able to combine Molecular Dynamics explorations and vibronic calculations. Moreover, the poor performance of HT approaches and the existence of two closely-lying states suggest the necessity of an improved fully-nonadiabatic vibronic approach. These findings demonstrate that even for such a simple system as the biarylcarbinol investigated here, a full reproduction of the fine details of the ECD spectrum requires the development of new improved methods.

Equation Chapter 1 Section 1Sequence-To-Conformation Relationships of Disordered Regions Tethered to Folded Domains of Proteins.

PubMed

Mittal, Anuradha; Holehouse, Alex S; Cohan, Megan C; Pappu, Rohit V

2018-05-12

Intrinsically disordered proteins and regions (IDPs / IDRs) are characterized by well-defined sequence-to-conformation relationships (SCRs). These relationships refer to the sequence-specific preferences for average sizes, shapes, residue-specific secondary structure propensities, and amplitudes of multiscale conformational fluctuations. SCRs are discerned from the sequence-specific conformational ensembles of IDPs. A vast majority of IDPs are actually tethered to folded domains (FDs). This raises the question of whether or not SCRs inferred for IDPs are applicable to IDRs tethered to folded domains. Here, we use atomistic simulations based on a well-established forcefield paradigm and an enhanced sampling method to obtain comparative assessments of SCRs for thirteen archetypal IDRs modeled as autonomous units, as C-terminal tails connected to folded domains, and as linkers between pairs of folded domains. Our studies uncover a set of general observations regarding context-independent versus context-dependent SCRs of IDRs. SCRs are minimally perturbed upon tethering to folded domains if the IDRs are deficient in charged residues and for polyampholytic IDRs where the oppositely charged residues within the sequence of the IDR are separated into distinct blocks. In contrast, the interplay between IDRs and tethered folded domains has a significant modulatory effect on SCRs if the IDRs have intermediate fractions of charged residues or if they have sequence-intrinsic conformational preferences for canonical random coils. Our findings suggest that IDRs with context-independent SCRs might be independent evolutionary modules whereas IDRs with context-dependent intrinsic SCRs might co-evolve with the FDs to which they are tethered. Copyright © 2018. Published by Elsevier Ltd.

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins.

PubMed

Marinelli, Fabrizio; Kuhlmann, Sonja I; Grell, Ernst; Kunte, Hans-Jörg; Ziegler, Christine; Faraldo-Gómez, José D

2011-12-06

Numerous membrane importers rely on accessory water-soluble proteins to capture their substrates. These substrate-binding proteins (SBP) have a strong affinity for their ligands; yet, substrate release onto the low-affinity membrane transporter must occur for uptake to proceed. It is generally accepted that release is facilitated by the association of SBP and transporter, upon which the SBP adopts a conformation similar to the unliganded state, whose affinity is sufficiently reduced. Despite the appeal of this mechanism, however, direct supporting evidence is lacking. Here, we use experimental and theoretical methods to demonstrate that an allosteric mechanism of enhanced substrate release is indeed plausible. First, we report the atomic-resolution structure of apo TeaA, the SBP of the Na(+)-coupled ectoine TRAP transporter TeaBC from Halomonas elongata DSM2581(T), and compare it with the substrate-bound structure previously reported. Conformational free-energy landscape calculations based upon molecular dynamics simulations are then used to dissect the mechanism that couples ectoine binding to structural change in TeaA. These insights allow us to design a triple mutation that biases TeaA toward apo-like conformations without directly perturbing the binding cleft, thus mimicking the influence of the membrane transporter. Calorimetric measurements demonstrate that the ectoine affinity of the conformationally biased triple mutant is 100-fold weaker than that of the wild type. By contrast, a control mutant predicted to be conformationally unbiased displays wild-type affinity. This work thus demonstrates that substrate release from SBPs onto their membrane transporters can be facilitated by the latter through a mechanism of allosteric modulation of the former.

Conformational diversity in contryphans from Conus venom: cis-trans isomerisation and aromatic/proline interactions in the 23-membered ring of a 7-residue peptide disulfide loop.

PubMed

Sonti, Rajesh; Gowd, Konkallu Hanumae; Rao, K N Shashanka; Ragothama, Srinivasarao; Rodriguez, Alex; Perez, Juan Jesus; Balaram, Padmanabhan

2013-11-04

Conformational diversity or "shapeshifting" in cyclic peptide natural products can, in principle, confer a single molecular entity with the property of binding to multiple receptors. Conformational equilibria have been probed in the contryphans, which are peptides derived from Conus venom possessing a 23-membered cyclic disulfide moiety. The natural sequences derived from Conus inscriptus, GCV(D)LYPWC* (In936) and Conus loroisii, GCP(D)WDPWC* (Lo959) differ in the number of proline residues within the macrocyclic ring. Structural characterisation of distinct conformational states arising from cis-trans equilibria about Xxx-Pro bonds is reported. Isomerisation about the C2-P3 bond is observed in the case of Lo959 and about the Y5-P6 bond in In936. Evidence is presented for as many as four distinct species in the case of the synthetic analogue V3P In936. The Tyr-Pro-Trp segment in In936 is characterised by distinct sidechain orientations as a consequence of aromatic/proline interactions as evidenced by specific sidechain-sidechain nuclear Overhauser effects and ring current shifted proton chemical shifts. Molecular dynamics simulations suggest that Tyr5 and Trp7 sidechain conformations are correlated and depend on the geometry of the Xxx-Pro bond. Thermodynamic parameters are derived for the cis↔trans equilibrium for In936. Studies on synthetic analogues provide insights into the role of sequence effects in modulating isomerisation about Xxx-Pro bonds. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Choriorétinite extensive bilatérale révélant une infection par le virus de l'immunodéficience humaine (VIH)

PubMed Central

El Yamouni, Oubaida; Tzili, Nazih; El Hassan, Abdallah; Slassi, Nadia; El Khaoua, Mahfoud; Jebbar, Zakaria; Berraho, Amina

2014-01-01

Au cours de l'infection par le virus de l'immunodéficience humaine(VIH), Les atteintes oculaires sont polymorphes, pouvant compromettre le pronostic fonctionnel. Nous rapportons l'observation d'un patient présentant une choriorétinite infectieuse sévère révélant une infection par le VIH. Patient âgé de 35 ans avec antécédent de tuberculose pulmonaire en 2007, consulte pour BAV bilatérale progressive depuis 6 mois. Une acuité visuelle à compte les doigts au niveau de l'oeil droit et à mouvement des doigts au niveau de l'oeil gauche, avec présence de foyers choriorétiniens diffus visualisés au fond d'oeil et à l'angiographie. Les sérologies VIH, toxoplasmose et CMV sont positives. Le patient a été mis sous traitement anti-toxoplasmose (Sulfadiazine et pyriméthamine) et anti-CMV (Ganciclovir per os). L’évolution sous traitement a été marquée par une régression de la hyalite avec la persistance des foyers choriorétiniens évolutifs et une acuité visuelle réduite à perception lumineuse. PMID:25709723

[Not Available].

PubMed

Belmir, R; Fejjal, N; El Omari, M; El Mazouz, S; Gharib, N; Abassi, A; Belmahi, A

2008-09-30

Les accidents électriques par haute tension (AEHT) provoquent des brûlures profondes par effet Joule le long des axes vasculo-nerveux entre les points d'entrée et de sortie, qui sont le siège de lésions délabrantes. Les Auteurs rapportent une série de dix cas d'AEHT admis au service de chirurgie réparatrice et de brûlés de l'Hôpital Ibn Sina de Rabat à travers laquelle ils étudient les caractéristiques épidémiologiques, cliniques et thérapeutiques. Tous les patients étaient des adultes de sexe masculin dont l'âge moyen était de 31 ans. Dans 70% des cas, ces brûlures étaient secondaires à un contact avec les distributeurs d'électricité avec une surface brûlée inférieure à 20%. Le traitement des lésions électrothermiques a nécessité des interventions itératives avec amputation des segments de membres nécrosés dans 70% des cas, dont les suites étaient marquées par des séquelles fonctionnelles invalidantes. La prévention des AEHT, en particulier pour les accidents du travail au sein des professions exposées, reste fondamentale.

Effect of B-ring substitution pattern on binding mode of propionamide selective androgen receptor modulators.

PubMed

Bohl, Casey E; Wu, Zengru; Chen, Jiyun; Mohler, Michael L; Yang, Jun; Hwang, Dong Jin; Mustafa, Suni; Miller, Duane D; Bell, Charles E; Dalton, James T

2008-10-15

Selective androgen receptor modulators (SARMs) are essentially prostate sparing androgens, which provide therapeutic potential in osteoporosis, male hormone replacement, and muscle wasting. Herein we report crystal structures of the androgen receptor (AR) ligand-binding domain (LBD) complexed to a series of potent synthetic nonsteroidal SARMs with a substituted pendant arene referred to as the B-ring. We found that hydrophilic B-ring para-substituted analogs exhibit an additional region of hydrogen bonding not seen with steroidal compounds and that multiple halogen substitutions affect the B-ring conformation and aromatic interactions with Trp741. This information elucidates interactions important for high AR binding affinity and provides new insight for structure-based drug design.

Clinical evaluation of intensity-modulated radiotherapy for head and neck cancers

PubMed Central

Bhide, S A; Newbold, K L; Harrington, K J; Nutting, C M

2012-01-01

Radiotherapy and surgery are the principal curative modalities in treatment of head and neck cancer. Conventional two-dimensional and three-dimensional conformal radiotherapy result in significant side effects and altered quality of life. Intensity-modulated radiotherapy (IMRT) can spare the normal tissues, while delivering a curative dose to the tumour-bearing tissues. This article reviews the current role of IMRT in head and neck cancer from the point of view of normal tissue sparing, and also reviews the current published literature by individual head and neck cancer subsites. In addition, we briefly discuss the role of image guidance in head and neck IMRT, and future directions in this area. PMID:22556403

Comparison of the progressive resolution optimizer and photon optimizer in VMAT optimization for stereotactic treatments.

PubMed

Liu, Han; Sintay, Benjamin; Pearman, Keith; Shang, Qingyang; Hayes, Lane; Maurer, Jacqueline; Vanderstraeten, Caroline; Wiant, David

2018-05-20

The photon optimization (PO) algorithm was recently released by Varian Medical Systems to improve volumetric modulated arc therapy (VMAT) optimization within Eclipse (Version 13.5). The purpose of this study is to compare the PO algorithm with its predecessor, progressive resolution optimizer (PRO) for lung SBRT and brain SRS treatments. A total of 30 patients were selected retrospectively. Previously, all the plans were generated with the PRO algorithm within Eclipse Version 13.6. In the new version of PO algorithm (Version 15), dynamic conformal arcs (DCA) were first conformed to the target, then VMAT inverse planning was performed to achieve the desired dose distributions. PTV coverages were forced to be identical for the same patient for a fair comparison. SBRT plan quality was assessed based on selected dose-volume parameters, including the conformity index, V 20 for lung, V 30 Gy for chest wall, and D 0.035 cc for other critical organs. SRS plan quality was evaluated based on the conformity index and normal tissue volumes encompassed by the 12 and 6 Gy isodose lines (V 12 and V 6 ). The modulation complexity score (MCS) was used to compare plan complexity of two algorithms. No statistically significant differences between the PRO and PO algorithms were found for any of the dosimetric parameters studied, which indicates both algorithms produce comparable plan quality. Significant improvements in the gamma passing rate (increased from 97.0% to 99.2% for SBRT and 96.1% to 98.4% for SRS), MCS (average increase of 0.15 for SBRT and 0.10 for SRS), and delivery efficiency (MU reduction of 29.8% for SBRT and 28.3% for SRS) were found for the PO algorithm. MCS showed a strong correlation with the gamma passing rate, and an inverse correlation with total MUs used. The PO algorithm offers comparable plan quality to the PRO, while minimizing MLC complexity, thereby improving the delivery efficiency and accuracy. © 2018 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Effect of Urea on G-Quadruplex Stability.

PubMed

Aslanyan, Lusine; Ko, Jordan; Kim, Byul G; Vardanyan, Ishkhan; Dalyan, Yeva B; Chalikian, Tigran V

2017-07-13

G-quadruplexes represent a class of noncanonical nucleic acid structures implicated in transcriptional regulation, cellular function, and disease. An understanding of the forces involved in stabilization and destabilization of the G-quadruplex conformation relative to the duplex or single-stranded conformation is a key to elucidating the biological role of G-quadruplex-based genomic switches and the quest for therapeutic means for controlled induction or suppression of a G-quadruplex at selected genomic loci. Solute-solvent interactions provide a ubiquitous and, in many cases, the determining thermodynamic force in maintaining and modulating the stability of nucleic acids. These interactions involve water as well as water-soluble cosolvents that may be present in the solution or in the crowded environment in the cell. We present here the first quantitative investigation of the effect of urea, a destabilizing cosolvent, on the conformational preferences of a G-quadruplex formed by the telomeric d[A(G 3 T 2 A) 3 G 3 ] sequence (Tel22). At 20 mM NaCl and room temperature, Tel22 undergoes a two-state urea-induced unfolding transition. An increase in salt mitigates the deleterious effect of urea on Tel22. The urea m-value of Tel22 normalized per change in solvent-accessible surface area, ΔS A , is similar to those for other DNA and RNA structures while being several-fold larger than that of proteins. Our results suggest that urea can be employed as an analytical tool in thermodynamic characterizations of G-quadruplexes in a manner similar to the use of urea in protein studies. We emphasize the need for further studies involving a larger selection of G-quadruplexes varying in sequence, topology (parallel, antiparallel, hybrid), and molecularity (monomolecular, bimolecular, tetramolecular) to outline the advantages and the limits of the use of urea in G-quadruplex studies. A deeper understanding of the effect of solvent and cosolvents on the differential stability of the G-quadruplex and duplex conformations is a step toward elucidation of the modulating influence of different types of cosolvents on duplex-G-quadruplex molecular switches triggering genomic events.

Cation Coordination Alters the Conformation of a Thrombin-Binding G-Quadruplex DNA Aptamer That Affects Inhibition of Thrombin.

PubMed

Zavyalova, Elena; Tagiltsev, Grigory; Reshetnikov, Roman; Arutyunyan, Alexander; Kopylov, Alexey

2016-10-01

Thrombin-binding aptamers are promising anticoagulants. HD1 is a monomolecular antiparallel G-quadruplex with two G-quartets linked by three loops. Aptamer-thrombin interactions are mediated with two TT-loops that bind thrombin exosite I. Several cations were shown to be coordinated inside the G-quadruplex, including K + , Na + , NH 4 + , Ba 2+ , and Sr 2+ ; on the contrary, Mn 2+ was coordinated in the grooves, outside the G-quadruplex. K + or Na + coordination provides aptamer functional activity. The effect of other cations on aptamer functional activity has not yet been described, because of a lack of relevant tests. Interactions between aptamer HD1 and a series of cations were studied. A previously developed enzymatic method was applied to evaluate aptamer inhibitory activity. The structure-function correlation was studied using the characterization of G-quadruplex conformation by circular dichroism spectroscopy. K + coordination provided the well-known high inhibitory activity of the aptamer, whereas Na + coordination supported low activity. Although NH 4 + coordination yielded a typical antiparallel G-quadruplex, no inhibitory activity was shown; a similar effect was observed for Ba 2+ and Sr 2+ coordination. Mn 2+ coordination destabilized the G-quadruplex that drastically diminished aptamer inhibitory activity. Therefore, G-quadruplex existence per se is insufficient for aptamer inhibitory activity. To elicit the nature of these effects, we thoroughly analyzed nuclear magnetic resonance (NMR) and X-ray data on the structure of the HD1 G-quadruplex with various cations. The most reasonable explanation is that cation coordination changes the conformation of TT-loops, affecting thrombin binding and inhibition. HD1 counterparts, aptamers 31-TBA and NU172, behaved similarly with some distinctions. In 31-TBA, an additional duplex module stabilized antiparallel G-quadruplex conformation at high concentrations of divalent cations; whereas in NU172, a different sequence of loops in the G-quadruplex module provided an equilibrium of antiparallel and parallel G-quadruplexes that shifted with cation binding. In conclusion, structures of G-quadruplex aptamers are flexible enough and are fine-tuned with different cation coordination.

