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1

Conformational transitions in model silk peptides.  

PubMed Central

Protein structural transitions and beta-sheet formation are a common problem both in vivo and in vitro and are of critical relevance in disparate areas such as protein processing and beta-amyloid and prion behavior. Silks provide a "databank" of well-characterized polymorphic sequences, acting as a window onto structural transitions. Peptides with conformationally polymorphic silk-like sequences, expected to exhibit an intractable beta-sheet form, were characterized using Fourier transform infrared spectroscopy, circular dichroism, and electron diffraction. Polymorphs resembling the silk I, silk II (beta-sheet), and silk III (threefold polyglycine II-like helix) crystal structures were identified for the peptide fibroin C (GAGAGS repetitive sequence). Two peptides based on silk amorphous sequences, fibroin A (GAGAGY) and fibroin V (GDVGGAGATGGS), crystallized as silk I under most conditions. Methanol treatment of fibroin A resulted in a gradual transition from silk I to silk II, with an intermediate state involving a high proportion of beta-turns. Attenuated total reflectance Fourier transform infrared spectroscopy has been used to observe conformational changes as the peptides adsorb from solution onto a hydrophobic surface. Fibroin C has a beta-strand structure in solution but adopts a silk I-like structure upon adsorption, which when dried on the ZnSe crystal contains silk III crystallites. PMID:10777765

Wilson, D; Valluzzi, R; Kaplan, D

2000-01-01

2

Atomistic simulations of the MS2 coat protein conformational transition  

NASA Astrophysics Data System (ADS)

During the replication of many viruses, hundreds to thousands of proteins self-assemble to form a protective protein coat, called a capsid, around the viral nucleic acid. Often these proteins have identical amino acid sequences with slightly different, or quasi-equivalent, conformations, which join in precise spatial arrangements. Although the structure of completed capsids is known to atomic resolution, little is known about the assembly intermediates and how protein conformations are selected during assembly. In this talk, we will use all-atom simulations to investigate how protein-RNA interactions guide conformational transitions of capsid proteins from the single-stranded RNA bacteriophage MS2. Since conformational changes occur on timescales which are not accessible to all-atom simulations, we use enhanced sampling methods to sample probable transition pathways and corresponding free energy profiles. Specifically, we will present free energy profiles associated with the MS2 capsid protein conformation in the presence and absence of RNA.

Perkett, Matthew; Pontiggia, Francesco; Hagan, Michael

2012-02-01

3

Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins  

NASA Astrophysics Data System (ADS)

A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-?s canonical MD simulation failed to sample such a rare event.

Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

2014-03-01

4

Intermediate conformations during viral fusion glycoprotein structural transition.  

PubMed

Entry of enveloped viruses into cells requires the fusion of viral and cellular membranes, driven by conformational changes in viral glycoproteins. Three different classes of viral fusion proteins have been hitherto identified based on common structural elements. Crystal structures have provided static pictures of pre-fusion and post-fusion conformations of these proteins and have revealed the dramatic reorganization of the molecules, but the transition pathway remains elusive. In this review, we will focus on recent data aiming to characterize intermediate structures during the conformational change. All these data support the existence of a pre-hairpin intermediate, but its oligomeric status is still a matter of debate. PMID:23562213

Baquero, Eduard; Albertini, Aurélie A; Vachette, Patrice; Lepault, Jean; Bressanelli, Stéphane; Gaudin, Yves

2013-04-01

5

Sequence Recognition of DNA by Protein-Induced Conformational Transitions  

E-print Network

bonding.2 In indirect readout, DNA sequence is detected by its propensity to assume noncanonical conformaSequence Recognition of DNA by Protein-Induced Conformational Transitions Derrick Watkins1 The binding of proteins to specific sequences of DNA is an important feature of virtually all DNA transactions

Williams, Loren

6

Conformation and Phase Transition of Poly-Glutamine  

NASA Astrophysics Data System (ADS)

In order to provide insights into the misfolding mechanism and the subsequent aggregate formation which cause what are known as the neurodegenerative polyglutamine diseases, we have simulated a 10-residue polyglutamine (poly-Q) chain in vacuum and in solvent by multicanonical method, which enabled us to study the system in a wide temperature range and discuss thermodynamic properties. It is understood that the system in vacuum shows two phase transitions, first of them occur at high temperature that is the well-known helix-coil transition and the second one is a solid-solid transition. However, the poly-Q chain in solvent is in a random coil state at higher temperatures, goes through a conformational change at T = 200 K and assumes predominantly a mixture of anti-parallel ?-sheet and ?-helix structures at low temperatures. One-residue glutamine dipeptide is also simulated and low-energy stable conformations are identified.

Göko?lu, Gökhan; Çelik, Tarik

7

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations  

PubMed Central

The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on ? -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

2011-01-01

8

Diversity of solvent dependent energy transfer pathways in heme proteins.  

PubMed

The time scales and pathways of heme cooling in both reduced cytochrome c and oxidized cytochrome c following heme photoexcitation were studied using molecular dynamics simulation. Five different solvent models, including normal water, heavy water, normal glycerol, deuterated glycerol, and a nonpolar solvent, were used in the simulation. Single exponential decay of the excess kinetic energy of the heme following photoexcitation was observed in all systems studied. The simulated time scale for heme cooling in normal water agrees with recent experimental results. In contrast to heme cooling in myoglobin, no solvent dependence was observed for the time scale for heme cooling in cytochrome c. The diversity of solvent dependence results from the different local heme environments in the two proteins. In myoglobin, it has been established that the dominant mechanism for heme cooling is direct energy transfer from the heme to the solvent. In cytochrome c, direct interaction between heme and protein residues forms the dominant energy transfer pathway. This distinction is dictated by protein topology and linked to function. PMID:19115811

Zhang, Yong; Straub, John E

2009-01-22

9

Conformation transitions of eukaryotic polyribosomes during multi-round translation  

PubMed Central

Using sedimentation and cryo electron tomography techniques, the conformations of eukaryotic polyribosomes formed in a long-term cell-free translation system were analyzed over all the active system lifetime (20–30 translation rounds during 6–8 h in wheat germ extract at 25°C). Three distinct types of the conformations were observed: (i) circular polyribosomes, varying from ring-shaped forms to circles collapsed into double rows, (ii) linear polyribosomes, tending to acquire planar zigzag-like forms and (iii) densely packed 3D helices. At the start, during the first two rounds of translation mostly the circular (ring-shaped and double-row) polyribosomes and the linear (free-shaped and zigzag-like) polyribosomes were formed (‘juvenile phase’). The progressive loading of the polyribosomes with translating ribosomes induced the opening of the circular polyribosomes and the transformation of a major part of the linear polyribosomes into the dense 3D helices (‘transitional phase’). After 2 h from the beginning (about 8–10 rounds of translation) this compact form of polyribosomes became predominant, whereas the circular and linear polyribosome fractions together contained less than half of polysomal ribosomes (‘steady-state phase’). The latter proportions did not change for several hours. Functional tests showed a reduced translational activity in the fraction of the 3D helical polyribosomes. PMID:25520190

Afonina, Zhanna A.; Myasnikov, Alexander G.; Shirokov, Vladimir A.; Klaholz, Bruno P.; Spirin, Alexander S.