Chloride concentration affects Kv channel voltage-gating kinetics: Importance of experimental anion concentrations.

PubMed

Bekar, L K; Loewen, M E; Forsyth, G W; Walz, W

2005-09-30

Chloride concentration has been shown to have a dramatic impact on protein folding and subsequent tertiary conformation [K.D. Collins, Ions from the Hofmeister series and osmolytes: effects on proteins in solution and in the crystallization process, Methods 34 (2004) 300-311; I. Jelesarov, E. Durr, R.M. Thomas, H.R. Bosshard, Salt effects on hydrophobic interaction and charge screening in the folding of a negatively charged peptide to a coiled coil (leucine zipper), Biochemistry 37 (1998) 7539-7550]. As it is known that Kv channel gating is linked to the stability of the cytoplasmic T1 multimerization domain conformation [D.L. Minor, Y.F. Lin, B.C. Mobley, A. Avelar, Y.N. Jan, L.Y. Jan, J.M. Berger, The polar T1 interface is linked to conformational changes that open the voltage-gated potassium channel, Cell 102 (2000) 657-670; B.A. Yi, D.L. Minor Jr., Y.F. Lin, Y.N. Jan, L.Y. Jan, Controlling potassium channel activities: interplay between the membrane and intracellular factors, Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 11016-11023] and that intracellular chloride concentration has been linked to Kv channel kinetics [L.K. Bekar, W. Walz, Intracellular chloride modulates A-type potassium currents in astrocytes, Glia 39 (2002) 207-216; W.B. Thoreson, S.L. Stella, Anion modulation of calcium current voltage dependence and amplitude in salamander rods, Biochim. Biophys. Acta 1464 (2000) 142-150], the objective of the present study was to address how chloride concentration changes affect Kv channel kinetics more closely in an isolated expression system. Initially, no significant chloride concentration-dependent effects on channel steady-state gating kinetics were observed. Only after disruption of the cytoskeleton with cytochalasin-D did we see significant chloride concentration-dependent shifts in gating kinetics. This suggests that the shift in gating kinetics is mediated through effects of intracellular chloride concentration on cytoplasmic domain tertiary conformation as cytoskeletal interaction appears to mask the effect. Furthermore, as cytoskeletal disruption only impacts channel gating kinetics at low physiological intracellular chloride concentrations, these studies highlight the importance of paying close attention to anion concentrations used under experimental conditions.

Activation helix orientation of the estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations.

PubMed

Fratev, Filip

2015-05-28

In recent years, the nuclear receptors (NR) dynamics have been studied extensively by various approaches. However, the transition path of helix 12 (H12) to an agonist or an antagonist conformation and the exchange pathway between these states is not clear yet. A number of accelerated molecular dynamics (aMD) runs were performed on both an ERα monomer and a homodimer with a total length of 2.2 μs. We have been able to sample reasonably well the H12 conformational landscape to reproduce precisely both the agonist and the antagonist conformations, starting from an unfolded position, and to describe the transition path between them, even in the presence of an agonist ligand. These conformations were the most prevalent, suggesting that the extended H12 state is not likely to exist and that the natural ERα H12 position might exist in both the agonist and antagonist states. Remarkably, the H12 transition occurs and is regulated only in a dimer form and the proper agonist or antagonist H12 conformation can be achieved solely in one of the dimer subunits. These results clearly demonstrate that clusters of the two well-known H12 states exist by themselves in the protein free energy landscape, i.e. they are not constituted directly by the ligands, and dimerization favors the switch between them. Conversely, in a monomer, no transitions have been observed. Thus, the dimer formation helps the constitution of populations of discrete H12 conformational states and reshapes the conformational landscape. Further analyses have shown that these observations can be explained by specific interface and long range protein-protein interactions, resulting in conformational fluctuations in helices 5 and 11. Based on these results, a new ERα activation/deactivation mechanism and a sequence of binding events during receptor activity modulation have been suggested according to which ligands control the H12 conformation via alterations of the inter-dimer interactions. These findings agree with the HDX and fluorescence experiments and provide an explanation on a structural basis of these data, demonstrating that the dynamics of H12 are not altered greatly upon ligand binding and large fluctuations at the end of H11 are present.

On staggered indecomposable Virasoro modules

NASA Astrophysics Data System (ADS)

Kytölä, Kalle; Ridout, David

2009-12-01

In this article, certain indecomposable Virasoro modules are studied. Specifically, the Virasoro mode L0 is assumed to be nondiagonalizable, possessing Jordan blocks of rank 2. Moreover, the module is further assumed to have a highest weight submodule, the "left module," and that the quotient by this submodule yields another highest weight module, the "right module." Such modules, which have been called staggered, have appeared repeatedly in the logarithmic conformal field theory literature, but their theory has not been explored in full generality. Here, such a theory is developed for the Virasoro algebra using rather elementary techniques. The focus centers on two different but related questions typically encountered in practical studies: How can one identify a given staggered module, and how can one demonstrate the existence of a proposed staggered module. Given just the values of the highest weights of the left and right modules, themselves subject to simple necessary conditions, invariants are defined which together with the knowledge of the left and right modules uniquely identify a staggered module. The possible values of these invariants form a vector space of dimension 0, 1, or 2, and the structures of the left and right modules limit the isomorphism classes of the corresponding staggered modules to an affine subspace (possibly empty). The number of invariants and affine restrictions is purely determined by the structures of the left and right modules. Moreover, in order to facilitate applications, the expressions for the invariants and restrictions are given by formulas as explicit as possible (they generally rely on expressions for Virasoro singular vectors). Finally, the text is liberally peppered throughout with examples illustrating the general concepts. These have been carefully chosen for their physical relevance or for the novel features they exhibit.

Sequelles de Brulures au Centre Hospitalier Universitaire Ibn Rochd de Casablanca: Aspects Epidemio-Cliniques

PubMed Central

Chafiki, N.; Fassi Fihri, J.; Boukind, E.H.

2007-01-01

Summary Il s'agit d'une étude épidémiologique des séquelles de brûlures à propos de 100 cas colligés au service de chirurgie réparatrice et de brûlés du centre hospitalier universitaire Ibn Rochd (Casablanca). Les adultes représentent 55% de la population étudiée, l'âge moyen global est de 20 ans. Le sexe féminin est le plus touché avec 61% des cas. Les brûlures survenues à domicile sont les plus fréquentes avec 80%. L'agent causal le plus incriminé est la petite bouteille de butane avec 44,4%. Plus de la moitié de la population brûlée (55%) sont accueillis initialement au niveau d'hôpitaux régionaux. Le délai de cicatrisation moyen de 7 mois et 11 jours et par conséquent les séquelles mineures (dyschromie dans 90% des cas et prurit dans 49% des cas) et majeures (rétractions dans 86% et l'hypertrophie dans 51%) sont fréquentes. La répartition globale des séquelles montre une prédominance du segment cervicocéphalique avec 89% des cas et des membres supérieurs dans 82% des cas. Les différents aspects anatomocliniques essentiels ont été décrits au niveau de chaque segment corporel. Nos résultats ont été comparés aux données de la littérature, ce qui nous amène à considérer qu'une large campagne de prévention couplée à une meilleure prise en charge initiale, précoce, bien conduite et multidisciplinaire permet non seulement de réduire le nombre de séquelles mais aussi de diminuer leur sévérité. PMID:21991060

Aménorrhée chimio induite chez une population marocaine: à propos d'une cohorte retrospective

PubMed Central

Brahmi, Sami Aziz; Ziani, Fatima Zahra; Youssef, Seddik; Afqir, Said

2016-01-01

Introduction Le cancer du sein est un des cancers les plus fréquents chez la femme en pré ménopause et son traitement peut compromettre la fertilité. En effet, la chimiothérapie utilisée dans le cancer du sein peut conduire à une aménorrhée transitoire ou permanente chez les femmes non ménopausées. Méthodes Nous avons mené une étude rétrospective au service d'oncologie médicale du CHU Mohammed VI d'Oujda sur une période de 3 ans allant de janvier 2009 à décembre 2011 incluant les patientes jeunes ayant un cancer du sein localisé, pour étudier l'incidence de l'aménorrhée chimio-induite (ACI), ainsi que les facteurs prédictifs intervenant dans sa survenue. Résultats Dans notre série 74% de nos patientes ont présenté une ACI et 33.6% de nos patientes ont présenté une aménorrhée chimio-induite définitive. Plusieurs facteurs ont été étudiés à la recherche d’élément prédictifs de la survenue de l'aménorrhée. Concernant le facteur âge, l'analyse a montré que les femmes avec un âge supérieur à 40 ans étaient plus susceptibles de présenter une aménorrhée que celles avec un âge inférieur à 40 avec un pourcentage de 95,7% versus 56,1% avec une différence significative (p = 0.003). Conclusion L'incidence dans notre étude de l'ACI semble comparable à celle retrouvé dans la littérature, l’âge dans notre étude est le facteur prédictif le plus prédominant dans sa survenue. PMID:27642399

[Not Available].

PubMed

Chafiki, N; Fassi Fihri, J; Boukind, E H

2007-03-31

Il s'agit d'une étude épidémiologique des séquelles de brûlures à propos de 100 cas colligés au service de chirurgie réparatrice et de brûlés du centre hospitalier universitaire Ibn Rochd (Casablanca). Les adultes représentent 55% de la population étudiée, l'âge moyen global est de 20 ans. Le sexe féminin est le plus touché avec 61% des cas. Les brûlures survenues à domicile sont les plus fréquentes avec 80%. L'agent causal le plus incriminé est la petite bouteille de butane avec 44,4%. Plus de la moitié de la population brûlée (55%) sont accueillis initialement au niveau d'hôpitaux régionaux. Le délai de cicatrisation moyen de 7 mois et 11 jours et par conséquent les séquelles mineures (dyschromie dans 90% des cas et prurit dans 49% des cas) et majeures (rétractions dans 86% et l'hypertrophie dans 51%) sont fréquentes. La répartition globale des séquelles montre une prédominance du segment cervicocéphalique avec 89% des cas et des membres supérieurs dans 82% des cas. Les différents aspects anatomocliniques essentiels ont été décrits au niveau de chaque segment corporel. Nos résultats ont été comparés aux données de la littérature, ce qui nous amène à considérer qu'une large campagne de prévention couplée à une meilleure prise en charge initiale, précoce, bien conduite et multidisciplinaire permet non seulement de réduire le nombre de séquelles mais aussi de diminuer leur sévérité.

Volumetric-modulated arc therapy (RapidArc) vs. conventional fixed-field intensity-modulated radiotherapy for {sup 18}F-FDG-PET-guided dose escalation in oropharyngeal cancer: A planning study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teoh, May, E-mail: m.teoh@nhs.net; Beveridge, Sabeena; Wood, Katie

2013-04-01

Fluorine-18-fluorodeoxyglucose-positron emission tomography ({sup 18}F-FDG-PET)–guided focal dose escalation in oropharyngeal cancer may potentially improve local control. We evaluated the feasibility of this approach using volumetric-modulated arc therapy (RapidArc) and compared these plans with fixed-field intensity-modulated radiotherapy (IMRT) focal dose escalation plans. Materials and methods: An initial study of 20 patients compared RapidArc with fixed-field IMRT using standard dose prescriptions. From this cohort, 10 were included in a dose escalation planning study. Dose escalation was applied to {sup 18}F-FDG-PET–positive regions in the primary tumor at dose levels of 5% (DL1), 10% (DL2), and 15% (DL3) above standard radical dose (65 Gymore » in 30 fractions). Fixed-field IMRT and double-arc RapidArc plans were generated for each dataset. Dose-volume histograms were used for plan evaluation and comparison. The Paddick conformity index (CI{sub Paddick}) and monitor units (MU) for each plan were recorded and compared. Both IMRT and RapidArc produced clinically acceptable plans and achieved planning objectives for target volumes. Dose conformity was significantly better in the RapidArc plans, with lower CI{sub Paddick} scores in both primary (PTV1) and elective (PTV2) planning target volumes (largest difference in PTV1 at DL3; 0.81 ± 0.03 [RapidArc] vs. 0.77 ± 0.07 [IMRT], p = 0.04). Maximum dose constraints for spinal cord and brainstem were not exceeded in both RapidArc and IMRT plans, but mean doses were higher with RapidArc (by 2.7 ± 1 Gy for spinal cord and 1.9 ± 1 Gy for brainstem). Contralateral parotid mean dose was lower with RapidArc, which was statistically significant at DL1 (29.0 vs. 29.9 Gy, p = 0.01) and DL2 (29.3 vs. 30.3 Gy, p = 0.03). MU were reduced by 39.8–49.2% with RapidArc (largest difference at DL3, 641 ± 94 vs. 1261 ± 118, p < 0.01). {sup 18}F-FDG-PET–guided focal dose escalation in oropharyngeal cancer is feasible with RapidArc. Compared with conventional fixed-field IMRT, RapidArc can achieve better dose conformity, improve contralateral parotid sparing, and uses fewer MU.« less

Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bokoch, Michael P.; Zou, Yaozhong; Rasmussen, Søren G.F.

G-protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters. They are the largest group of therapeutic targets for a broad spectrum of diseases. Recent crystal structures of GPCRs have revealed structural conservation extending from the orthosteric ligand-binding site in the transmembrane core to the cytoplasmic G-protein-coupling domains. In contrast, the extracellular surface (ECS) of GPCRs is remarkably diverse and is therefore an ideal target for the discovery of subtype-selective drugs. However, little is known about the functional role of the ECS in receptor activation, or about conformational coupling of this surface to the nativemore » ligand-binding pocket. Here we use NMR spectroscopy to investigate ligand-specific conformational changes around a central structural feature in the ECS of the {beta}{sub 2} adrenergic receptor: a salt bridge linking extracellular loops 2 and 3. Small-molecule drugs that bind within the transmembrane core and exhibit different efficacies towards G-protein activation (agonist, neutral antagonist and inverse agonist) also stabilize distinct conformations of the ECS. We thereby demonstrate conformational coupling between the ECS and the orthosteric binding site, showing that drugs targeting this diverse surface could function as allosteric modulators with high subtype selectivity. Moreover, these studies provide a new insight into the dynamic behaviour of GPCRs not addressable by static, inactive-state crystal structures.« less

Stretching and Controlled Motion of Single-Stranded DNA in Locally-Heated Solid-State Nanopores

PubMed Central

Belkin, Maxim; Maffeo, Christopher; Wells, David B.

2013-01-01

Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated via a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4–8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA. PMID:23876013

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

PubMed Central

Lambrughi, Matteo; De Gioia, Luca; Gervasio, Francesco Luigi; Lindorff-Larsen, Kresten; Nussinov, Ruth; Urani, Chiara; Bruschi, Maurizio; Papaleo, Elena

2016-01-01

Binding-induced conformational changes of a protein at regions distant from the binding site may play crucial roles in protein function and regulation. The p53 tumour suppressor is an example of such an allosterically regulated protein. Little is known, however, about how DNA binding can affect distal sites for transcription factors. Furthermore, the molecular details of how a local perturbation is transmitted through a protein structure are generally elusive and occur on timescales hard to explore by simulations. Thus, we employed state-of-the-art enhanced sampling atomistic simulations to unveil DNA-induced effects on p53 structure and dynamics that modulate the recruitment of cofactors and the impact of phosphorylation at Ser215. We show that DNA interaction promotes a conformational change in a region 3 nm away from the DNA binding site. Specifically, binding to DNA increases the population of an occluded minor state at this distal site by more than 4-fold, whereas phosphorylation traps the protein in its major state. In the minor conformation, the interface of p53 that binds biological partners related to p53 transcription-independent functions is not accessible. Significantly, our study reveals a mechanism of DNA-mediated protection of p53 from interactions with partners involved in the p53 transcription-independent signalling. This also suggests that conformational dynamics is tightly related to p53 signalling. PMID:27604871

The structure of amylosucrase from Deinococcus radiodurans has an unusual open active-site topology.

PubMed

Skov, Lars K; Pizzut-Serin, Sandra; Remaud-Simeon, Magali; Ernst, Heidi A; Gajhede, Michael; Mirza, Osman

2013-09-01

Amylosucrases (ASes) catalyze the formation of an α-1,4-glucosidic linkage by transferring a glucosyl unit from sucrose onto an acceptor α-1,4-glucan. To date, several ligand-bound crystal structures of wild-type and mutant ASes from Neisseria polysaccharea and Deinococcus geothermalis have been solved. These structures all display a very similar overall conformation with a deep pocket leading to the site for transglucosylation, subsite -1. This has led to speculation on how sucrose enters the active site during glucan elongation. In contrast to previous studies, the AS structure from D. radiodurans presented here has a completely empty -1 subsite. This structure is strikingly different from other AS structures, as an active-site-lining loop comprising residues Leu214-Asn225 is found in a previously unobserved conformation. In addition, a large loop harbouring the conserved active-site residues Asp133 and Tyr136 is disordered. The result of the changed loop conformations is that the active-site topology is radically changed, leaving subsite -1 exposed and partially dismantled. This structure provides novel insights into the dynamics of ASes and comprises the first structural support for an elongation mechanism that involves considerable conformational changes to modulate accessibility to the sucrose-binding site and thereby allows successive cycles of glucosyl-moiety transfer to a growing glucan chain.

AnchorDock for Blind Flexible Docking of Peptides to Proteins.

PubMed

Slutzki, Michal; Ben-Shimon, Avraham; Niv, Masha Y

2017-01-01

Due to increasing interest in peptides as signaling modulators and drug candidates, several methods for peptide docking to their target proteins are under active development. The "blind" docking problem, where the peptide-binding site on the protein surface is unknown, presents one of the current challenges in the field. AnchorDock protocol was developed by Ben-Shimon and Niv to address this challenge.This protocol narrows the docking search to the most relevant parts of the conformational space. This is achieved by pre-folding the free peptide and by computationally detecting anchoring spots on the surface of the unbound protein. Multiple flexible simulated annealing molecular dynamics (SAMD) simulations are subsequently carried out, starting from pre-folded peptide conformations, constrained to the various precomputed anchoring spots.Here, AnchorDock is demonstrated using two known protein-peptide complexes. A PDZ-peptide complex provides a relatively easy case due to the relatively small size of the protein, and a typical peptide conformation and binding region; a more challenging example is a complex between USP7 N-term and a p53-derived peptide, where the protein is larger, and the peptide conformation and a binding site are generally assumed to be unknown. AnchorDock returned native-like solutions ranked first and third for the PDZ and USP7 complexes, respectively. We describe the procedure step by step and discuss possible modifications where applicable.

Unraveling HIV protease flaps dynamics by Constant pH Molecular Dynamics simulations.

PubMed

Soares, Rosemberg O; Torres, Pedro H M; da Silva, Manuela L; Pascutti, Pedro G

2016-08-01

The active site of HIV protease (HIV-PR) is covered by two flaps. These flaps are known to be essential for the catalytic activity of the HIV-PR, but their exact conformations at the different stages of the enzymatic pathway remain subject to debate. Understanding the correct functional dynamics of the flaps might aid the development of new HIV-PR inhibitors. It is known that, the HIV-PR catalytic efficiency is pH-dependent, likely due to the influence of processes such as charge transfer and protonation/deprotonation of ionizable residues. Several Molecular Dynamics (MD) simulations have reported information about the HIV-PR flaps. However, in MD simulations the protonation of a residue is fixed and thus it is not possible to study the correlation between conformation and protonation state. To address this shortcoming, this work attempts to capture, through Constant pH Molecular Dynamics (CpHMD), the conformations of the apo, substrate-bound and inhibitor-bound HIV-PR, which differ drastically in their flap arrangements. The results show that the HIV-PR flaps conformations are defined by the protonation of the catalytic residues Asp25/Asp25' and that these residues are sensitive to pH changes. This study suggests that the catalytic aspartates can modulate the opening of the active site and substrate binding. Copyright © 2016 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Yang; Glover, Karen; Su, Minfei

BECN1 (Beclin 1), a highly conserved eukaryotic protein, is a key regulator of autophagy, a cellular homeostasis pathway, and also participates in vacuolar protein sorting, endocytic trafficking, and apoptosis. BECN1 is important for embryonic development, the innate immune response, tumor suppression, and protection against neurodegenerative disorders, diabetes, and heart disease. BECN1 mediates autophagy as a core component of the class III phosphatidylinositol 3-kinase complexes. However, the exact mechanism by which it regulates the activity of these complexes, or mediates its other diverse functions is unclear. BECN1 interacts with several diverse protein partners, perhaps serving as a scaffold or interaction hubmore » for autophagy. Based on extensive structural, biophysical and bioinformatics analyses, BECN1 consists of an intrinsically disordered region (IDR), which includes a BH3 homology domain (BH3D); a flexible helical domain (FHD); a coiled-coil domain (CCD); and a β-α-repeated autophagy-specific domain (BARAD). Each of these BECN1 domains mediates multiple diverse interactions that involve concomitant conformational changes. Thus, BECN1 conformational flexibility likely plays a key role in facilitating diverse protein interactions. Further, BECN1 conformation and interactions are also modulated by numerous post-translational modifications. A better structure-based understanding of the interplay between different BECN1 conformational and binding states, and the impact of post-translational modifications will be essential to elucidating the mechanism of its multiple biological roles.« less

Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling

PubMed Central

Gadkari, Varun V; Harvey, Sophie R; Raper, Austin T; Chu, Wen-Ting; Wang, Jin; Wysocki, Vicki H; Suo, Zucai

2018-01-01

Abstract Proliferating cell nuclear antigen (PCNA) is a trimeric ring-shaped clamp protein that encircles DNA and interacts with many proteins involved in DNA replication and repair. Despite extensive structural work to characterize the monomeric, dimeric, and trimeric forms of PCNA alone and in complex with interacting proteins, no structure of PCNA in a ring-open conformation has been published. Here, we use a multidisciplinary approach, including single-molecule Förster resonance energy transfer (smFRET), native ion mobility-mass spectrometry (IM-MS), and structure-based computational modeling, to explore the conformational dynamics of a model PCNA from Sulfolobus solfataricus (Sso), an archaeon. We found that Sso PCNA samples ring-open and ring-closed conformations even in the absence of its clamp loader complex, replication factor C, and transition to the ring-open conformation is modulated by the ionic strength of the solution. The IM-MS results corroborate the smFRET findings suggesting that PCNA dynamics are maintained in the gas phase and further establishing IM-MS as a reliable strategy to investigate macromolecular motions. Our molecular dynamic simulations agree with the experimental data and reveal that ring-open PCNA often adopts an out-of-plane left-hand geometry. Collectively, these results implore future studies to define the roles of PCNA dynamics in DNA loading and other PCNA-mediated interactions. PMID:29529283

Probing Vitamine C, Aspirin and Paracetamol in the Gas Phase: High Resolution Rotational Studies

NASA Astrophysics Data System (ADS)

Mata, S.; Cabezas, C.; Varela, M.; Pena, I.; Nino, A.; López, J. C.; Alonso, J. L.; Grabow, J.-U.

2011-06-01

A solid sample of Vitamin C (m.p. 190°C) vaporized by laser ablation has been investigated in gas phase and characterized through their rotational spectra. Two spectroscopy techniques has been used to obtain the spectra: a new design of broadband chirped pulse Fourier transform microwave spectroscopy with in-phase/quadrature-phase-modulation passage-acquired-coherence technique (IMPACT) and conventional laser ablation molecular beam Fourier transform microwave spectroscopy (LA-MB-FTMW). Up to now, two low-energy conformer have been observed and their rotational constants determined. Ab initio calculations at the MP2/6-311++G (d,p) level of theory predicted rotational constants which helped us to identify these conformers unequivocally. Among the molecules to benefit from the LA-MB-FTMW technique there are common important drugs never observed in the gas phase through rotational spectroscopy. We present here the results on acetyl salicylic acid and acetaminophen (m.p. 136°C), commonly known as aspirin and paracetamol respectively. We have observed two stable conformers of aspirin and two for paracetamol. The internal rotation barrier of the methyl group in aspirin has been determined for both conformers from the analysis of the A-E splittings due to the coupling of internal and overall rotation. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys. Chem. Chem. Phys. 11,617-627 (2009)and references therein

The Autism Diagnostic Observation Schedule, Module 4: Application of the Revised Algorithms in an Independent, Well-Defined, Dutch Sample (n = 93).

PubMed

de Bildt, Annelies; Sytema, Sjoerd; Meffert, Harma; Bastiaansen, Jojanneke A C J

2016-01-01

This study examined the discriminative ability of the revised Autism Diagnostic Observation Schedule module 4 algorithm (Hus and Lord in J Autism Dev Disord 44(8):1996-2012, 2014) in 93 Dutch males with Autism Spectrum Disorder (ASD), schizophrenia, psychopathy or controls. Discriminative ability of the revised algorithm ASD cut-off resembled the original algorithm ASD cut-off: highly specific for psychopathy and controls, lower sensitivity than Hus and Lord (2014; i.e. ASD .61, AD .53). The revised algorithm AD cut-off improved sensitivity over the original algorithm. Discriminating ASD from schizophrenia was still challenging, but the better-balanced sensitivity (.53) and specificity (.78) of the revised algorithm AD cut-off may aide clinicians' differential diagnosis. Findings support using the revised algorithm, being conceptually conform the other modules, thus improving comparability across the lifespan.

Structural Basis for Prereceptor Modulation of Plant Hormones by GH3 Proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Westfall, Corey S.; Zubieta, Chloe; Herrmann, Jonathan

Acyl acid amido synthetases of the GH3 family act as critical prereceptor modulators of plant hormone action; however, the molecular basis for their hormone selectivity is unclear. Here, we report the crystal structures of benzoate-specific Arabidopsis thaliana AtGH3.12/PBS3 and jasmonic acid-specific AtGH3.11/JAR1. These structures, combined with biochemical analysis, define features for the conjugation of amino acids to diverse acyl acid substrates and highlight the importance of conformational changes in the carboxyl-terminal domain for catalysis. We also identify residues forming the acyl acid binding site across the GH3 family and residues critical for amino acid recognition. Our results demonstrate how amore » highly adaptable three-dimensional scaffold is used for the evolution of promiscuous activity across an enzyme family for modulation of plant signaling molecules.« less

A synthetic intrabody-based selective and generic inhibitor of GPCR endocytosis

NASA Astrophysics Data System (ADS)

Ghosh, Eshan; Srivastava, Ashish; Baidya, Mithu; Kumari, Punita; Dwivedi, Hemlata; Nidhi, Kumari; Ranjan, Ravi; Dogra, Shalini; Koide, Akiko; Yadav, Prem N.; Sidhu, Sachdev S.; Koide, Shohei; Shukla, Arun K.

2017-12-01

Beta-arrestins (βarrs) critically mediate desensitization, endocytosis and signalling of G protein-coupled receptors (GPCRs), and they scaffold a large number of interaction partners. However, allosteric modulation of their scaffolding abilities and direct targeting of their interaction interfaces to modulate GPCR functions selectively have not been fully explored yet. Here we identified a series of synthetic antibody fragments (Fabs) against different conformations of βarrs from phage display libraries. Several of these Fabs allosterically and selectively modulated the interaction of βarrs with clathrin and ERK MAP kinase. Interestingly, one of these Fabs selectively disrupted βarr-clathrin interaction, and when expressed as an intrabody, it robustly inhibited agonist-induced endocytosis of a broad set of GPCRs without affecting ERK MAP kinase activation. Our data therefore demonstrate the feasibility of selectively targeting βarr interactions using intrabodies and provide a novel framework for fine-tuning GPCR functions with potential therapeutic implications.

Role for the MED21-MED7 Hinge in Assembly of the Mediator-RNA Polymerase II Holoenzyme*

PubMed Central

Sato, Shigeo; Tomomori-Sato, Chieri; Tsai, Kuang-Lei; Yu, Xiaodi; Sardiu, Mihaela; Saraf, Anita; Washburn, Michael P.; Florens, Laurence; Asturias, Francisco J.; Conaway, Ronald C.

2016-01-01

Mediator plays an integral role in activation of RNA polymerase II (Pol II) transcription. A key step in activation is binding of Mediator to Pol II to form the Mediator-Pol II holoenzyme. Here, we exploit a combination of biochemistry and macromolecular EM to investigate holoenzyme assembly. We identify a subset of human Mediator head module subunits that bind Pol II independent of other subunits and thus probably contribute to a major Pol II binding site. In addition, we show that binding of human Mediator to Pol II depends on the integrity of a conserved “hinge” in the middle module MED21-MED7 heterodimer. Point mutations in the hinge region leave core Mediator intact but lead to increased disorder of the middle module and markedly reduced affinity for Pol II. These findings highlight the importance of Mediator conformation for holoenzyme assembly. PMID:27821593

Volumetric modulated arc therapy: a review of current literature and clinical use in practice

PubMed Central

Teoh, M; Clark, C H; Wood, K; Whitaker, S; Nisbet, A

2011-01-01

Volumetric modulated arc therapy (VMAT) is a novel radiation technique, which can achieve highly conformal dose distributions with improved target volume coverage and sparing of normal tissues compared with conventional radiotherapy techniques. VMAT also has the potential to offer additional advantages, such as reduced treatment delivery time compared with conventional static field intensity modulated radiotherapy (IMRT). The clinical worldwide use of VMAT is increasing significantly. Currently the majority of published data on VMAT are limited to planning and feasibility studies, although there is emerging clinical outcome data in several tumour sites. This article aims to discuss the current use of VMAT techniques in practice and review the available data from planning and clinical outcome studies in various tumour sites including prostate, pelvis (lower gastrointestinal, gynaecological), head and neck, thoracic, central nervous system, breast and other tumour sites. PMID:22011829

Differential operators on the supercircle S1|2 and symbol map

NASA Astrophysics Data System (ADS)

Hamza, Raouafi; Selmi, Zeineb; Boujelben, Jamel

2017-09-01

We consider the supercircle S1|2 equipped with the standard contact structure. The conformal Lie superalgebra 𝒦(2) acts on S1|2 as the Lie superalgebra of contact vector fields; it contains the Möbius superalgebra 𝔬𝔰𝔭(2|2). We study the space of linear differential operators on weighted densities as a module over 𝔬𝔰𝔭(2|2). We introduce the canonical isomorphism between this space and the corresponding space of symbols. This result allows us to give, in contrast to the classical setting, a classification of the 𝒦(2)-modules 𝔇λ,μk of linear differential operators of order k acting on the superspaces of weighted densities. This work is the simplest superization of a result by Gargoubi and Ovsienko [Modules of differential operators on the real line, Funct. Anal. Appl. 35(1) (2001) 13-18.