2015-01-01

10

Conformation transitions of eukaryotic polyribosomes during multi-round translation.  

PubMed

Using sedimentation and cryo electron tomography techniques, the conformations of eukaryotic polyribosomes formed in a long-term cell-free translation system were analyzed over all the active system lifetime (20-30 translation rounds during 6-8 h in wheat germ extract at 25°C). Three distinct types of the conformations were observed: (i) circular polyribosomes, varying from ring-shaped forms to circles collapsed into double rows, (ii) linear polyribosomes, tending to acquire planar zigzag-like forms and (iii) densely packed 3D helices. At the start, during the first two rounds of translation mostly the circular (ring-shaped and double-row) polyribosomes and the linear (free-shaped and zigzag-like) polyribosomes were formed ('juvenile phase'). The progressive loading of the polyribosomes with translating ribosomes induced the opening of the circular polyribosomes and the transformation of a major part of the linear polyribosomes into the dense 3D helices ('transitional phase'). After 2 h from the beginning (about 8-10 rounds of translation) this compact form of polyribosomes became predominant, whereas the circular and linear polyribosome fractions together contained less than half of polysomal ribosomes ('steady-state phase'). The latter proportions did not change for several hours. Functional tests showed a reduced translational activity in the fraction of the 3D helical polyribosomes. PMID:25520190

Afonina, Zhanna A; Myasnikov, Alexander G; Shirokov, Vladimir A; Klaholz, Bruno P; Spirin, Alexander S

2015-01-01

11

Conformational Transitions of Subunit ? in ATP Synthase from Thermophilic Bacillus PS3  

Microsoft Academic Search

Subunit ? of bacterial and chloroplast FOF1-ATP synthase is responsible for inhibition of ATPase activity. In Bacillus PS3 enzyme, subunit ? can adopt two conformations. In the “extended”, inhibitory conformation, its two C-terminal ?-helices are stretched along subunit ?. In the “contracted”, noninhibitory conformation, these helices form a hairpin. The transition of subunit ? from an extended to a contracted

Boris A. Feniouk; Yasuyuki Kato-Yamada; Masasuke Yoshida; Toshiharu Suzuki

2010-01-01

12

Sequence Recognition of DNA by Protein-Induced Conformational Transitions  

SciTech Connect

The binding of proteins to specific sequences of DNA is an important feature of virtually all DNA transactions. Proteins recognize specific DNA sequences using both direct readout (sensing types and positions of DNA functional groups) and indirect readout (sensing DNA conformation and deformability). Previously we showed that the P22 c2 repressor N-terminal domain (P22R NTD) forces the central non-contacted 5{prime}-ATAT-3{prime} sequence of the DNA operator into the B{prime} state, a state known to affect DNA hydration, rigidity and bending. Usually the B{prime} state, with a narrow minor groove and a spine of hydration, is reserved for A-tract DNA (TpA steps disrupt A-tracts). Here, we have co-crystallized P22R NTD with an operator containing a central 5{prime}-ACGT-3{prime} sequence in the non-contacted region. C {center_dot} G base pairs have not previously been observed in the B{prime} state and are thought to prevent it. However, P22R NTD induces a narrow minor groove and a spine of hydration to 5{prime}-ACGT-3{prime}. We observe that C {center_dot} G base pairs have distinctive destabilizing and disordering effects on the spine of hydration. It appears that the reduced stability of the spine results in a higher energy cost for the B to B{prime} transition. The differential effect of DNA sequence on the barrier to this transition allows the protein to sense the non-contacted DNA sequence.

Watkins, Derrick; Mohan, Srividya; Koudelka, Gerald B.; Williams, Loren Dean (GIT); (SUNYB)

2010-11-09

13

Conformational Transitions of Subunit ? in ATP Synthase from Thermophilic Bacillus PS3  

PubMed Central

Abstract Subunit ? of bacterial and chloroplast FOF1-ATP synthase is responsible for inhibition of ATPase activity. In Bacillus PS3 enzyme, subunit ? can adopt two conformations. In the “extended”, inhibitory conformation, its two C-terminal ?-helices are stretched along subunit ?. In the “contracted”, noninhibitory conformation, these helices form a hairpin. The transition of subunit ? from an extended to a contracted state was studied in ATP synthase incorporated in Bacillus PS3 membranes at 59°C. Fluorescence energy resonance transfer between fluorophores introduced in the C-terminus of subunit ? and in the N-terminus of subunit ? was used to follow the conformational transition in real time. It was found that ATP induced the conformational transition from the extended to the contracted state (half-maximum transition extent at 140 ?M ATP). ADP could neither prevent nor reverse the ATP-induced conformational change, but it did slow it down. Acid residues in the DELSEED region of subunit ? were found to stabilize the extended conformation of ?. Binding of ATP directly to ? was not essential for the ATP-induced conformational change. The ATP concentration necessary for the half-maximal transition (140 ?M) suggests that subunit ? probably adopts the extended state and strongly inhibits ATP hydrolysis only when the intracellular ATP level drops significantly below the normal value. PMID:20141757

Feniouk, Boris A.; Kato-Yamada, Yasuyuki; Yoshida, Masasuke; Suzuki, Toshiharu

2010-01-01

14

Pseudorotation and conformational transitions in crystal structures having trigonal prismatic coordination  

SciTech Connect

Kinematic regularities have been examined for the conformational rearrangement of clusters showing trigonal prismatic coordination. Pseudorotation is postulated in an MX/sub 6/ coordination polyhedron, and it has been found that conformation transitions can occur without disrupting most of the bonds. A kinematic cell has been identified in the transition-metal dichalcogenides MX/sub 2/ as a pair of trigonal prisms linked by lateral edges, whose conformation features are similar to those of boat-shaped rings. It is found that the conformation changes in parts of the MX/sub 2/ structure can occur in two ways: by matched rearrangements of chains linking flexible rings or by local transformation of the ring segments. The equilibrium conformations of structurally flexible fragments have been examined: linear, clump-convoluted, and spiral. There is a discussion of the scope for a rotational isomeric mechanism for rearrangement involving trigonal prismatic coordination in glide and in polytype transitions.

Shchegolev, V.A.; Derlugyan, I.D.; Derlugyan, P.D.

1987-09-01

15

Monte Carlo analysis of conformational transitions in superhelical DNA Hongzhi Sun  

E-print Network

Monte Carlo analysis of conformational transitions in superhelical DNA Hongzhi Sun Department August 1995 Metropolis­Monte Carlo algorithms are developed to analyze the strand separation transition the results of Monte Carlo calculations that use shuffling operations are compared with those from statistical

Benham, Craig J.