Reconstruction de la surface de Fermi dans l'etat normal d'un supraconducteur a haute Tc: Une etude du transport electrique en champ magnetique intense

NASA Astrophysics Data System (ADS)

Le Boeuf, David

Des mesures de resistance longitudinale et de resistance de Hall en champ magnetique intense transverse (perpendiculaire aux plans CuO2) ont ete effectuees au sein de monocristaux de YBa2Cu3Oy (YBCO) demacles, ordonnes et de grande purete, afin d'etudier l'etat fondamental des supraconducteurs a haute Tc dans le regime sous-dope. Cette etude a ete realisee en fonction du dopage et de l'orientation du courant d'excitation J par rapport a l'axe orthorhombique b de la structure cristalline. Les mesures en champ magnetique intense revelent par suppression de la supraconductivite des oscillations magnetiques des resistances longitudinale et de Hall dans YBa2Cu 3O6.51 et YBa2Cu4O8. La conformite du comportement de ces oscillations quantiques au formalisme de Lifshitz-Kosevich, apporte la preuve de l'existence d'une surface de Fermi fermee a caractere quasi-2D, abritant des quasiparticules coherentes respectant la statistique de Fermi-Dirac, dans la phase pseudogap d'YBCO. La faible frequence des oscillations quantiques, combinee avec l'etude de la partie monotone de la resistance de Hall en fonction de la temperature indique que la surface de Fermi d'YBCO sous-dope comprend une petite poche de Fermi occupee par des porteurs de charge negative. Cette particularite de la surface de Fermi dans le regime sous-dope incompatible avec les calculs de structure de bande est en fort contraste avec la structure electronique presente dans le regime surdope. Cette observation implique ainsi l'existence d'un point critique quantique dans le diagramme de phase d'YBCO, au voisinage duquel la surface de Fermi doit subir une reconstruction induite par l'etablissement d'une brisure de la symetrie de translation du reseau cristallin sous-jacent. Enfin, l'etude en fonction du dopage de la resistance de Hall et de la resistance longitudinale en champ magnetique intense suggere qu'un ordre du type onde de densite (DW) est responsable de la reconstruction de la surface de Fermi. L'analogie de la phenomenologie entourant le comportement des resistances longitudinale et de Hall dans YBa2Cu3Oy, avec des systemes dans lesquels l'existence d'un ordre du type DW est etablie, notamment des cuprates a structure tetragonale a basse temperature ("Low Temperature Tetragonal", LTT), indique que l'ordre causant la reconstruction de la surface de Fermi est stabilise au voisinage du dopage p = 1/8, et est en competition directe avec la supraconductivite.

Effets des electrons secondaires sur l'ADN

NASA Astrophysics Data System (ADS)

Boudaiffa, Badia

Les interactions des electrons de basse energie (EBE) representent un element important en sciences des radiations, particulierement, les sequences se produisant immediatement apres l'interaction de la radiation ionisante avec le milieu biologique. Il est bien connu que lorsque ces radiations deposent leur energie dans la cellule, elles produisent un grand nombre d'electrons secondaires (4 x 104/MeV), qui sont crees le long de la trace avec des energies cinetiques initiales bien inferieures a 20 eV. Cependant, il n'y a jamais eu de mesures directes demontrant l'interaction de ces electrons de tres basse energie avec l'ADN, du principalement aux difficultes experimentales imposees par la complexite du milieu biologique. Dans notre laboratoire, les dernieres annees ont ete consacrees a l'etude des phenomenes fondamentaux induits par impact des EBE sur differentes molecules simples (e.g., N2, CO, O2, H2O, NO, C2H 4, C6H6, C2H12) et quelques molecules complexes dans leur phase solide. D'autres travaux effectues recemment sur des bases de l'ADN et des oligonucleotides ont montre que les EBE produisent des bris moleculaires sur les biomolecules. Ces travaux nous ont permis d'elaborer des techniques pour mettre en evidence et comprendre les interactions fondamentales des EBE avec des molecules d'interet biologique, afin d'atteindre notre objectif majeur d'etudier l'effet direct de ces particules sur la molecule d'ADN. Les techniques de sciences des surfaces developpees et utilisees dans les etudes precitees peuvent etre etendues et combinees avec des methodes classiques de biologie pour etudier les dommages de l'ADN induits par l'impact des EBE. Nos experiences ont montre l'efficacite des electrons de 3--20 eV a induire des coupures simple et double brins dans l'ADN. Pour des energies inferieures a 15 eV, ces coupures sont induites par la localisation temporaire d'un electron sur une unite moleculaire de l'ADN, ce qui engendre la formation d'un ion negatif transitoire dans un etat electronique dissociatif, cette localisation est suivie d'une fragmentation. A plus haute energie, la dissociation dipolaire (i.e., la formation simultanee d'un ion positif et negatif) et l'ionisation jouent un role important dans le dommage de l'ADN. L'ensemble de nos resultats permet d'expliquer les mecanismes de degradation de l'ADN par les EBE et d'obtenir des sections efficaces effectives des differents types de dommages.

Apport de l'orientation clinique dans le diagnostic des hypertensions arterielles endocriniennes

PubMed Central

El Aziz, Siham; Chadli, Asma; Louda, Fatima; El Ghomari, Hassan; Farouqi, Ahmed

2014-01-01

L'hypertension artérielle d'origine endocrinienne représente une cause curable d'hypertension artérielle (HTA), ce qui en justifie le dépistage. Une orientation clinique est souhaitable afin de prescrire les bilans adéquats, notamment dans les pays en voie de développement. L'objectif de notre étude est décrire les aspects cliniques des patients ayant une HTA endocrinienne diagnostiquée au CHU de Casablanca. Méthodes: Il s'agit d'une étude descriptive rétrospective de 2004 à 2011, incluant tout patient ayant une HTA endocrinienne (en dehors des dysthyroïdies) admis en Endocrinologie. Les données concernant les facteurs cliniques, paracliniques et thérapeutiques ont été colligées. Au cours de la période étudiée, 53 cas d'HTA endocrinienne ont été admis, avec une age moyen au diagnostic de 39,3 ans et un sex-ratio F/H de 3,9. Trente patients (56.6%) ont un age ont un âge inférieur à 40 ans. On ne retrouve pas d'hérédité tensionelle chez 88.7% des patients. Les étiologies sont le Syndrome de cushing (41.5%), le phéochromocytome (32%), les adénomes somatotropes (15%) et les hyperaldostéronismes primaire (7.5%). L'HTA est essentiellement de grade un ou deux (69.8%), avec un retentissement cardio-vasculaire chez 11 patients (20.7%). Les patients ayant un SC avaient tous des signes cutanés spécifiques. Il s'agissait de sujets jeunes avec plusieurs facteurs de risque cardiovasculaire. Nous avons retrouvé un amaigrissement chez 37.5% des patients ayant un phéochromocytome avec un indice de masse corporel moyen de 20 kg/m2. L'HTA était permanente dans 5 cas de phéochromocytomes. Il n'existait pas d'hypokaliémie chez 50% des patients ayant un hyperaldostéronisme. Les signes cliniques des patients ayant une acromégalie étaient francs, avec un age moyen plus élevé de 50 ans. Nous avons noté une régression de l'HTA chez 59% de ces patients après guérison de l'endocrinopathie en cause. Plusieurs signes cliniques peuvent nous orienter vers une HTA endocrinienne, notamment chez l'adulte jeune, et devraient indiquer les bilans adéquats afin d’éviter une méconnaissance du diagnostic. PMID:25422689

"Click" saccharide/beta-lactam hybrids for lectin inhibition.

PubMed

Palomo, Claudio; Aizpurua, Jesus M; Balentová, Eva; Azcune, Itxaso; Santos, J Ignacio; Jiménez-Barbero, Jesús; Cañada, Javier; Miranda, José Ignacio

2008-06-05

Hybrid glycopeptide beta-lactam mimetics designed to bind lectins or carbohydrate recognition domains in selectins have been prepared according to a "shape-modulating linker" design. This approach was implemented using the azide-alkyne "click" cycloaddition reaction, and as shown by NMR/MD experiments, binding of the resulting mimetics to Ulex Europaeus Lectin-1 (UEL-1) occurred after a "bent-to-extended" conformational change around a partially rotatable triazolylmethylene moiety.

Intensity-modulated radiotherapy in the standard management of head and neck cancer: promises and pitfalls.

PubMed

Mendenhall, William M; Amdur, Robert J; Palta, Jatinder R

2006-06-10

The purpose of this article is to review the role of intensity-modulated radiotherapy (IMRT) in the standard management of patients with head and neck cancer through a critical review of the pertinent literature. IMRT may result in a dose distribution that is more conformal than that achieved with three-dimensional conformal radiotherapy (3D CRT), allowing dose reduction to normal structures and thus decreasing toxicity and possibly enhancing locoregional control through dose escalation. Disadvantages associated with IMRT include increased risk of a marginal miss, decreased dose homogeneity, increased total body dose, and increased labor and expense. Outcomes data after IMRT are limited, and follow-up is relatively short. Locoregional control rates appear to be comparable to those achieved with 3D CRT and, depending on the location and extent of the tumor, late toxicity may be lower. Despite limited data on clinical outcomes, IMRT has been widely adopted as a standard technique in routine practice and clinical trials. The use of IMRT involves a learning curve for the practitioner and will continue to evolve, requiring continuing education and monitoring of outcomes from routine practice. Additional standards pertaining to a variety of issues, including target definitions and dose specification, need to be developed. Phase III trials will better define the role of IMRT in coming years.

The chaperonin CCT inhibits assembly of α-synuclein amyloid fibrils by a specific, conformation-dependent interaction

PubMed Central

Sot, Begoña; Rubio-Muñoz, Alejandra; Leal-Quintero, Ahudrey; Martínez-Sabando, Javier; Marcilla, Miguel; Roodveldt, Cintia; Valpuesta, José M.

2017-01-01

The eukaryotic chaperonin CCT (chaperonin containing TCP-1) uses cavities built into its double-ring structure to encapsulate and to assist folding of a large subset of proteins. CCT can inhibit amyloid fibre assembly and toxicity of the polyQ extended mutant of huntingtin, the protein responsible for Huntington’s disease. This raises the possibility that CCT modulates other amyloidopathies, a still-unaddressed question. We show here that CCT inhibits amyloid fibre assembly of α-synuclein A53T, one of the mutants responsible for Parkinson’s disease. We evaluated fibrillation blockade in α-synuclein A53T deletion mutants and CCT interactions of full-length A53T in distinct oligomeric states to define an inhibition mechanism specific for α-synuclein. CCT interferes with fibre assembly by interaction of its CCTζ and CCTγ subunits with the A53T central hydrophobic region (NAC). This interaction is specific to NAC conformation, as it is produced once soluble α-synuclein A53T oligomers form and blocks the reaction before fibres begin to grow. Finally, we show that this association inhibits α-synuclein A53T oligomer toxicity in neuroblastoma cells. In summary, our results and those for huntingtin suggest that CCT is a general modulator of amyloidogenesis via a specific mechanism. PMID:28102321

Endoxifen, 4-Hydroxytamoxifen and an Estrogenic Derivative Modulate Estrogen Receptor Complex Mediated Apoptosis in Breast Cancer.

PubMed

Maximov, Philipp Y; Abderrahman, Balkees; Fanning, Sean W; Sengupta, Surojeet; Fan, Ping; Curpan, Ramona F; Quintana Rincon, Daniela Maria; Greenland, Jeffery A; Rajan, Shyamala S; Greene, Geoffrey L; Jordan, V Craig

2018-05-08

Estrogen therapy was used to treat advanced breast cancer in postmenopausal women for decades until the introduction of tamoxifen. Resistance to long-term estrogen deprivation (LTED) with tamoxifen and aromatase inhibitors used as a treatment for breast cancer inevitably occurs, but unexpectedly low dose estrogen can cause regression of breast cancer and increase disease free survival in some patients. This therapeutic effect is attributed to estrogen-induced apoptosis in LTED breast cancer. Here we describe modulation of the estrogen receptor liganded with antiestrogens (endoxifen, 4-hydroxytamoxifen) and an estrogenic triphenylethylene (TPE) EthoxyTPE (EtOXTPE) on estrogen-induced apoptosis in LTED breast cancer cells. Our results show that the angular TPE estrogen (EtOXTPE) is able to induce the ER-mediated apoptosis only at a later time compared to planar estradiol in these cells. Using RT-PCR, ChIP, Western blotting, molecular modelling and X-ray crystallography techniques we report novel conformations of the ER complex with an angular estrogen EtOXTPE and endoxifen. We propose that alteration of the conformation of the ER complexes, with changes in coactivator binding, governs estrogen-induced apoptosis through the PERK sensor system to trigger an Unfolded Protein Response (UPR). The American Society for Pharmacology and Experimental Therapeutics.

Modulating the Intrinsic Disorder in the Cytoplasmic Domain Alters the Biological Activity of the N-Methyl-d-aspartate-sensitive Glutamate Receptor*

PubMed Central

Choi, Ucheor B.; Kazi, Rashek; Stenzoski, Natalie; Wollmuth, Lonnie P.; Uversky, Vladimir N.; Bowen, Mark E.

2013-01-01

The NMDA-sensitive glutamate receptor is a ligand-gated ion channel that mediates excitatory synaptic transmission in the nervous system. Extracellular zinc allosterically regulates the NMDA receptor by binding to the extracellular N-terminal domain, which inhibits channel gating. Phosphorylation of the intrinsically disordered intracellular C-terminal domain alleviates inhibition by extracellular zinc. The mechanism for this functional effect is largely unknown. Proline is a hallmark of intrinsic disorder, so we used proline mutagenesis to modulate disorder in the cytoplasmic domain. Proline depletion selectively uncoupled zinc inhibition with little effect on receptor biogenesis, surface trafficking, or ligand-activated gating. Proline depletion also reduced the affinity for a PDZ domain involved in synaptic trafficking and affected small molecule binding. To understand the origin of these phenomena, we used single molecule fluorescence and ensemble biophysical methods to characterize the structural effects of proline mutagenesis. Proline depletion did not eliminate intrinsic disorder, but the underlying conformational dynamics were changed. Thus, we altered the form of intrinsic disorder, which appears sufficient to affect the biological activity. These findings suggest that conformational dynamics within the intrinsically disordered cytoplasmic domain are important for the allosteric regulation of NMDA receptor gating. PMID:23782697

W-band PELDOR with 1 kW microwave power: molecular geometry, flexibility and exchange coupling.

PubMed

Reginsson, Gunnar W; Hunter, Robert I; Cruickshank, Paul A S; Bolton, David R; Sigurdsson, Snorri Th; Smith, Graham M; Schiemann, Olav

2012-03-01

A technique that is increasingly being used to determine the structure and conformational flexibility of biomacromolecules is Pulsed Electron-Electron Double Resonance (PELDOR or DEER), an Electron Paramagnetic Resonance (EPR) based technique. At X-band frequencies (9.5 GHz), PELDOR is capable of precisely measuring distances in the range of 1.5-8 nm between paramagnetic centres but the orientation selectivity is weak. In contrast, working at higher frequencies increases the orientation selection but usually at the expense of decreased microwave power and PELDOR modulation depth. Here it is shown that a home-built high-power pulsed W-band EPR spectrometer (HiPER) with a large instantaneous bandwidth enables one to achieve PELDOR data with a high degree of orientation selectivity and large modulation depths. We demonstrate a measurement methodology that gives a set of PELDOR time traces that yield highly constrained data sets. Simulating the resulting time traces provides a deeper insight into the conformational flexibility and exchange coupling of three bisnitroxide model systems. These measurements provide strong evidence that W-band PELDOR may prove to be an accurate and quantitative tool in assessing the relative orientations of nitroxide spin labels and to correlate those orientations to the underlying biological structure and dynamics. Copyright © 2012 Elsevier Inc. All rights reserved.