16

Conformational transition of response regulator RR468 in a two-component system signal transduction process.  

PubMed

Signal transduction can be accomplished via a two-component system (TCS) consisting of a histidine kinase (HK) and a response regulator (RR). In this work, we simulate the response regulator RR468 from Thermotoga maritima, in which phosphorylation and dephosphorylation of a conserved aspartate residue acts as a switch via a large conformational change concentrated in three proximal loops. A detailed view of the conformational transition is obscured by the lack of stability of the intermediate states, which are difficult to detect using common structural biology techniques. Molecular dynamics (MD) trajectories of the inactive and active conformations were run, and show that the inactive (or active) trajectories do not exhibit sampling of the active (or inactive) conformations on this time scale. Targeted MD (TMD) was used to generate trajectories that span the inactive and active conformations and provide a view of how a localized event like phosphorylation can lead to conformational changes elsewhere in the protein, especially in the three proximal loops. The TMD trajectories are clustered to identify stages along the transition path. Residue interaction networks are identified that point to key residues having to rearrange in the process of transition. These are identified using both hydrogen bond analysis and residue interaction strength measurements. Potentials of mean force are generated for key residue rearrangements to ascertain their free energy barriers. We introduce methods that attempt to extrapolate from one conformation to the other and find that the most fluctuating proximal loop can transit part way from one to the other, suggesting that this conformational information is embedded in the sequence. PMID:24731214

Banerjee, Rahul; Yan, Honggao; Cukier, Robert I

2014-05-01

17

Anomalous conformational transitions in cytochrome C adsorbing to Langmuir-Blodgett films  

NASA Astrophysics Data System (ADS)

Helix to beta conformational transitions in proteins has attracted much attention due to their relevance to fibril formation which is implicated in many neurological diseases. This study reports on unusual conformational transition of cytochrome C adsorbing to hydrophilic surface containing pure cationic lipid and mixed Langmuir-Blodgett films (LB films) of cationic and neutral lipids. Evidence for conformational changes of the protein from its native helical state to beta sheet comes from Circular dichroic spectroscopy (CD spectroscopy). Analysis of these samples using High resolution TEM (HRTEM) shows a typical fibrillar pattern with each strand spacing of about 0.41 nm across which can be attributed to the repeat distance of interdigitated neighboring hydrogen-bonded ribbons in a beta sheet. Changes in contact angles of protein adsorbing to the LB films together with the increased mass uptake of water using quartz crystal microbalance (QCM) confirm the role of positive charges in the conformational transition. Dehydration of the protein resulting from the excess water entrainment in the polar planes of the cationic lipid in hydrophilic surface seems to trigger the refolding of the protein to beta sheet while it retains its native conformation in hydrophobic films. The results suggest that drastic conformational changes in CytC adsorbing to cationic lipids may be of significance in its role as a peripheral membrane protein.

Sankaranarayanan, Kamatchi; Nair, B. U.; Dhathathreyan, A.

2013-05-01

18

Conformational transitions in human translin enable nucleic acid binding  

PubMed Central

Translin is a highly conserved RNA- and DNA-binding protein that plays essential roles in eukaryotic cells. Human translin functions as an octamer, but in the octameric crystallographic structure, the residues responsible for nucleic acid binding are not accessible. Moreover, electron microscopy data reveal very different octameric configurations. Consequently, the functional assembly and the mechanism of nucleic acid binding by the protein remain unclear. Here, we present an integrative study combining small-angle X-ray scattering (SAXS), site-directed mutagenesis, biochemical analysis and computational techniques to address these questions. Our data indicate a significant conformational heterogeneity for translin in solution, formed by a lesser-populated compact octameric state resembling the previously solved X-ray structure, and a highly populated open octameric state that had not been previously identified. On the other hand, our SAXS data and computational analyses of translin in complex with the RNA oligonucleotide (GU)12 show that the internal cavity found in the octameric assemblies can accommodate different nucleic acid conformations. According to this model, the nucleic acid binding residues become accessible for binding, which facilitates the entrance of the nucleic acids into the cavity. Our data thus provide a structural basis for the functions that translin performs in RNA metabolism and transport. PMID:23980029

Pérez-Cano, Laura; Eliahoo, Elad; Lasker, Keren; Wolfson, Haim J.; Glaser, Fabian; Manor, Haim; Bernadó, Pau; Fernández-Recio, Juan

2013-01-01

19

Conformal Dynamics and Thermal/Bulk Phase Transition in Lattice Gauge Theory with Many Fermion Species  

NASA Astrophysics Data System (ADS)

We summarize our recent results1,2 which investigate the conformal dynamics associated with the infra-red fixed point in colour SU(Nc = 3) gauge theory with a variable number (Nf) of fundamental fermions by using lattice Monte-Carlo simulations. We evaluate the thermal chiral phase transition as a function of Nf, and investigate the vanishing of the chiral dynamics in the large Nf region. Then, three independent analyses consistently indicate the onset of the conformal phase for Nf ? N*f ˜ 9.2 - 14.1. Furthermore, we study the bulk transition in Nf = 12 system with a focus on the interplay between the transition property and the improvements for the lattice action. We show that the bulk transition observed in the case of the naive action evolves into two rapid crossovers due to the improvement for the fermion sector.

Miura, Kohtaroh; Lombardo, Maria Paola; Pallante, Elisabetta; da Silva, Tiago Nunes; Deuzeman, Albert

20

Conformational DNA transition in the in vitro torsionally strained chicken beta-globin 5' region.  

PubMed Central

A sequence of 86 bp within the 5' region of the adult chicken beta-globin gene was found to undergo a DNA conformational transition at elevated levels of negative superhelical stress (- sigma = 0.068). In vitro chemical DNA modification studies which detect purine hyperreactivity (HR) to the alkylating agent diethyl pyrocarbonate (DEP) have identified this 86 bp long DEP-HR element. The DEP-HR element is composed of small, tandem segments with imperfect purine-pyrimidine alternations. Methylation of cytosines within GCGC sequences of the DEP-HR element facilitates this structural change. The binding of a monoclonal anti-Z-DNA antibody to the element has been revealed by chemical footprinting with DEP. These data suggest that the DEP-HR sequence can undergo a conformational transition to Z-DNA. It is unknown whether the conformational flexibility observed here occurs in vivo. Images PMID:3763402

Runkel, L; Nordheim, A

1986-01-01

21

The role of the 132–160 region in prion protein conformational transitions  

PubMed Central

The native conformation of host-encoded cellular prion protein (PrPC) is metastable. As a result of a post-translational event, PrPC can convert to the scrapie form (PrPSc), which emerges as the essential constituent of infectious prions. Despite thorough research, the mechanism underlying this conformational transition remains unknown. However, several studies have highlighted the importance of the N-terminal region spanning residues 90–154 in PrP folding. In order to understand why PrP folds into two different conformational states exhibiting distinct secondary and tertiary structure, and to gain insight into the involvement of this particular region in PrP transconformation, we studied the pressure-induced unfolding/ refolding of recombinant Syrian hamster PrP expanding from residues 90–231, and compared it with heat unfolding. By using two intrinsic fluorescent variants of this protein (Y150W and F141W), conformational changes confined to the 132–160 segment were monitored. Multiple conformational states of the Trp variants, characterized by their spectroscopic properties (fluorescence and UV absorbance in the fourth derivative mode), were achieved by tuning the experimental conditions of pressure and temperature. Further insight into unexplored conformational states of the prion protein, likely to mimic the in vivo structural change, was obtained from pressure-assisted cold unfolding. Furthermore, salt-induced conformational changes suggested a structural stabilizing role of Tyr150 and Phe141 residues, slowing down the conversion to a ?-sheet form. PMID:15772306

Torrent, Joan; Alvarez-Martinez, Maria Teresa; Liautard, Jean-Pierre; Balny, Claude; Lange, Reinhard

2005-01-01

22

"Wet to dry" conformational transition of polymer layers grafted to nanoparticles in nanocomposite  

E-print Network

in nanocomposite ! " # $ % & ' % ( ' 1 Laboratoire Léon Brillouin, CEA Saclay 91191 Gif sur Yvette Cedex France 2 corona grafted around silica nano particles dispersed inside a nanocomposite, a matrix of the same to the nanocomposite: a transition from a stretched and swollen form in solution to a Gaussian conformation

Paris-Sud XI, Université de

23

Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway  

NASA Astrophysics Data System (ADS)

Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is proposed as a molecular simulation method to generate conformational transition pathway under the condition that a set of "reactant" and "product" structures is known a priori. In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the product structure for the next cycle are repeated until the simulated structures move sufficiently close to the product. Folding of 10-residue mini-protein chignolin from the extended to native structures and open-close conformational transition of T4 lysozyme were investigated by PaCS-MD. In both cases, tens of cycles of 100-ps MD were sufficient to reach the product structures, indicating the efficient generation of conformational transition pathway in PaCS-MD with a series of conventional MD without additional external biases. Using the snapshots along the pathway as the initial coordinates, free energy landscapes were calculated by the combination with multiple independent umbrella samplings to statistically elucidate the conformational transition pathways.

Harada, Ryuhei; Kitao, Akio

2013-07-01

24

Supramolecular chemical shift reagents inducing conformational transitions: NMR analysis of carbohydrate homooligomer mixtures.  

PubMed

We introduce the concept of supramolecular chemical shift reagents as a tool to improve signal resolution for the NMR analysis of homooligomers. Non-covalent interactions with the shift reagent can constrain otherwise flexible analytes inducing a conformational transition that results in signal separation. Here we use this approach for the quantitative analysis of a complex homooligomeric glycan mixture. PMID:25604578

Beeren, Sophie R; Meier, Sebastian

2015-02-01

25

Constrained Proper Sampling of Conformations of Transition State Ensemble during Protein Folding  

E-print Network

Constrained Proper Sampling of Conformations of Transition State Ensemble during Protein Folding) is important for studying protein folding. A promising approach pioneered by Vendruscolo et al40 to study TSE to understand how proteins fold to its native state8,29,37 . Protein folding is a complex process that involves

Dai, Yang

26

Mapping the structure and conformational movements of proteins with transition metal ion FRET  

E-print Network

Mapping the structure and conformational movements of proteins with transition metal ion FRET of most allosteric proteins are unknown. Here we report that fluorescence resonance energy transfer (FRET structural rearrangements in proteins. This method provides several key advantages over classical FRET

Cai, Long

27

The impact of N-terminal phosphorylation on LHCII conformation in state transition  

NASA Astrophysics Data System (ADS)

State transition is an important protection mechanism of plants for maintaining optimal efficiency through redistributing unbalanced excitation energy between photo-system II (PSII) and photosystem I (PSI). This process depends on the reversible phosphorylation/dephosphorylation of the major light-harvesting complex II (LHCII) and its bi-directional migration between PSII and PSI. But it remains unclear how phosphorylation/dephosphorylation modulates the LHCII conformation and further regulates its reversible migration. Here molecular dynamics simulations (MDS) were employed to elucidate the impact of phosphorylation on LHCII conformation. The results indicated that N-terminal phosphorylation loosened LHCII trimer with decreased hydrogen bond (H-bond) interactions and extended the distances between neighboring monomers, which stemmed from the conformational adjustment of each monomer itself. Global conformational change of LHCII monomer started from its stromal Nterminal (including the phosphorylation sites) by enhancing its interaction to lipid membrane and by adjusting the interaction network with surrounded inter-monomer and intra-monomer transmembrane helixes of B, C, and A, and finally triggered the reorientation of transmembrane helixes and transferred the conformational change to luminal side helixes and loops. These results further our understanding in molecular mechanism of LHCII migration during state transition from the phosphorylation-induced microstructural feature of LHCII.

Ding, Jin-Hong; Li, Ning; Wang, Man-Liu; Zhang, Yan; Lü, Shou-Qin; Long, Mian

2014-06-01

28

Lithium Diisopropylamide-Mediated Enolizations: Solvent-Dependent Mixed Aggregation Effects  

E-print Network

Lithium Diisopropylamide-Mediated Enolizations: Solvent-Dependent Mixed Aggregation Effects Xiufeng spectroscopic investigations of lithium diisopropylamide-mediated ester enolization in THF, t-BuOMe, HMPA that the metalations by lithium diisopropylamide (LDA) homonuclear dimers proceed at nearly solvent-independent rates

Collum, David B.

29

Molecular dynamics study of the weakly solvent dependent relaxation dynamics following chlorine dioxide photoexcitation  

E-print Network

Molecular dynamics study of the weakly solvent dependent relaxation dynamics following chlorine The solvation dynamics following photoexcitation of chlorine dioxide OClO in different solvents are investigated chemistry.1­3 Representative of this group of compounds, chlorine dioxide OClO has been the subject of much

30

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model  

PubMed Central

Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results. PMID:24699246

Jo, Sunhwan; Bahar, Ivet; Roux, Benoît

2014-01-01

31

Statistical Mechanical Theory of Protein Conformation and Its Transition  

NASA Astrophysics Data System (ADS)

The statistical mechanical theory of the structural transitions of proteins is developed in accordance with the island model by considering the hydrophobic interactions and the entropy factors while connecting the two hydrophobic residues. The proteins treated here are apo-?-lactalbumin (1B9O), lysozyme (1LZ1), ferrocytochrome c (1CYC), cytochrome c (isozyme 1) (1YCC), chymotrypsin inhibitor 2 (2CI2), and ubiquitin (1UBQ). Among them, according to the experiments, 2CI2 and 1UBQ do not exhibit intermediate structures (two-state model), but others do exhibit intermediate structures that are sometimes termed molten globules (three-state model). The theory related to these facts is given in terms of the island model, specifically 1B9O and 1LZ1. The stability or instability of the intermediate structures is explained by the effects of entropy during folding and the amino acid sequence. The intermediate structure is composed of several stable islands, which become unstable during unfolding.