Docking, thermodynamics and molecular dynamics (MD) studies of a non-canonical protease inhibitor, MP-4, from Mucuna pruriens.

PubMed

Kumar, Ashish; Kaur, Harmeet; Jain, Abha; Nair, Deepak T; Salunke, Dinakar M

2018-01-12

Sequence and structural homology suggests that MP-4 protein from Mucuna pruriens belongs to Kunitz-type protease inhibitor family. However, biochemical assays showed that this protein is a poor inhibitor of trypsin. To understand the basis of observed poor inhibition, thermodynamics and molecular dynamics (MD) simulation studies on binding of MP-4 to trypsin were carried out. Molecular dynamics simulations revealed that temperature influences the spectrum of conformations adopted by the loop regions in the MP-4 structure. At an optimal temperature, MP-4 achieves maximal binding while above and below the optimum temperature, its functional activity is hampered due to unfavourable flexibility and relative rigidity, respectively. The low activity at normal temperature is due to the widening of the conformational spectrum of the Reactive Site Loop (RSL) that reduces the probability of formation of stabilizing contacts with trypsin. The unique sequence of the RSL enhances flexibility at ambient temperature and thus reduces its ability to inhibit trypsin. This study shows that temperature influences the function of a protein through modulation in the structure of functional domain of the protein. Modulation of function through appearance of new sequences that are more sensitive to temperature may be a general strategy for evolution of new proteins.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dirix, Piet, E-mail: piet.dirix@uzleuven.b; Vanstraelen, Bianca; Jorissen, Mark

Purpose: To evaluate clinical outcome and toxicity of postoperative intensity-modulated radiotherapy (IMRT) for malignancies of the nasal cavity and paranasal sinuses. Methods and Materials: Between 2003 and 2008, 40 patients with cancer of the paranasal sinuses (n = 34) or nasal cavity (n = 6) received postoperative IMRT to a dose of 60 Gy (n = 21) or 66 Gy (n = 19). Treatment outcome and toxicity were retrospectively compared with that of a previous patient group (n = 41) who were also postoperatively treated to the same doses but with three-dimensional conformal radiotherapy without intensity modulation, from 1992 tomore » 2002. Results: Median follow-up was 30 months (range, 4-74 months). Two-year local control, overall survival, and disease-free survival were 76%, 89%, and 72%, respectively. Compared to the three-dimensional conformal radiotherapy treatment, IMRT resulted in significantly improved disease-free survival (60% vs. 72%; p = 0.02). No grade 3 or 4 toxicity was reported in the IMRT group, either acute or chronic. The use of IMRT significantly reduced the incidence of acute as well as late side effects, especially regarding skin toxicity, mucositis, xerostomia, and dry-eye syndrome. Conclusions: Postoperative IMRT for sinonasal cancer significantly improves disease-free survival and reduces acute as well as late toxicity. Consequently, IMRT should be considered the standard treatment modality for malignancies of the nasal cavity and paranasal sinuses.« less

Variation of the chemical reactivity of Thermus thermophilus HB8 ribosomal proteins as a function of pH.

PubMed

Running, William E; Reilly, James P

2010-10-01

Ribosomes occupy a central position in cellular metabolism, converting stored genetic information into active cellular machinery. Ribosomal proteins modulate both the intrinsic function of the ribosome and its interaction with other cellular complexes, such as chaperonins or the signal recognition particle. Chemical modification of proteins combined with mass spectrometric detection of the extent and position of covalent modifications is a rapid, sensitive method for the study of protein structure and flexibility. By altering the pH of the solution, we have induced non-denaturing changes in the structure of bacterial ribosomal proteins and detected these conformational changes by covalent labeling. Changes in ribosomal protein modification across a pH range from 6.6 to 8.3 are unique to each protein, and correlate with their structural environment in the ribosome. Lysine residues whose extent of modification increases as a function of increasing pH are on the surface of proteins, but in close proximity either to glutamate and aspartate residues, or to rRNA backbone phosphates. Increasing pH disrupts tertiary and quaternary interactions mediated by hydrogen bonding or ionic interactions, and regions of protein structure whose conformations are sensitive to these changes are of potential importance in modulating the flexibility of the ribosome or its interaction with other cellular complexes.

NFκB is a central regulator of protein quality control in response to protein aggregation stresses via autophagy modulation

PubMed Central

Nivon, Mathieu; Fort, Loïc; Muller, Pascale; Richet, Emma; Simon, Stéphanie; Guey, Baptiste; Fournier, Maëlenn; Arrigo, André-Patrick; Hetz, Claudio; Atkin, Julie D.; Kretz-Remy, Carole

2016-01-01

During cell life, proteins often misfold, depending on particular mutations or environmental changes, which may lead to protein aggregates that are toxic for the cell. Such protein aggregates are the root cause of numerous diseases called “protein conformational diseases,” such as myofibrillar myopathy and familial amyotrophic lateral sclerosis. To fight against aggregates, cells are equipped with protein quality control mechanisms. Here we report that NFκB transcription factor is activated by misincorporation of amino acid analogues into proteins, inhibition of proteasomal activity, expression of the R120G mutated form of HspB5 (associated with myofibrillar myopathy), or expression of the G985R and G93A mutated forms of superoxide dismutase 1 (linked to familial amyotrophic lateral sclerosis). This noncanonical stimulation of NFκB triggers the up-regulation of BAG3 and HspB8 expression, two activators of selective autophagy, which relocalize to protein aggregates. Then NFκB-dependent autophagy allows the clearance of protein aggregates. Thus NFκB appears as a central and major regulator of protein aggregate clearance by modulating autophagic activity. In this context, the pharmacological stimulation of this quality control pathway might represent a valuable strategy for therapies against protein conformational diseases. PMID:27075172

Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations.

PubMed

Jiang, Jun; Aduri, Raviprasad; Chow, Christine S; SantaLucia, John

2014-04-01

Helix 69 (H69) is a 19-nt stem-loop region from the large subunit ribosomal RNA. Three pseudouridine (Ψ) modifications clustered in H69 are conserved across phylogeny and known to affect ribosome function. To explore the effects of Ψ on the conformations of Escherichia coli H69 in solution, nuclear magnetic resonance spectroscopy was used to reveal the structural differences between H69 with (ΨΨΨ) and without (UUU) Ψ modifications. Comparison of the two structures shows that H69 ΨΨΨ has the following unique features: (i) the loop region is closed by a Watson-Crick base pair between Ψ1911 and A1919, which is potentially reinforced by interactions involving Ψ1911N1H and (ii) Ψ modifications at loop residues 1915 and 1917 promote base stacking from Ψ1915 to A1918. In contrast, the H69 UUU loop region, which lacks Ψ modifications, is less organized. Structure modulation by Ψ leads to alteration in conformational behavior of the 5' half of the H69 loop region, observed as broadening of C1914 non-exchangeable base proton resonances in the H69 ΨΨΨ nuclear magnetic resonance spectra, and plays an important biological role in establishing the ribosomal intersubunit bridge B2a and mediating translational fidelity.

Arthrose due au genu varum: traitement par osteotomie tibiale de valgisation

PubMed Central

Moussa, Abdou Kadri; Lukulunga, Loubet Unyendje; Mahfoud, Mustapha; El Bardouni, Ahmed; Ismail, Farid; Kharmaz, Mohamed; Berrada, Mohammed Saleh; El Yaacoubi, Moradh

2014-01-01

Le traitement du genu varum est le plus souvent conservateur (ostéotomie tibiale de valgisation) permettant de corriger le trouble architectural afin de rétablir l'axe physiologique du membre inférieur. Le but de l’étude était d’évaluer les résultats du traitement et comparer à ceux de la littérature. Il s'est agi d'une étude rétrospective portant sur des patients présentant un genu varum qui s'est déroulée dans le Service de Chirurgie Orthopédique et Traumatologie de CHU Ibn SINA de RABAT, sur une période de 9 ans (2000 au 31 Décembre 2008). Nous avons inclus dans notre étude: les patients qui avaient un genu-varum clinique avec examen radiographique standard ainsi qu'un pangonogramme; traités par différents procédés d'ostéotomie tibiale de valgisation; avec un suivis d’ au moins deux ans. Nos critères d’évaluation ont été appréciés selon le score HSS. Nous avons colligé 115 cas de genu-varum par ostéotomie de valgisation. L’âge de nos patients variait entre 40 et 69 ans, avec une moyenne de 53 ans. Le pic de fréquence se situait entre 52et 63 ans. Le sexe féminin prédominait avec 87 cas (75,6%) avec un sex ratio 3,1. Un Indice de masse corporelle supérieur à 30 a été noté dans 44 cas (38%). Quant aux antécédents chirurgicaux,18 patients de la série (soit 14%) ont été opérés pour le genu varum d'un autre genou. Le délai de consultation a varié entre 4 mois à 6 ans, avec une moyenne de 2 ans. La douleur était le principal motif de consultation et était de siège médial dans 70% des cas et bicompartimental dans 30% cas. Il s'agissait d'une douleur mécanique dans 76% des cas, mixte 21% des cas et inflammatoire 4% des cas. La déformation du genou appréciée par l’écart intercondylien a été en moyenne de 8,7 cm avec des extrêmes de 3 cm et 33cm. Le bilan de l'imagerie médicale reposait essentiellement sur les radiographies standards du genou de face et de profil, ainsi que la goniométrie. Ces clichés nous ont permis de classer l'arthrose du genou selon Ahlbäck. 72,5% des patients, présentaient une arthrose débutante. Le pangonogramme a été réalisé pour mesurer la déviation axiale du génu varum. La déviation angulaire: HKA (angle entre le centre de la tête fémorale et le milieu de la cheville) préopératoire a varié entre 163° et 176°, soit une moyenne de 175,46°. Une correction moyenne de déviation de 11,3° a été réalisée avec des extrêmes de 7 à 19°. Cet angle de correction (DAC) qui variait de 7 à 19° a été supérieur à 15° dans 57,39%s inférieur à 15° chez 38%. 27,4% des patients avaient une déviation angulaire importante avec une arthrose avancée. Après un bilan préopératoire et une planification opératoire 73% des patients ont été opérés sous anesthésie loco-régionale. Pour l'ostéotomie tibiale de fermeture, la voie d'abord a été la voie de Gernez antérolatérale, utilisée chez 56 cas (48,6%), l'ostéotomie tibiale d'ouverture (la voie d'abord était Gernez antéro-médiale) effectuée dans 20 cas (17,3%);et l'ostéotomie curviplane, a été réalisée par une voie d'abord longitudinale médiane dans 39%. Les ostéosynthèses ont été réalisées dans 51 cas (44,3%) par les agrafes de Blount, dans 54 cas (46,9%) par la plaque en T ou en L et dans 11 cas par une plaque en col de cygne. En per-opératoire nous avons enregistré deux (02) cas de fractures du plateau tibial médial, en post-opératoire on a eu 1 cas d'infection superficielle et comme complications tardives une raideur du genou (18,2%) et 3,4% de pseudarthrose, une récidive du génu varum dans 19,1% (n = 22) après 3 années de recul. Les résultats du traitement ont été bons dans 78,4% selon le score HSS. L'OTV sur genu varum a été réalisé chez des patients relativement âgés avec la prédominance du sexe féminin. Les techniques utilisées dépendaient de la préférence du chirurgien. Les résultats sont probants malgré la fréquence des récidives. Quelle que soit la technique utilisée les résultats sont satisfaisants, et malgré l’âge élevé l'OTV pourrait être une alternative intéressante et toujours d'actualité dans nos pays où la population est à majorité analphabète avec un niveau socioéconomique bas. PMID:25810807

Differential Modulation of Functional Dynamics and Allosteric Interactions in the Hsp90-Cochaperone Complexes with p23 and Aha1: A Computational Study

PubMed Central

Blacklock, Kristin; Verkhivker, Gennady M.

2013-01-01

Allosteric interactions of the molecular chaperone Hsp90 with a large cohort of cochaperones and client proteins allow for molecular communication and event coupling in signal transduction networks. The integration of cochaperones into the Hsp90 system is driven by the regulatory mechanisms that modulate the progression of the ATPase cycle and control the recruitment of the Hsp90 clientele. In this work, we report the results of computational modeling of allosteric regulation in the Hsp90 complexes with the cochaperones p23 and Aha1. By integrating protein docking, biophysical simulations, modeling of allosteric communications, protein structure network analysis and the energy landscape theory we have investigated dynamics and stability of the Hsp90-p23 and Hsp90-Aha1 interactions in direct comparison with the extensive body of structural and functional experiments. The results have revealed that functional dynamics and allosteric interactions of Hsp90 can be selectively modulated by these cochaperones via specific targeting of the regulatory hinge regions that could restrict collective motions and stabilize specific chaperone conformations. The protein structure network parameters have quantified the effects of cochaperones on conformational stability of the Hsp90 complexes and identified dynamically stable communities of residues that can contribute to the strengthening of allosteric interactions. According to our results, p23-mediated changes in the Hsp90 interactions may provide “molecular brakes” that could slow down an efficient transmission of the inter-domain allosteric signals, consistent with the functional role of p23 in partially inhibiting the ATPase cycle. Unlike p23, Aha1-mediated acceleration of the Hsp90-ATPase cycle may be achieved via modulation of the equilibrium motions that facilitate allosteric changes favoring a closed dimerized form of Hsp90. The results of our study have shown that Aha1 and p23 can modulate the Hsp90-ATPase activity and direct the chaperone cycle by exerting the precise control over structural stability, global movements and allosteric communications in Hsp90. PMID:23977182

Enthalpy-Entropy Compensation in the Binding of Modulators at Ionotropic Glutamate Receptor GluA2.

PubMed

Krintel, Christian; Francotte, Pierre; Pickering, Darryl S; Juknaitė, Lina; Pøhlsgaard, Jacob; Olsen, Lars; Frydenvang, Karla; Goffin, Eric; Pirotte, Bernard; Kastrup, Jette S

2016-06-07

The 1,2,4-benzothiadiazine 1,1-dioxide type of positive allosteric modulators of the ionotropic glutamate receptor A2 (GluA2) are promising lead compounds for the treatment of cognitive disorders, e.g., Alzheimer's disease. The modulators bind in a cleft formed by the interface of two neighboring ligand binding domains and act by stabilizing the agonist-bound open-channel conformation. The driving forces behind the binding of these modulators can be significantly altered with only minor substitutions to the parent molecules. In this study, we show that changing the 7-fluorine substituent of modulators BPAM97 (2) and BPAM344 (3) into a hydroxyl group (BPAM557 (4) and BPAM521 (5), respectively), leads to a more favorable binding enthalpy (ΔH, kcal/mol) from -4.9 (2) and -7.5 (3) to -6.2 (4) and -14.5 (5), but also a less favorable binding entropy (-TΔS, kcal/mol) from -2.3 (2) and -1.3 (3) to -0.5 (4) and 4.8 (5). Thus, the dissociation constants (Kd, μM) of 4 (11.2) and 5 (0.16) are similar to those of 2 (5.6) and 3 (0.35). Functionally, 4 and 5 potentiated responses of 10 μM L-glutamate at homomeric rat GluA2(Q)i receptors with EC50 values of 67.3 and 2.45 μM, respectively. The binding mode of 5 was examined with x-ray crystallography, showing that the only change compared to that of earlier compounds was the orientation of Ser-497 pointing toward the hydroxyl group of 5. The favorable enthalpy can be explained by the formation of a hydrogen bond from the side-chain hydroxyl group of Ser-497 to the hydroxyl group of 5, whereas the unfavorable entropy might be due to desolvation effects combined with a conformational restriction of Ser-497 and 5. In summary, this study shows a remarkable example of enthalpy-entropy compensation in drug development accompanied with a likely explanation of the underlying structural mechanism. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Conformal phased surfaces for wireless powering of bioelectronic microdevices

PubMed Central

Agrawal, Devansh R.; Tanabe, Yuji; Weng, Desen; Ma, Andrew; Hsu, Stephanie; Liao, Song-Yan; Zhen, Zhe; Zhu, Zi-Yi; Sun, Chuanbowen; Dong, Zhenya; Yang, Fengyuan; Tse, Hung Fat; Poon, Ada S. Y.; Ho, John S.