Kobayashi, Yukio; Wako, Hiroshi; Saitô, Nobuhiko

2007-07-01

32

Finite-Size Conformational Transitions: A Unifying Concept Underlying Chromosome Dynamics  

NASA Astrophysics Data System (ADS)

Investigating average thermodynamic quantities is not sufficient to understand conformational transitions of a finite-size polymer. We propose that such transitions are better described in terms of the probability distribution of some finite-size order parameter, and the evolution of this distribution as a control parameter varies. We demonstrate this claim for the coil-globule transition of a linear polymer and its mapping onto a two-state model. In a biological context, polymer models delineate the physical constraints experienced by the genome at different levels of organization, from DNA to chromatin to chromosome. We apply our finite-size approach to the formation of plectonemes in a DNA segment submitted to an applied torque and the ensuing helix-coil transition that can be numerically observed, with a coexistence of the helix and coil states in a range of parameters. Polymer models are also essential to analyze recent in vivo experiments providing the frequency of pairwise contacts between genomic loci. The probability distribution of these contacts yields quantitative information on the conformational fluctuations of chromosome regions. The changes observed in the shape of the distribution when the cell type or the physiological conditions vary may reveal an epigenetic modulation of the conformational constraints experienced by the chromosomes.

Bertrand, R. Caré; Pascal, Carrivain; Thierry, Forné; Jean-Marc, Victor; Annick, Lesne

2014-10-01

33

Mechanistic picture for conformational transition of a membrane transporter at atomic resolution  

PubMed Central

During their transport cycle, ATP-binding cassette (ABC) transporters undergo large-scale conformational changes between inward- and outward-facing states. Using an approach based on designing system-specific reaction coordinates and using nonequilibrium work relations, we have performed extensive all-atom molecular dynamics simulations in the presence of explicit membrane/solvent to sample a large number of mechanistically distinct pathways for the conformational transition of MsbA, a bacterial ABC exporter whose structure has been solved in multiple functional states. The computational approach developed here is based on (i) extensive exploration of system-specific biasing protocols (e.g., using collective variables designed based on available low-resolution crystal structures) and (ii) using nonequilibrium work relations for comparing the relevance of the transition pathways. The most relevant transition pathway identified using this approach involves several distinct stages reflecting the complex nature of the structural changes associated with the function of the protein. The opening of the cytoplasmic gate during the outward- to inward-facing transition of apo MsbA is found to be disfavored when the periplasmic gate is open and facilitated by a twisting motion of the nucleotide-binding domains that involves a dramatic change in their relative orientation. These results highlight the cooperativity between the transmembrane and the nucleotide-binding domains in the conformational transition of ABC exporters. The approach introduced here provides a framework to study large-scale conformational changes of other membrane transporters whose computational investigation at an atomic resolution may not be currently feasible using conventional methods. PMID:24191018

Moradi, Mahmoud; Tajkhorshid, Emad

2013-01-01

34

Mechanistic picture for conformational transition of a membrane transporter at atomic resolution.  

PubMed

During their transport cycle, ATP-binding cassette (ABC) transporters undergo large-scale conformational changes between inward- and outward-facing states. Using an approach based on designing system-specific reaction coordinates and using nonequilibrium work relations, we have performed extensive all-atom molecular dynamics simulations in the presence of explicit membrane/solvent to sample a large number of mechanistically distinct pathways for the conformational transition of MsbA, a bacterial ABC exporter whose structure has been solved in multiple functional states. The computational approach developed here is based on (i) extensive exploration of system-specific biasing protocols (e.g., using collective variables designed based on available low-resolution crystal structures) and (ii) using nonequilibrium work relations for comparing the relevance of the transition pathways. The most relevant transition pathway identified using this approach involves several distinct stages reflecting the complex nature of the structural changes associated with the function of the protein. The opening of the cytoplasmic gate during the outward- to inward-facing transition of apo MsbA is found to be disfavored when the periplasmic gate is open and facilitated by a twisting motion of the nucleotide-binding domains that involves a dramatic change in their relative orientation. These results highlight the cooperativity between the transmembrane and the nucleotide-binding domains in the conformational transition of ABC exporters. The approach introduced here provides a framework to study large-scale conformational changes of other membrane transporters whose computational investigation at an atomic resolution may not be currently feasible using conventional methods. PMID:24191018

Moradi, Mahmoud; Tajkhorshid, Emad

2013-11-19

35

The Conformational Transition Pathways of ATP-Binding Cassette Transporter BtuCD Revealed by Targeted Molecular Dynamics Simulation  

PubMed Central

BtuCD is a member of the ATP-binding cassette transporters in Escherichia coli that imports vitamin B12 into the cell by utilizing the energy of ATP hydrolysis. Crystal structures of BtuCD and its homologous protein HI1470/1 in various conformational states support the “alternating access” mechanism which proposes the conformational transitions of the substrate translocation pathway at transmembrane domain (TMD) between the outward-facing and inward-facing states. The conformational transition at TMD is assumed to couple with the movement of the cytoplasmic nucleotide-binding domains (NBDs) driven by ATP hydrolysis/binding. In this study, we performed targeted molecular dynamics (MD) simulations to explore the atomic details of the conformational transitions of BtuCD importer. The outward-facing to inward-facing (O?I) transition was found to be initiated by the conformational movement of NBDs. The subsequent reorientation of the substrate translocation pathway at TMD began with the closing of the periplasmic gate, followed by the opening of the cytoplamic gate in the last stage of the conformational transition due to the extensive hydrophobic interactions at this region, consistent with the functional requirement of unidirectional transport of the substrates. The reverse inward-facing to outward-facing (I?O) transition was found to exhibit intrinsic diversity of the conformational transition pathways and significant structural asymmetry, suggesting that the asymmetric crystal structure of BtuCD-F is an intermediate state in this process. PMID:22272354

Weng, Jingwei; Fan, Kangnian; Wang, Wenning

2012-01-01

36

Binding to the lipid monolayer induces conformational transition in A? monomer.  

PubMed

Using implicit solvent atomistic model and replica exchange molecular dynamics, we study binding of A? monomer to zwitterionic dimyristoylphosphatidylcholine (DMPC) lipid monolayer. Our results suggest that A? binding to the monolayer is governed primarily by positively charged and aromatic amino acids. Lysine residues tend to interact with surface choline and phosphorous lipid groups, whereas aromatic amino acids penetrate deeper into the monolayer, reaching its hydrophobic core. We show that binding to the DMPC monolayer causes a dramatic conformational transition in A? monomer, resulting in chain extension, loss of intrapeptide interactions, and formation of ?-structure. This conformational transition is far more significant than that occurring during the initial stages of aggregation in water. We also found that A? binding perturbs surface ordering of lipids interacting with A?. PMID:23053007

Kim, Seongwon; Klimov, Dmitri K

2013-02-01

37

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition  

SciTech Connect

One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet, E-mail: msayar@ku.edu.tr [College of Engineering, Koç University, 34450 Istanbul (Turkey)] [College of Engineering, Koç University, 34450 Istanbul (Turkey); Peter, Christine [Max Planck Institute for Polymer Research, 55128 Mainz (Germany) [Max Planck Institute for Polymer Research, 55128 Mainz (Germany); Department of Chemistry, University of Konstanz, 78547 Konstanz (Germany)

2013-12-21

38

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition  

NASA Astrophysics Data System (ADS)

One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

Dalgicdir, Cahit; Sensoy, Ozge; Peter, Christine; Sayar, Mehmet

2013-12-01

39

Solid-to-hybrid transitioning armature railgun with non-conforming-to-prejudice bore profile  

DOEpatents

An improved railgun, railgun barrel, railgun projectile, and railgun system for accelerating a solid-to-hybrid transitioning armature projectile using a barrel having a bore that does not conform to a cross-sectional profile of the projectile, to contact and guide the projectile only by the rails in a low pressure bore volume so as to minimize damage, failure, and/or underperformance caused by plasma armatures, insulator ablation, and/or restrikes.

Solberg, Jerome Michael

2012-12-04

40

STIM1 couples to ORAI1 via an intramolecular transition into an extended conformation  

PubMed Central

Stromal interaction molecule (STIM1) and ORAI1 are key components of the Ca2+ release-activated Ca2+ (CRAC) current having an important role in T-cell activation and mast cell degranulation. CRAC channel activation occurs via physical interaction of ORAI1 with STIM1 when endoplasmic reticulum Ca2+ stores are depleted. Here we show, utilizing a novel STIM1-derived Förster resonance energy transfer sensor, that the ORAI1 activating small fragment (OASF) undergoes a C-terminal, intramolecular transition into an extended conformation when activating ORAI1. The C-terminal rearrangement of STIM1 does not require a functional CRAC channel, suggesting interaction with ORAI1 as sufficient for this conformational switch. Extended conformations were also engineered by mutations within the first and third coiled-coil domains in the cytosolic portion of STIM1 revealing the involvement of hydrophobic residues in the intramolecular transition. Corresponding full-length STIM1 mutants exhibited enhanced interaction with ORAI1 inducing constitutive CRAC currents, even in the absence of store depletion. We suggest that these mutant STIM1 proteins imitate a physiological activated state, which mimics the intramolecular transition that occurs in native STIM1 upon store depletion. PMID:21427704

Muik, Martin; Fahrner, Marc; Schindl, Rainer; Stathopulos, Peter; Frischauf, Irene; Derler, Isabella; Plenk, Peter; Lackner, Barbara; Groschner, Klaus; Ikura, Mitsuhiko; Romanin, Christoph

2011-01-01

41

Solvent dependent supramolecular self-assembly and surface reversal of a modified porphyrin.  

PubMed

In this paper, a novel core-modified porphyrin with meso-aryl substituents and phenanthrene-fused pyrrole rings (N2S2-OR) is synthesized. Scanning tunneling microscopy (STM) has been used to probe its self-assembly behavior on a highly-oriented pyrolytic graphite (HOPG) surface. Our STM results have shown that there is an obvious solvent-dependent self-assembly for the surface-confined target molecules. In n-tetradecane, N2S2-OR assembles into a perfect alternating structure. At the 1-phenyloctane-graphite interface, disordered structures are formed and nonperiodic alternation is observed, whereas the target molecule in 1-heptanoic acid is assumed to form homogeneous close-packed monolayers with no alternating. Interestingly, such solvent-dependent supramolecular assembled behavior also involves the structural transformation of the backbone of the core-modified porphyrin derivative from saddle to reversed-saddle in these three solvents with different polarities. PMID:23764927

Zhang, Xuemei; Xu, Haijun; Shen, Yongtao; Wang, Yibing; Shen, Zhen; Zeng, Qingdao; Wang, Chen

2013-08-14

42

Solvent dependent Raman bandshape analysis on Cdbnd O containing molecules: Vibrational relaxation study  

NASA Astrophysics Data System (ADS)

Solvent dependent Raman band studies of some carbonyl containing molecules have been carried out in chlorobenzene (CLB) and chloroform (CLF) solvents. The variation of bandwidth with the solvent concentration was discussed using different mechanisms. The vibrational and reorientational correlation times were studied corresponding to solvent concentrations. The reorientational correlation time follows with the liquid viscosity in molecules under study. It reflects about the nature of solvent molecules hindering to the orientational motion of solute in liquid solution.

Gomti Devi, Th.; Upadhayay, Ganesh

2012-06-01

43

Conformational transitions in beta-lactoglobulin induced by cationic amphiphiles: equilibrium studies.  

PubMed

The conformational transition from the native state in water ("beta-state") to a state containing a considerable amount of alpha-helices ("alpha-state") was studied for the protein beta-lactoglobulin (BLG), from bovine milk, in several colloidal solutions containing mixed micelles or spontaneous vesicles. These aggregates were formed in the bicationic system containing the surfactant dodecyltrimethylammonium chloride (DTAC) and the lipid didodecyldimethylammonium bromide (DDAB). The beta-->alpha transition in BLG, investigated by far-ultraviolet circular dichroism spectroscopy, is induced to the same protein alpha-state by pure and mixed DDAB/DTAC micelles or vesicles. This implies a similar interaction mechanism of BLG with DDAB or DTAC, once the colloidal aggregates are formed. In premicelle DTAC solutions, the fraction of alpha-helix is lower and increases with the DTAC concentration. DDAB and DTAC also promote conformational changes in the protein tertiary structure that expose the tryptophans to a less constrained environment. These unfolding transitions were investigated by near-ultraviolet circular dichroism and steady-state fluorescence spectroscopies. In equilibrium conditions, it was found that higher DTAC (and, probably, DDAB) concentrations are needed to induce the beta-->alpha transition than to unfold the protein. beta-Lactoglobulin may therefore be considered as a model for protein-surfactant and protein-lipid interactions. PMID:15041677

Viseu, Maria Isabel; Carvalho, Teresa Isabel; Costa, Sílvia M B

2004-04-01

44

Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores.  