2017-01-01

Wireless powering could enable the long-term operation of advanced bioelectronic devices within the human body. Although both enhanced powering depth and device miniaturization can be achieved by shaping the field pattern within the body, existing electromagnetic structures do not provide the spatial phase control required to synthesize such patterns. Here, we describe the design and operation of conformal electromagnetic structures, termed phased surfaces, that interface with non-planar body surfaces and optimally modulate the phase response to enhance the performance of wireless powering. We demonstrate that the phased surfaces can wirelessly transfer energy across anatomically heterogeneous tissues in large animal models, powering miniaturized semiconductor devices (<12 mm3) deep within the body (>4 cm). As an illustration of in vivo operation, we wirelessly regulated cardiac rhythm by powering miniaturized stimulators at multiple endocardial sites in a porcine animal model. PMID:29226018

The structure of the β-barrel assembly machinery complex

DOE PAGES

Bakelar, Jeremy; Buchanan, Susan K.; Noinaj, Nicholas

2016-01-08

β-Barrel outer membrane proteins (OMPs) are found in the outer membranes of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. A 200-kilodalton five-component complex called the β-barrel assembly machinery (BAM) complex has been implicated in the biogenesis of OMPs. In this paper, we report the structure of the BAM complex from Escherichia coli, revealing that binding of BamCDE modulates the conformation of BamA, the central component, which may serve to regulate the BAM complex. The periplasmic domain of BamA was in a closed state that prevents access to the barrel lumen, which indicates substrate OMPs may notmore » be threaded through the barrel during biogenesis. Finally and further, conformational shifts in the barrel domain lead to opening of the exit pore and rearrangement at the lateral gate.« less

The structure of the β-barrel assembly machinery complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bakelar, Jeremy; Buchanan, Susan K.; Noinaj, Nicholas

β-Barrel outer membrane proteins (OMPs) are found in the outer membranes of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. A 200-kilodalton five-component complex called the β-barrel assembly machinery (BAM) complex has been implicated in the biogenesis of OMPs. In this paper, we report the structure of the BAM complex from Escherichia coli, revealing that binding of BamCDE modulates the conformation of BamA, the central component, which may serve to regulate the BAM complex. The periplasmic domain of BamA was in a closed state that prevents access to the barrel lumen, which indicates substrate OMPs may notmore » be threaded through the barrel during biogenesis. Finally and further, conformational shifts in the barrel domain lead to opening of the exit pore and rearrangement at the lateral gate.« less

Allosteric transcriptional regulation via changes in the overall topology of the core promoter

DOE PAGES

Philips, Steven J.; Canalizo-Hernandez, Monica; Yildirim, Ilyas; ...

2015-08-21

Many transcriptional activators act at a distance from core promoter elements and work by recruiting RNA polymerase through protein-protein interactions. We show here how the prokaryotic regulatory protein CueR both represses and activates transcription by differentially modulating local DNA structure within the promoter. Structural studies reveal that the repressor state slightly bends the promoter DNA, precluding optimal RNA polymerase-promoter recognition. Upon binding a metal ion in the allosteric site, CueR switches into an activator conformation. It maintains all protein-DNA contacts but introduces torsional stresses that kink and undertwist the promoter, stabilizing an A-DNA-like conformation. Finally, these factors switch on andmore » off transcription by exerting dynamic control of DNA stereochemistry, reshaping the core promoter and making it a better or worse substrate for polymerase.« less

Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics.

PubMed

Miao, Yinglong; Nichols, Sara E; McCammon, J Andrew

2014-04-14

G-protein coupled receptors (GPCRs) mediate cellular responses to various hormones and neurotransmitters and are important targets for treating a wide spectrum of diseases. They are known to adopt multiple conformational states (e.g., inactive, intermediate and active) during their modulation of various cell signaling pathways. Here, the free energy landscape of GPCRs is explored using accelerated molecular dynamics (aMD) simulations as demonstrated on the M2 muscarinic receptor, a key GPCR that regulates human heart rate and contractile forces of cardiomyocytes. Free energy profiles of important structural motifs that undergo conformational transitions upon GPCR activation and allosteric signaling are analyzed in detail, including the Arg(3.50)-Glu(6.30) ionic lock, the Trp(6.48) toggle switch and the hydrogen interactions between Tyr(5.58)-Tyr(7.53).

A lattice approach to the conformal OSp(2S+2|2S) supercoset sigma model. Part I: Algebraic structures in the spin chain. The Brauer algebra

NASA Astrophysics Data System (ADS)

Candu, Constantin; Saleur, Hubert

2009-02-01

We define and study a lattice model which we argue is in the universality class of the OSp(2S+2|2S) supercoset sigma model for a large range of values of the coupling constant gσ2. In this first paper, we analyze in details the symmetries of this lattice model, in particular the decomposition of the space of the quantum spin chain V as a bimodule over OSp(2S+2|2S) and its commutant, the Brauer algebra B(2). It turns out that V is a nonsemisimple module for both OSp(2S+2|2S) and B(2). The results are used in the companion paper to elucidate the structure of the (boundary) conformal field theory.

Light manipulation with flat and conformal inhomogeneous dispersive impedance sheets: an efficient FDTD modeling.

PubMed

Jafar-Zanjani, Samad; Cheng, Jierong; Mosallaei, Hossein

2016-04-10

An efficient auxiliary differential equation method for incorporating 2D inhomogeneous dispersive impedance sheets in the finite-difference time-domain solver is presented. This unique proposed method can successfully solve optical problems of current interest involving 2D sheets. It eliminates the need for ultrafine meshing in the thickness direction, resulting in a significant reduction of computation time and memory requirements. We apply the method to characterize a novel broad-beam leaky-wave antenna created by cascading three sinusoidally modulated reactance surfaces and also to study the effect of curvature on the radiation characteristic of a conformal impedance sheet holographic antenna. Considerable improvement in the simulation time based on our technique in comparison with the traditional volumetric model is reported. Both applications are of great interest in the field of antennas and 2D sheets.

Intensity-Modulated and 3D-Conformal Radiotherapy for Whole-Ventricular Irradiation as Compared With Conventional Whole-Brain Irradiation in the Management of Localized Central Nervous System Germ Cell Tumors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Michael Jenwei, E-mail: michaelchen@einstein.b; Silva Santos, Adriana da; Sakuraba, Roberto Kenji

Purpose: To compare the sparing potential of cerebral hemispheres with intensity-modulated radiotherapy (IMRT) and three-dimensional conformal radiotherapy (3D-CRT) for whole-ventricular irradiation (WVI) and conventional whole-brain irradiation (WBI) in the management of localized central nervous system germ cell tumors (CNSGCTs). Methods and Materials: Ten cases of patients with localized CNSGCTs and submitted to WVI by use of IMRT with or without a 'boost' to the primary lesion were selected. For comparison purposes, similar treatment plans were produced by use of 3D-CRT (WVI with or without boost) and WBI (opposed lateral fields with or without boost), and cerebral hemisphere sparing was evaluatedmore » at dose levels ranging from 2 Gy to 40 Gy. Results: The median prescription dose for WVI was 30.6 Gy (range, 25.2-37.5 Gy), and that for the boost was 16.5 Gy (range, 0-23.4 Gy). Mean irradiated cerebral hemisphere volumes were lower for WVI with IMRT than for 3D-CRT and were lower for WVI with 3D-CRT than for WBI. Intensity-modulated radiotherapy was associated with the lowest irradiated volumes, with reductions of 7.5%, 12.2%, and 9.0% at dose levels of 20, 30, and 40 Gy, respectively, compared with 3D-CRT. Intensity-modulated radiotherapy provided statistically significant reductions of median irradiated volumes at all dose levels (p = 0.002 or less). However, estimated radiation doses to peripheral areas of the body were 1.9 times higher with IMRT than with 3D-CRT. Conclusions: Although IMRT is associated with increased radiation doses to peripheral areas of the body, its use can spare a significant amount of normal central nervous system tissue compared with 3D-CRT or WBI in the setting of CNSGCT treatment.« less

Membrane proteins bind lipids selectively to modulate their structure and function.

PubMed

Laganowsky, Arthur; Reading, Eamonn; Allison, Timothy M; Ulmschneider, Martin B; Degiacomi, Matteo T; Baldwin, Andrew J; Robinson, Carol V

2014-06-05

Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments and that lipids can bind to specific sites, for example, in potassium channels. Fundamental questions remain however regarding the extent of membrane protein selectivity towards lipids. Here we report a mass spectrometry approach designed to determine the selectivity of lipid binding to membrane protein complexes. We investigate the mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis and aquaporin Z (AqpZ) and the ammonia channel (AmtB) from Escherichia coli, using ion mobility mass spectrometry (IM-MS), which reports gas-phase collision cross-sections. We demonstrate that folded conformations of membrane protein complexes can exist in the gas phase. By resolving lipid-bound states, we then rank bound lipids on the basis of their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability; however, the highest-ranking lipid is phosphatidylinositol phosphate, in line with its proposed functional role in mechanosensation. AqpZ is also stabilized by many lipids, with cardiolipin imparting the most significant resistance to unfolding. Subsequently, through functional assays we show that cardiolipin modulates AqpZ function. Similar experiments identify AmtB as being highly selective for phosphatidylglycerol, prompting us to obtain an X-ray structure in this lipid membrane-like environment. The 2.3 Å resolution structure, when compared with others obtained without lipid bound, reveals distinct conformational changes that re-position AmtB residues to interact with the lipid bilayer. Our results demonstrate that resistance to unfolding correlates with specific lipid-binding events, enabling a distinction to be made between lipids that merely bind from those that modulate membrane protein structure and/or function. We anticipate that these findings will be important not only for defining the selectivity of membrane proteins towards lipids, but also for understanding the role of lipids in modulating protein function or drug binding.

Intensity modulated radiotherapy and 3D conformal radiotherapy for whole breast irradiation: a comparative dosimetric study and introduction of a novel qualitative index for plan evaluation, the normal tissue index

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yim, Jackie; Suttie, Clare; Bromley, Regina

We report on a retrospective dosimetric study, comparing 3D conformal radiotherapy (3DCRT) and hybrid intensity modulated radiotherapy (hIMRT). We evaluated plans based on their planning target volume coverage, dose homogeneity, dose to organs at risk (OARs) and exposure of normal tissue to radiation. The Homogeneity Index (HI) was used to assess the dose homogeneity in the target region, and we describe a new index, the normal tissue index (NTI), to assess the dose in the normal tissue inside the tangent treatment portal. Plans were generated for 25 early-stage breast cancer patients, using a hIMRT technique. These were compared with themore » 3DCRT plans of the treatment previously received by the patients. Plan quality was evaluated using the HI, NTI and dose to OARs. The hIMRT technique was significantly more homogenous than the 3DCRT technique, while maintaining target coverage. The hIMRT technique was also superior at minimising the amount of tissue receiving D{sub 105%} and above (P < 0.0001). The ipsilateral lung and contralateral breast maximum were significantly lower in the hIMRT plans (P < 0.05 and P < 0.005), but the 3DCRT technique achieved a lower mean heart dose in left-sided breast cancer patients (P < 0.05). Hybrid intensity modulated radiotherapy plans achieved improved dose homogeneity compared to the 3DCRT plans and superior outcome with regard to dose to normal tissues. We propose that the addition of both HI and NTI in evaluating the quality of intensity modulated radiotherapy (IMRT) breast plans provides clinically relevant comparators which more accurately reflect the new paradigm of treatment goals and outcomes in the era of breast IMRT.« less

Cardiac Exposure in the Dynamic Conformal Arc Therapy, Intensity-Modulated Radiotherapy and Volumetric Modulated Arc Therapy of Lung Cancer

PubMed Central

Ming, Xin; Feng, Yuanming; Liu, Huan; Zhang, Ying; Zhou, Li; Deng, Jun

2015-01-01

Purpose To retrospectively evaluate the cardiac exposure in three cohorts of lung cancer patients treated with dynamic conformal arc therapy (DCAT), intensity-modulated radiotherapy (IMRT), or volumetric modulated arc therapy (VMAT) at our institution in the past seven years. Methods and Materials A total of 140 lung cancer patients were included in this institutional review board approved study: 25 treated with DCAT, 70 with IMRT and 45 with VMAT. All plans were generated in a same commercial treatment planning system and have been clinically accepted and delivered. The dose distribution to the heart and the effects of tumor laterality, the irradiated heart volume and the beam-to-heart distance on the cardiac exposure were investigated. Results The mean dose to the heart among all 140 plans was 4.5 Gy. Specifically, the heart received on average 2.3, 5.2 and 4.6 Gy in the DCAT, IMRT and VMAT plans, respectively. The mean heart doses for the left and right lung tumors were 4.1 and 4.8 Gy, respectively. No patients died with evidence of cardiac disease. Three patients (2%) with preexisting cardiac condition developed cardiac disease after treatment. Furthermore, the cardiac exposure was found to increase linearly with the irradiated heart volume while decreasing exponentially with the beam-to-heart distance. Conclusions Compared to old technologies for lung cancer treatment, modern radiotherapy treatment modalities demonstrated better heart sparing. But the heart dose in lung cancer radiotherapy is still higher than that in the radiotherapy of breast cancer and Hodgkin’s disease where cardiac complications have been extensively studied. With strong correlations of mean heart dose with beam-to-heart distance and irradiated heart volume, cautions should be exercised to avoid long-term cardiac toxicity in the lung cancer patients undergoing radiotherapy. PMID:26630566

Comparison of three-dimensional conformal radiation therapy, intensity-modulated radiation therapy, and volumetric-modulated arc therapy in the treatment of cervical esophageal carcinoma.

PubMed

Yang, Hao; Feng, Cong; Cai, Bo-Ning; Yang, Jun; Liu, Hai-Xia; Ma, Lin

2017-02-01

The aim of this study was to evaluate the effectiveness and toxicities of three-dimensional conformal radiation therapy (3DCRT), intensity-modulated radiation therapy (IMRT), and volumetric-modulated arc therapy (VMAT) in patients with cervical esophageal cancer. Specifically, we asked whether technological advances conferred an advantage with respect to the clinical curative effect. Seventy-eight patients with cervical esophageal cancer treated with definitive radiotherapy with or without concomitant chemotherapy at our institution between 2007 and 2014 were enrolled in the study: 26 received 3DCRT, 30 were treated with IMRT, and 22 underwent VMAT. Kaplan-Meier analysis and the Cox proportional hazard model were used to analyze overall survival (OS) and failure-free survival (FFS). Treatment-related toxicity was also assessed. For all patients, the 2-year OS and FFS rates were 56.2 and 53.9%, respectively. The 2-year OS for the 3DCRT, IMRT, and VMAT groups was 53.6, 55.6, and 60.6%, respectively (P = 0.965). The corresponding 2-year FFS rates were 49.5, 56.7, and 60.1% (P = 0.998). A univariate analysis of the complete response to treatment showed an advantage of treatment modality with respect to OS (P < 0.001). The development of acute hematologic toxicity was not significantly different among the three groups. The survival rates of patients treated with IMRT and VMAT were comparable to the survival of patients administered 3DCRT, while lower lung mean dose, V20, maximum dose of brachial plexus and spinal cord. Grade 1 radiation pneumonitis occurred significantly less in patients treated with IMRT and VMAT than with 3DCRT (P = 0.011). A complete response was the most important prognostic factor of the patients with cervical esophageal cancer. © 2016 International Society for Diseases of the Esophagus.