PubMed

Mechanical manipulation of DNA by forced extension can lead double-stranded DNA (dsDNA) to structurally transform from a helical form to a linear zipper-like form. By employing classical molecular dynamics and quantum mechanical nonequilibrium Green's function-based transport simulations, we show the ability of graphene nanopores to discern different dsDNA conformations, in a helical to zipper transition, using transverse electronic conductance. In particular, conductance oscillations due to helical dsDNA vanish as dsDNA extends from a helical form to a zipper form while it is transported through the nanopore. The predicted ability to detect conformational changes in dsDNA via transverse electronic conductance can widen the potential use of graphene-based nanosensors for DNA detection. PMID:25325530

Sathe, Chaitanya; Girdhar, Anuj; Leburton, Jean-Pierre; Schulten, Klaus

2014-11-01

45

Structural Basis of Lipid-Driven Conformational Transitions in the KvAP Voltage Sensing Domain  

PubMed Central

Voltage-gated ion channels respond to transmembrane electric fields through reorientations of the positively charged S4 helix within the voltage-sensing domain (VSD). Despite a wealth of structural and functional data, the details of this conformational change remain controversial. Recent electrophysiological evidence showed that equilibrium between the resting (Down) and activated (Up) conformations of KvAP-VSD from Aeropyrum pernix can be biased through reconstitution in lipids with or without phosphate groups. We investigated the structural transition between these functional states using site-directed spin labeling and EPR spectroscopic methods. Solvent accessibility and inter-helical distance determinations suggest that KvAP gates through S4 movements involving a ~3 Å upward tilt and simultaneous ~2 Å axial shift. This motion leads to large accessibly changes in the intracellular water-filled crevice and supports a novel model of gating that combines structural rearrangements and electric field remodeling. PMID:24413055

Li, Qufei; Wanderling, Sherry; Somponspisut, Pornthep; Perozo, Eduardo

2013-01-01

46

Mapping the Structure and Conformational Movements of Proteins with Transition Metal Ion FRET  

SciTech Connect

Visualizing conformational dynamics in proteins has been difficult, and the atomic-scale motions responsible for the behavior of most allosteric proteins are unknown. Here we report that fluorescence resonance energy transfer (FRET) between a small fluorescent dye and a nickel ion bound to a dihistidine motif can be used to monitor small structural rearrangements in proteins. This method provides several key advantages over classical FRET, including the ability to measure the dynamics of close-range interactions, the use of small probes with short linkers, a low orientation dependence, and the ability to add and remove unique tunable acceptors. We used this 'transition metal ion FRET' approach along with X-ray crystallography to determine the structural changes of the gating ring of the mouse hyperpolarization-activated cyclic nucleotide-regulated ion channel HCN2. Our results suggest a general model for the conformational switch in the cyclic nucleotide-binding site of cyclic nucleotide-regulated ion channels.

Taraska, J.; Puljung, M; Olivier, N; Olivier, G; Zagotta, W

2009-01-01

47

A Conformational Transition Observed in Single HIV-1 Gag Molecules during In Vitro Assembly of Virus-Like Particles  

PubMed Central

ABSTRACT The conformational changes within single HIV-1 Gag molecules that occur during assembly into immature viruses are poorly understood. Using an in vitro assembly assay, it has been proposed that HIV-1 Gag undergoes a conformational transition from a compact conformation in solution to an extended rod-like conformation in virus-like particles (VLPs). Here we used single-molecule Förster resonance energy transfer (smFRET) to test this model by directly probing the conformation of single HIV-1 Gag molecules. We demonstrate that monomeric HIV-1 Gag lacking the p6 domain and the N-terminal myristoyl moiety is found in solution predominantly in a compact conformation. Gag in this conformation, and in the presence of nucleic acid, assembles into 30-nm-diameter particles. However, with the addition of inositol hexakisphosphate, Gag adopts a linear conformation and assembles into full-sized ?100-to-150-nm-diameter VLPs. Parallel fluorescence correlation spectroscopy measurements show that this conformational transition occurs early in the assembly process when Gag oligomers are small, perhaps as early as upon dimerization. Thus, smFRET measurements confirm that HIV-1 Gag transitions from a compact to a linear conformation during the formation of VLPs. Our results are consistent with a model whereby binding of HIV-1 Gag to phosphoinositides at the plasma membrane stabilizes an extended conformation and promotes oligomerization into the radially aligned immature capsid. IMPORTANCE The establishment of single-molecule fluorescence techniques reveals the conformational state of individual HIV-1 Gag molecules prior to and during in vitro assembly into virus-like particles. The data demonstrate that Gag in distinct conformations forms particles with different morphologies. In the compact conformation, in the presence of nucleic acid, Gag forms spherical particles of a diameter of approximately 30 nm. In the extended conformation, Gag forms spherical virus-like particles of approximately 100-nm diameter. The adoption of the extended conformation required the presence of inositol hexakisphosphate in addition to nucleic acid. Our results are consistent with a model whereby binding of HIV-1 Gag to phosphoinositides at the plasma membrane stabilizes an extended conformation and promotes oligomerization into the radially aligned immature capsid. PMID:24403576

Nath, Abhinav; Färber, Michael; Datta, Siddhartha A. K.; Rein, Alan; Rhoades, Elizabeth

2014-01-01

48

"Wet-to-Dry" Conformational Transition of Polymer Layers Grafted to Nanoparticles in Nanocomposite  

E-print Network

The present communication reports the first direct measurement of the conformation of a polymer corona grafted around silica nano-particles dispersed inside a nanocomposite, a matrix of the same polymer. This measurement constitutes an experimental breakthrough based on a refined combination of chemical synthesis, which permits to match the contribution of the neutron silica signal inside the composite, and the use of complementary scattering methods SANS and SAXS to extract the grafted polymer layer form factor from the inter-particles silica structure factor. The modelization of the signal of the grafted polymer on nanoparticles inside the matrix and the direct comparison with the form factor of the same particles in solution show a clear-cut change of the polymer conformation from bulk to the nanocomposite: a transition from a stretched and swollen form in solution to a Gaussian conformation in the matrix followed with a compression of a factor two of the grafted corona. In the probed range, increasing the interactions between the grafted particles (by increasing the particle volume fraction) or between the grafted and the free matrix chains (decreasing the grafted-free chain length ratio) does not influence the amplitude of the grafted brush compression. This is the first direct observation of the wet-to-dry conformational transition theoretically expected to minimize the free energy of swelling of grafted chains in interaction with free matrix chains, illustrating the competition between the mixing entropy of grafted and free chains, and the elastic deformation of the grafted chains. In addition to the experimental validation of the theoretical prediction, this result constitutes a new insight for the nderstanding of the general problem of dispersion of nanoparticles inside a polymer matrix for the design of new nanocomposites materials.

Chloé Chevigny; Jacques Jestin; Didier Gigmes; Ralph Schweins; Emanuela Null Di Cola; Florent Dalmas; Denis Bertin; François Boué

2010-05-10

49

Long-range conformational transition of a photoswitchable allosteric protein: molecular dynamics simulation study.  