Dosimetric study of the protection level of the bone marrow in patients with cervical or endometrial cancer for three radiotherapy techniques - 3D CRT, IMRT and VMAT. Study protocol.

NASA Astrophysics Data System (ADS)

Jodda, Agata; Urbański, Bartosz; Piotrowski, Tomasz; Malicki, Julian

2016-03-01

Background: The paper shows the methodology of an in-phantom study of the protection level of the bone marrow in patients with cervical or endometrial cancer for three radiotherapy techniques: three-dimensional conformal radiotherapy, intensity modulated radiotherapy, and volumetric modulated arc therapy, preceded by the procedures of image guidance. Methods/Design: The dosimetric evaluation of the doses will be performed in an in-house multi-element anthropomorphic phantom of the female pelvic area created by three-dimensional printing technology. The volume and position of the structures will be regulated according to the guidelines from the Bayesian network. The input data for the learning procedure of the model will be obtained from the retrospective analysis of imaging data obtained for 96 patients with endometrial cancer or cervical cancer treated with radiotherapy in our centre in 2008-2013. Three anatomical representations of the phantom simulating three independent clinical cases will be chosen. Five alternative treatment plans (1 × three-dimensional conformal radiotherapy, 2 × intensity modulated radiotherapy and 2 × volumetric modulated arc therapy) will be created for each representation. To simulate image-guided radiotherapy, ten specific recombinations will be designated, for each anatomical representation separately, reflecting possible changes in the volume and position of the phantom components. Discussion: The comparative analysis of planned measurements will identify discrepancies between calculated doses and doses that were measured in the phantom. Finally, differences between the doses cumulated in the hip plates performed by different techniques simulating the gynaecological patients' irradiation of dose delivery will be established. The results of this study will form the basis of the prospective clinical trial that will be designed for the assessment of hematologic toxicity and its correlation with the doses cumulated in the hip plates, for gynaecologic patients undergoing radiation therapy.

A retrospective planning analysis comparing intensity modulated radiation therapy (IMRT) to volumetric modulated arc therapy (VMAT) using two optimization algorithms for the treatment of early-stage prostate cancer

PubMed Central

Elith, Craig A; Dempsey, Shane E; Warren-Forward, Helen M

2013-01-01

Introduction The primary aim of this study is to compare intensity modulated radiation therapy (IMRT) to volumetric modulated arc therapy (VMAT) for the radical treatment of prostate cancer using version 10.0 (v10.0) of Varian Medical Systems, RapidArc radiation oncology system. Particular focus was placed on plan quality and the implications on departmental resources. The secondary objective was to compare the results in v10.0 to the preceding version 8.6 (v8.6). Methods Twenty prostate cancer cases were retrospectively planned using v10.0 of Varian's Eclipse and RapidArc software. Three planning techniques were performed: a 5-field IMRT, VMAT using one arc (VMAT-1A), and VMAT with two arcs (VMAT-2A). Plan quality was assessed by examining homogeneity, conformity, the number of monitor units (MUs) utilized, and dose to the organs at risk (OAR). Resource implications were assessed by examining planning and treatment times. The results obtained using v10.0 were also compared to those previously reported by our group for v8.6. Results In v10.0, each technique was able to produce a dose distribution that achieved the departmental planning guidelines. The IMRT plans were produced faster than VMAT plans and displayed improved homogeneity. The VMAT plans provided better conformity to the target volume, improved dose to the OAR, and required fewer MUs. Treatments using VMAT-1A were significantly faster than both IMRT and VMAT-2A. Comparison between versions 8.6 and 10.0 revealed that in the newer version, VMAT planning was significantly faster and the quality of the VMAT dose distributions produced were of a better quality. Conclusion VMAT (v10.0) using one or two arcs provides an acceptable alternative to IMRT for the treatment of prostate cancer. VMAT-1A has the greatest impact on reducing treatment time. PMID:26229615

Luxation traumatique invétérée de la hanche

PubMed Central

Rachid, Abdelillah; Abdeljaouad, Najib; Abdelkrim, Daoudi; Hicham, Yacoubi

2015-01-01

La luxation traumatique invétérée de la hanche est une affection rare et grave avec une prise en charge difficile et non encore codifiée. L'arthroplastie totale de la hanche reste le traitement chirurgical de choix. Nous rapportons un cas de luxation iliaque invétérée de la hanche chez un jeune patient de 19 ans, traitée par une arthroplastie totale de la hanche. Après un recul de 2 ans, le résultat fonctionnel est satisfaisant, avec une marche indolore sans aide. Le Score de Harris est de 96 et le score de Merle d'aubigné-Postel est de 17. PMID:26848347

Laser femtoseconde, filamentation, nuage et orage

NASA Astrophysics Data System (ADS)

Courvoisier, F.; Boutou, V.; Kasparian, J.; Salmon, E.; Méjean, G.; Yu, J.; Wolf, J.-P.

2005-06-01

Les applications telles que le contrôle de foudre grâce aux filaments autoguidés générés par un laser femtoseconde nécessitent de propager un tel filament à travers des aérosols de gouttes d'eau. Nous montrons qu'un filament survit à son interaction avec une goutte de diamètre comparable au sien (95 μ m), ainsi qu'à des nuages d'épaisseur optique 3,2, soit 5% de transmission. Cette transmission est permise par la présence d'un “bain de photons” autour du filament. Ce bain forme un réservoir contenant une part importante de l'énergie du faisceau, en équilibre avec le filament, et favorisant son alimentation.

Perception de la verticale avec Un cadre visuel solidaire de la tete: implications pour la conception des afficheurs de casques en ae’ronauflque (Perception of the Vertical With a Head-Mounted Visual Frame: Implication for the Design of Helmet-Mounted Displays in Aeronautics)

DTIC Science & Technology

2003-02-01

de celle de la tete. MWthodes Douze sujets, 9 hommes et 3 femmes, dg6s de 23 it 41 ans, se...qui donne la sensation de voir un 6cran informatique, centr6 sur l’axe interoculaire, d’une taille angulaire de 300 X 22,5’. L ’&ran virtuel apparait...inclin6s de faqon identique par rapport ýt la gravit6. Le premier essai 6tait toujours r6alis6 avec la tete droite . Ensuite, une nouvelle orientation de

Coulometrische titration von hypochloriten und chloraten.

PubMed

Gründler, P; Holzapfel, H

1970-03-01

Hypochlorite was determined by direct coulometric titration with iron(II) in an acetate buffered solution. Chlorate was titrated with titanium(III) in 2M hydrochloric acid. Amperometric indication with one and two electrodes, respectively, was used. Mixtures of hypochlorites and chlorates, e.g., in industrial electrolytes, may be analysed. On a déterminé l'hypochlorite par titrage coulométrique direct avec le fer(II) dans une solution tamponnée à l'acétate. On a titré le chlorate avec le titane(III) en acide chlorhydrique 2M. On a utilisé l'indication ampérométrique une et deux électrodes respectivement. On peut analyser des mélanges d'hypochlorites et de chlorates, par exemple dans des électrolytes industriels.

Pseudo-HELLP syndrome par carence en folates et/ou en vitamine B12: à propos d'un cas

PubMed Central

Benali, Mechaal; Bouassida, Mahdi; Dhouib, Firas; Bouzeidi, Kaled

2014-01-01

Plusieurs pathologies médicales peuvent interférer avec la grossesse et mimer le tableau biologique de HELLP syndrome. L’évolution naturelle de ce syndrome est d'une particulière gravité pour la mère et le fœtus, il convient d’éliminer rapidement les autres diagnostics afin d’éviter une extraction fœtale prématurée injustifiée. Nous rapportons le cas d'une parturiente qui s'est présentée avec un tableau évocateur d'un HELLP syndrome, rapporté finalement à une carence en folates et en vitamine B12. PMID:25404961

Dosimetric comparison of 3D conformal, IMRT, and V-MAT techniques for accelerated partial-breast irradiation (APBI)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qiu, Jian-Jian; Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai

2014-07-01

The purpose is to dosimetrically compare the following 3 delivery techniques: 3-dimensional conformal radiation therapy (3D-CRT), intensity-modulated arc therapy (IMRT), and volumetric-modulated arc therapy (V-MAT) in the treatment of accelerated partial-breast irradiation (APBI). Overall, 16 patients with T1/2N0 breast cancer were treated with 3D-CRT (multiple, noncoplanar photon fields) on the RTOG 0413 partial-breast trial. These cases were subsequently replanned using static gantry IMRT and V-MAT technology to understand dosimetric differences among these 3 techniques. Several dosimetric parameters were used in plan quality evaluation, including dose conformity index (CI) and dose-volume histogram analysis of normal tissue coverage. Quality assurance studies includingmore » gamma analysis were performed to compare the measured and calculated dose distributions. The IMRT and V-MAT plans gave more conformal target dose distributions than the 3D-CRT plans (p < 0.05 in CI). The volume of ipsilateral breast receiving 5 and 10 Gy was significantly less using the V-MAT technique than with either 3D-CRT or IMRT (p < 0.05). The maximum lung dose and the ipsilateral lung volume receiving 10 (V{sub 10}) or 20 Gy (V{sub 20}) were significantly less with both V-MAT and IMRT (p < 0.05). The IMRT technique was superior to 3D-CRT and V-MAT of low dose distributions in ipsilateral lung (p < 0.05 in V{sub 5} and D{sub 5}). The total mean monitor units (MUs) for V-MAT (621.0 ± 111.9) were 12.2% less than those for 3D-CRT (707.3 ± 130.9) and 46.5% less than those for IMRT (1161.4 ± 315.6) (p < 0.05). The average machine delivery time was 1.5 ± 0.2 minutes for the V-MAT plans, 7.0 ± 1.6 minutes for the 3D-CRT plans, and 11.5 ± 1.9 minutes for the IMRT plans, demonstrating much less delivery time for V-MAT. Based on this preliminary study, V-MAT and IMRT techniques offer improved dose conformity as compared with 3D-CRT techniques without increasing dose to the ipsilateral lung. In terms of MU and delivery time, V-MAT is significantly more efficient for APBI than for conventional 3D-CRT and static-beam IMRT.« less

A comprehensive dosimetric study of pancreatic cancer treatment using three-dimensional conformal radiation therapy (3DCRT), intensity-modulated radiation therapy (IMRT), volumetric-modulated radiation therapy (VMAT), and passive-scattering and modulated-scanning proton therapy (PT)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Xuanfeng; Dionisi, Francesco; Tang, Shikui

With traditional photon therapy to treat large postoperative pancreatic target volume, it often leads to poor tolerance of the therapy delivered and may contribute to interrupted treatment course. This study was performed to evaluate the potential advantage of using passive-scattering (PS) and modulated-scanning (MS) proton therapy (PT) to reduce normal tissue exposure in postoperative pancreatic cancer treatment. A total of 11 patients with postoperative pancreatic cancer who had been previously treated with PS PT in University of Pennsylvania Roberts Proton Therapy Center from 2010 to 2013 were identified. The clinical target volume (CTV) includes the pancreatic tumor bed as wellmore » as the adjacent high-risk nodal areas. Internal (iCTV) was generated from 4-dimensional (4D) computed tomography (CT), taking into account target motion from breathing cycle. Three-field and 4-field 3D conformal radiation therapy (3DCRT), 5-field intensity-modulated radiation therapy, 2-arc volumetric-modulated radiation therapy, and 2-field PS and MS PT were created on the patients’ average CT. All the plans delivered 50.4 Gy to the planning target volume (PTV). Overall, 98% of PTV was covered by 95% of the prescription dose and 99% of iCTV received 98% prescription dose. The results show that all the proton plans offer significant lower doses to the left kidney (mean and V{sub 18} {sub Gy}), stomach (mean and V{sub 20} {sub Gy}), and cord (maximum dose) compared with all the photon plans, except 3-field 3DCRT in cord maximum dose. In addition, MS PT also provides lower doses to the right kidney (mean and V{sub 18} {sub Gy}), liver (mean dose), total bowel (V{sub 20} {sub Gy} and mean dose), and small bowel (V{sub 15} {sub Gy} absolute volume ratio) compared with all the photon plans and PS PT. The dosimetric advantage of PT points to the possibility of treating tumor bed and comprehensive nodal areas while providing a more tolerable treatment course that could be used for dose escalation and combining with radiosensitizing chemotherapy.« less

Symetries et integrabilite des equations aux differences finies

NASA Astrophysics Data System (ADS)

Lafortune, Stephane

2000-09-01

La présente thèse porte sur l'étude des symétries et des propriétés d'intégrabilité des équations aux différences finies. Dans le chapitre 1, le groupe de symétrie ponctuelle d'un système couplé à deux équations différentielles aux différences est étudié. On montre que dans certains cas, la dimension du groupe peut être infinie. Les équations peuvent décrire l'interaction de deux longues chaînes moléculaires, chacune étant composée d'atomes d'un même type. Dans le chapitre 2, une classe de théories de champs avec interaction exponentielle est introduite. L'interaction dépend de deux matrices de ``couplage'' et est suffisamment générale pour inclure toutes les théories de champs de Toda existant dans la littérature. Les symétries de Lie ponctuelles sont obtenues pour les cas où l'on a un nombre fini, infini ou semi-infini de champs. Une attention spéciale est accordée à la présence de l'invariance conforme. Dans le chapitre 3, nous procédons à la classification et à l'étude d'équations linéarisables. Nous examinons tout d'abord l'équation de Gambier continue qui contient, comme réductions, toutes les équations de deuxième ordre intégrables par linéarisation. Nous introduisons par la suite la forme discrète de cette équation et obtenons les conditions d'intégrabilité à l'aide du confinement des singularités. Nous étudions aussi les différentes réductions du cas discret. De plus, nous obtenons des transformations de Schlesinger pour les équations de Gambier discrète et continue. Dans la dernière partie du chapitre, nous étudions une famille d'équations discrètes du deuxième ordre incluant des équations résolubles par linéarisation. Plusieurs cas intégrables sont obtenus. Dans le cas discret, l'étude de l'intégrabilité est faite à l'aide du confinement des singularités. Dans le chapitre 4, nous étudions un autre critère d'intégrabilité: l'entropie algébrique. Nous montrons que les résultats obtenus avec ce critère pour les équations linéarisables sont les mêmes que ceux obtenus avec le confinement des singularités. Nous obtenons de plus une méthode algorithmique pour la détection de la linéarisabilité. Le chapitre 5 est consacré à l'étude d'équations du troisième ordre. Nous obtenons des équations intégrables par des couplages d'équations du premier et du deuxième ordre. Les équations continues sont étudiées à l'aide de l'analyse de Painlevé et le confinement des singularités est utilisé dans le cas discret.

Expanding the Interactome of TES by Exploiting TES Modules with Different Subcellular Localizations.

PubMed

Sala, Stefano; Van Troys, Marleen; Medves, Sandrine; Catillon, Marie; Timmerman, Evy; Staes, An; Schaffner-Reckinger, Elisabeth; Gevaert, Kris; Ampe, Christophe

2017-05-05

The multimodular nature of many eukaryotic proteins underlies their temporal or spatial engagement in a range of protein cocomplexes. Using the multimodule protein testin (TES), we here report a proteomics approach to increase insight in cocomplex diversity. The LIM-domain containing and tumor suppressor protein TES is present at different actin cytoskeleton adhesion structures in cells and influences cell migration, adhesion and spreading. TES module accessibility has been proposed to vary due to conformational switching and variants of TES lacking specific domains target to different subcellular locations. By applying iMixPro AP-MS ("intelligent Mixing of Proteomes"-affinity purification-mass spectrometry) to a set of tagged-TES modular variants, we identified proteins residing in module-specific cocomplexes. The obtained distinct module-specific interactomes combine to a global TES interactome that becomes more extensive and richer in information. Applying pathway analysis to the module interactomes revealed expected actin-related canonical pathways and also less expected pathways. We validated two new TES cocomplex partners: TGFB1I1 and a short form of the glucocorticoid receptor. TES and TGFB1I1 are shown to oppositely affect cell spreading providing biological validity for their copresence in complexes since they act in similar processes.

Application Reuse Library for Software, Requirements, and Guidelines

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Thronesbery, Carroll

1994-01-01

Better designs are needed for expert systems and other operations automation software, for more reliable, usable and effective human support. A prototype computer-aided Application Reuse Library shows feasibility of supporting concurrent development and improvement of advanced software by users, analysts, software developers, and human-computer interaction experts. Such a library expedites development of quality software, by providing working, documented examples, which support understanding, modification and reuse of requirements as well as code. It explicitly documents and implicitly embodies design guidelines, standards and conventions. The Application Reuse Library provides application modules with Demo-and-Tester elements. Developers and users can evaluate applicability of a library module and test modifications, by running it interactively. Sub-modules provide application code and displays and controls. The library supports software modification and reuse, by providing alternative versions of application and display functionality. Information about human support and display requirements is provided, so that modifications will conform to guidelines. The library supports entry of new application modules from developers throughout an organization. Example library modules include a timer, some buttons and special fonts, and a real-time data interface program. The library prototype is implemented in the object-oriented G2 environment for developing real-time expert systems.

SU-G-BRC-14: Multi-Lesion, Multi-Rx, Brain Radiosurgery with Novel Single Isocenter Technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Honig, N; Alani, S; Schlocker, A

Purpose: There is a strong trend to treat multiple brain metastases with radiosurgery rather than whole brain irradiation. This feasibility study investigates a novel planning technique for radio-surgical treatment of multiple brain lesions with differing dose prescriptions, a single isocenter, and dynamic conformal arcs. The novel technique will be compared to the well-established single-isocenter volumetric modulated arc therapy (VMAT) technique commonly used for treating brain lesions. Methods: Six patients with metastatic brain lesions were selected for a prospective treatment planning study to evaluate Interdigitating MLC Dynamic Conformal Arc (IMDCA) technique. Arcs were planned for simultaneous irradiation to maximize beam deliverymore » efficiency. To accommodate varying PTV dose prescriptions, selected arcs were re-irradiated in reverse. Beam weights were adjusted until all prescription constraints were met. The number of lesions ranged between 2 to 4 (mode = 3). For comparison, SRS VMAT plans were generated utilizing an established single-isocenter, 3 arc planning template. All plans were compared by means of Paddick conformity index (PCI), RTOG Conformity Index (RCI), gradient index (GI), and the normal brain volume receiving 10% (V10) of the highest prescription dose. The monitor units and delivery time were tabulated for each plan. Results: IMDCA achieved conformal plans (PCI = 0.72±0.03, RCI = 1.33±0.03) with steep dose fall-off (GI = 3.79±0.03) on average for all of the plans evaluated. The VMAT plans had slightly better conformity (PCI = 0.85 ± 0.03, RCI = 1.13 ± 0.03) than IMDCA, but overall worse GI (4.29 ± 0.06). IMDCA plans had lower V10% values, required 50% fewer MUs, and had 34% shorter beam delivery time on average compared to VMAT plans. Conclusion: IMDCA plans with varying dose prescriptions for multiple lesions, had comparable dosimetric coverage as VMAT plans, but were obtained with significantly lower integral dose, fewer monitor units, and quicker delivery time.« less

How cholesterol constrains glycolipid conformation for optimal recognition of Alzheimer's beta amyloid peptide (Abeta1-40).

PubMed

Yahi, Nouara; Aulas, Anaïs; Fantini, Jacques

2010-02-05

Membrane lipids play a pivotal role in the pathogenesis of Alzheimer's disease, which is associated with conformational changes, oligomerization and/or aggregation of Alzheimer's beta-amyloid (Abeta) peptides. Yet conflicting data have been reported on the respective effect of cholesterol and glycosphingolipids (GSLs) on the supramolecular assembly of Abeta peptides. The aim of the present study was to unravel the molecular mechanisms by which cholesterol modulates the interaction between Abeta(1-40) and chemically defined GSLs (GalCer, LacCer, GM1, GM3). Using the Langmuir monolayer technique, we show that Abeta(1-40) selectively binds to GSLs containing a 2-OH group in the acyl chain of the ceramide backbone (HFA-GSLs). In contrast, Abeta(1-40) did not interact with GSLs containing a nonhydroxylated fatty acid (NFA-GSLs). Cholesterol inhibited the interaction of Abeta(1-40) with HFA-GSLs, through dilution of the GSL in the monolayer, but rendered the initially inactive NFA-GSLs competent for Abeta(1-40) binding. Both crystallographic data and molecular dynamics simulations suggested that the active conformation of HFA-GSL involves a H-bond network that restricts the orientation of the sugar group of GSLs in a parallel orientation with respect to the membrane. This particular conformation is stabilized by the 2-OH group of the GSL. Correspondingly, the interaction of Abeta(1-40) with HFA-GSLs is strongly inhibited by NaF, an efficient competitor of H-bond formation. For NFA-GSLs, this is the OH group of cholesterol that constrains the glycolipid to adopt the active L-shape conformation compatible with sugar-aromatic CH-pi stacking interactions involving residue Y10 of Abeta(1-40). We conclude that cholesterol can either inhibit or facilitate membrane-Abeta interactions through fine tuning of glycosphingolipid conformation. These data shed some light on the complex molecular interplay between cell surface GSLs, cholesterol and Abeta peptides, and on the influence of this molecular ballet on Abeta-membrane interactions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Small, Katherine; Kelly, Chris; Beldham-Collins, Rachael

A comparative study was conducted comparing the difference between (1) conformal radiotherapy (CRT) to the whole breast with sequential boost excision cavity plans and (2) intensity-modulated radiation therapy (IMRT) to the whole breast with simultaneously integrated boost to the excision cavity. The computed tomography (CT) data sets of 25 breast cancer patients were used and the results analysed to determine if either planning method produced superior plans. CT data sets from 25 past breast cancer patients were planned using (1) CRT prescribed to 50 Gy in 25 fractions (Fx) to the whole-breast planning target volume (PTV) and 10 Gy inmore » 5Fx to the excision cavity and (2) IMRT prescribed to 60 Gy in 25Fx, with 60 Gy delivered to the excision cavity PTV and 50 Gy delivered to the whole-breast PTV, treated simultaneously. In total, 50 plans were created, with each plan evaluated by PTV coverage using conformity indices, plan maximum dose, lung dose, and heart maximum dose for patients with left-side lesions. CRT plans delivered the lowest plan maximum doses in 56% of cases (average CRT = 6314.34 cGy, IMRT = 6371.52 cGy). They also delivered the lowest mean lung dose in 68% of cases (average CRT = 1206.64 cGy, IMRT = 1288.37 cGy) and V20 in 88% of cases (average CRT = 20.03%, IMRT = 21.73%) and V30 doses in 92% of cases (average CRT = 16.82%, IMRT = 17.97%). IMRT created more conformal plans, using both conformity index and conformation number, in every instance, and lower heart maximum doses in 78.6% of cases (average CRT = 5295.26 cGy, IMRT = 5209.87 cGy). IMRT plans produced superior dose conformity and shorter treatment duration, but a slightly higher planning maximum and increased lung doses. IMRT plans are also faster to treat on a daily basis, with shorter fractionation.« less

Insight into structural rearrangements and interdomain interactions related to electron transfer between flavin mononucleotide and heme in nitric oxide synthase: A molecular dynamics study.

PubMed

Sheng, Yinghong; Zhong, Linghao; Guo, Dahai; Lau, Gavin; Feng, Changjian

2015-12-01

Calmodulin (CaM) binding to nitric oxide synthase (NOS) enables a conformational change, in which the FMN domain shuttles between the FAD and heme domains to deliver electrons to the active site heme center. A clear understanding of this large conformational change is critical, since this step is the rate-limiting in NOS catalysis. Herein molecular dynamics simulations were conducted on a model of an oxygenase/FMN (oxyFMN) construct of human inducible NOS (iNOS). This is to investigate the structural rearrangements and the domain interactions related to the FMN-heme interdomain electron transfer (IET). We carried out simulations on the iNOS oxyFMN·CaM complex models in [Fe(III)][FMNH(-)] and [Fe(II)][FMNH] oxidation states, the pre- and post-IET states. The comparison of the dynamics and conformations of the iNOS construct at the two oxidation states has allowed us to identify key factors related to facilitating the FMN-heme IET process. The computational results demonstrated, for the first time, that the conformational change is redox-dependent. Predictions of the key interacting sites in optimal interdomain FMN/heme docking are well supported by experimental data in the literature. An intra-subunit pivot region is predicted to modulate the FMN domain motion and correlate with existence of a bottleneck in the conformational sampling that leads to the electron transfer-competent state. Interactions of the residues identified in this work are proposed to ensure that the FMN domain moves with appropriate degrees of freedom and docks to proper positions at the heme domain, resulting in efficient IET and nitric oxide production. Copyright © 2015 Elsevier Inc. All rights reserved.

Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase.

PubMed

Liu, C Tony; Layfield, Joshua P; Stewart, Robert J; French, Jarrod B; Hanoian, Philip; Asbury, John B; Hammes-Schiffer, Sharon; Benkovic, Stephen J

2014-07-23

Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and (13)C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor-acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for significant electrostatic changes in the active site microenvironments due to conformational motion occurring over the catalytic cycle of ecDHFR.

Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase

PubMed Central

2015-01-01

Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and 13C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor–acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for significant electrostatic changes in the active site microenvironments due to conformational motion occurring over the catalytic cycle of ecDHFR. PMID:24977791

Computational investigation of the effect of pH on the color of firefly bioluminescence by DFT.

PubMed

Pinto da Silva, Luís; Esteves da Silva, Joaquim C G

2011-04-04

In spite of recent advances towards understanding the mechanism of firefly bioluminescence, there is no consensus about which oxyluciferin (OxyLH(2)) species are the red and yellow-green emitters. The crystal structure of Luciola cruciata luciferase (LcLuc) revealed different conformations for the various steps of the bioluminescence reaction, with different degrees of polarity and rigidity of the active-site microenvironment. In this study, these different conformations of luciferase (Luc) are simulated and their effects on the different chemical equilibria of OxyLH(2) are investigated as a function of pH by means of density functional theory with the PBE0 functional. In particular, the thermodynamic properties and the absorption spectra of each species, as well as their relative stabilities in the ground and excited states, were computed in the different conformations of Luc. From the calculations it is possible to derive the acid dissociation and tautomeric constants, and the corresponding distribution diagrams. It is observed that the anionic keto form of OxyLH(2) is both the red and the yellow-green emitter. Consequently, the effect of Luc conformations on the structural and electronic properties of the Keto-(-1) form are studied. Finally, insights into the Luc-catalyzed light-emitting reaction are derived from the calculations. The multicolor bioluminescence can be explained by interactions of the emitter with active-site molecules, the effects of which on light emission are modulated by the internal dielectric constant of the different conformations. These interactions can suffer also from rearrangement due to entry of external solvent and changes in the protonation state of some amino acid residues and adenosine monophosphate (AMP). Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mode shift of the voltage sensors in Shaker K+ channels is caused by energetic coupling to the pore domain

PubMed Central

Haddad, Georges A.

2011-01-01

The voltage sensors of voltage-gated ion channels undergo a conformational change upon depolarization of the membrane that leads to pore opening. This conformational change can be measured as gating currents and is thought to be transferred to the pore domain via an annealing of the covalent link between voltage sensor and pore (S4-S5 linker) and the C terminus of the pore domain (S6). Upon prolonged depolarizations, the voltage dependence of the charge movement shifts to more hyperpolarized potentials. This mode shift had been linked to C-type inactivation but has recently been suggested to be caused by a relaxation of the voltage sensor itself. In this study, we identified two ShakerIR mutations in the S4-S5 linker (I384N) and S6 (F484G) that, when mutated, completely uncouple voltage sensor movement from pore opening. Using these mutants, we show that the pore transfers energy onto the voltage sensor and that uncoupling the pore from the voltage sensor leads the voltage sensors to be activated at more negative potentials. This uncoupling also eliminates the mode shift occurring during prolonged depolarizations, indicating that the pore influences entry into the mode shift. Using voltage-clamp fluorometry, we identified that the slow conformational change of the S4 previously correlated with the mode shift disappears when uncoupling the pore. The effects can be explained by a mechanical load that is imposed upon the voltage sensors by the pore domain and allosterically modulates its conformation. Mode shift is caused by the stabilization of the open state but leads to a conformational change in the voltage sensor. PMID:21518834

Virulence Regulation with Venus Flytrap Domains: Structure and Function of the Periplasmic Moiety of the Sensor-Kinase BvgS

PubMed Central

Lensink, Marc F.; Wintjens, René; Vagin, Alexey; Lebedev, Andrey; Crosson, Sean; Villeret, Vincent; Locht, Camille; Antoine, Rudy; Jacob-Dubuisson, Françoise

2015-01-01

Two-component systems (TCS) represent major signal-transduction pathways for adaptation to environmental conditions, and regulate many aspects of bacterial physiology. In the whooping cough agent Bordetella pertussis, the TCS BvgAS controls the virulence regulon, and is therefore critical for pathogenicity. BvgS is a prototypical TCS sensor-kinase with tandem periplasmic Venus flytrap (VFT) domains. VFT are bi-lobed domains that typically close around specific ligands using clamshell motions. We report the X-ray structure of the periplasmic moiety of BvgS, an intricate homodimer with a novel architecture. By combining site-directed mutagenesis, functional analyses and molecular modeling, we show that the conformation of the periplasmic moiety determines the state of BvgS activity. The intertwined structure of the periplasmic portion and the different conformation and dynamics of its mobile, membrane-distal VFT1 domains, and closed, membrane-proximal VFT2 domains, exert a conformational strain onto the transmembrane helices, which sets the cytoplasmic moiety in a kinase-on state by default corresponding to the virulent phase of the bacterium. Signaling the presence of negative signals perceived by the periplasmic domains implies a shift of BvgS to a distinct state of conformation and activity, corresponding to the avirulent phase. The response to negative modulation depends on the integrity of the periplasmic dimer, indicating that the shift to the kinase-off state implies a concerted conformational transition. This work lays the bases to understand virulence regulation in Bordetella. As homologous sensor-kinases control virulence features of diverse bacterial pathogens, the BvgS structure and mechanism may pave the way for new modes of targeted therapeutic interventions. PMID:25738876