PubMed

A local perturbation of a protein may lead to functional changes at some distal site. An example is the PDZ2 domain of human tyrosine phosphatase 1E, which shows an allosteric transition upon binding to a peptide ligand. Recently Buchli et al. presented a time-resolved study of this transition by covalently linking an azobenzene photoswitch across the binding groove and using a femtosecond laser pulse that triggers the cis-trans photoisomerization of azobenzene. To aid the interpretation of these experiments, in this work seven microsecond runs of all-atom molecular dynamics simulations each for the wild-type PDZ2 in the ligand-bound and -free state, as well as the photoswitchable protein (PDZ2S) in the cis and trans states of the photoswitch, in explicit water were conducted. First the theoretical model is validated by recalculating the available NMR data from the simulations. By comparing the results for PDZ2 and PDZ2S, it is analyzed to what extent the photoswitch indeed mimics the free-bound transition. A detailed description of the conformational rearrangement following the cis-trans photoisomerization of PDZ2S reveals a series of photoinduced structural changes that propagate from the anchor residues of the photoswitch via intermediate secondary structure segments to the C-terminus of PDZ2S. The changes of the conformational distribution of the C-terminal region is considered as the distal response of the isolated allosteric protein. PMID:25365469

Buchenberg, Sebastian; Knecht, Volker; Walser, Reto; Hamm, Peter; Stock, Gerhard

2014-11-26

50

Conformational transitions of alternating purine-pyrimidine DNAs in perchlorate ethanol solutions.  

PubMed Central

Conformational transitions of poly(dA-dC).poly(dG-dT), poly(dA-dT).poly(dA-dT), and other alternating purine-pyrimidine DNAs were studied in aqueous ethanol solutions containing molar concentrations of sodium perchlorate, which is a novel solvent stabilizing non-B duplexes of DNA. Using CD and UV absorption spectroscopies, we show that this solvent unstacks bases and unwinds the B-forms of the DNAs to transform them into the A-form or Z-form. In the absence of divalent cations poly(dA-dC).poly(dG-dT) can adopt both of these conformations. Its transition into the Z-form is induced at higher salt and lower ethanol concentrations, and at higher temperatures than the transition into the A-form. Submillimolar concentrations of NiCl2 induce a highly cooperative and slow A-Z transition or Z-Z' transition, which is fast and displays low cooperativity. Poly(dA-dT).poly(dA-dT) easily isomerizes into the A-form in perchlorate-ethanol solutions, whereas high perchlorate concentrations denature the polynucleotide, which then cannot adopt the Z-form. At low temperatures, however, NiCl2 also cooperatively induces the Z'-form in poly(dA-dT).poly(dA-dT). Poly(dI-dC).poly(dI-dC) is known to adopt an unusual B-form in low-salt aqueous solution, which is transformed into a standard B-form by the combination of perchlorate and ethanol. NiCl2 then transforms poly(dI-dC).poly(dI-dC) into the Z'-form, which is also adopted by poly(dI-br5dC).poly(dI-br5dC). PMID:8580346

Vorlícková, M

1995-01-01

51

Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods  

PubMed Central

Background Obtaining atomic-scale information about large-amplitude conformational transitions in proteins is a challenging problem for both experimental and computational methods. Such information is, however, important for understanding the mechanisms of interaction of many proteins. Methods This paper presents a computationally efficient approach, combining methods originating from robotics and computational biophysics, to model protein conformational transitions. The ability of normal mode analysis to predict directions of collective, large-amplitude motions is applied to bias the conformational exploration performed by a motion planning algorithm. To reduce the dimension of the problem, normal modes are computed for a coarse-grained elastic network model built on short fragments of three residues. Nevertheless, the validity of intermediate conformations is checked using the all-atom model, which is accurately reconstructed from the coarse-grained one using closed-form inverse kinematics. Results Tests on a set of ten proteins demonstrate the ability of the method to model conformational transitions of proteins within a few hours of computing time on a single processor. These results also show that the computing time scales linearly with the protein size, independently of the protein topology. Further experiments on adenylate kinase show that main features of the transition between the open and closed conformations of this protein are well captured in the computed path. Conclusions The proposed method enables the simulation of large-amplitude conformational transitions in proteins using very few computational resources. The resulting paths are a first approximation that can directly provide important information on the molecular mechanisms involved in the conformational transition. This approximation can be subsequently refined and analyzed using state-of-the-art energy models and molecular modeling methods. PMID:24564964

2013-01-01

52

Conformational transitions during FtsK translocase activation of individual XerCD–dif recombination complexes  

PubMed Central

Three single-molecule techniques have been used simultaneously and in tandem to track the formation in vitro of single XerCD–dif recombination complexes. We observed the arrival of the FtsK translocase at individual preformed synaptic complexes and demonstrated the conformational change that occurs during their activation. We then followed the reaction intermediate transitions as Holliday junctions formed through catalysis by XerD, isomerized, and were converted by XerC to reaction products, which then dissociated. These observations, along with the calculated intermediate lifetimes, inform the reaction mechanism, which plays a key role in chromosome unlinking in most bacteria with circular chromosomes. PMID:24101525

Zawadzki, Pawel; May, Peter F. J.; Baker, Rachel A.; Pinkney, Justin N. M.; Kapanidis, Achillefs N.; Sherratt, David J.; Arciszewska, Lidia K.

2013-01-01

53

Bicyclic amino acid-carbohydrate-conjugates as conformationally restricted hydroxyethylamine (HEA) transition-state isosteres.  

PubMed

This communication describes a general synthetic route to bicyclic amino acid-carbohydrate-conjugates, which would be useful as conformationally restricted hydroxyethylamine (HEA) transition-state isosteres. The synthesis was achieved in 12 steps starting from D-glucose. The striking features of this system are the bicyclic rigid core displaying an ?-amino acid side chain and hydroxyethylamine moiety--both of which would be potentially important for receptor interactions, leading to various biomedical responses, as described in the literature. Crystal structure investigation suggested extensive intermolecular hydrogen-bonding interactions in this system, involving the backbone amide and hydroxyl groups. PMID:21915421

Kale, Sangram S; Chavan, Sanjay T; Sabharwal, Sushma G; Puranik, Vedavati G; Sanjayan, Gangadhar J

2011-11-01

54

Solvent dependent triphenylamine based D-(pi-A)n type dye molecules and optical properties.  

PubMed

D-(pi-A)n type dyes of triphenylamine derivatives were synthesized and their absorption and luminescence in different solvents were examined to investigate solvent dependent properties observed for their emissions in solvents with different dielectric constants. The emission wavelengths showed a dramatic blue shift with increasing solvent polarity. The results of molecular orbital calculations by computer simulation, based on Material Studio suite of programs, were found to reasonably account for the spectral properties. Relative levels of HOMO and LUMO were measured and calculated and all derivatives exhibited strong solid fluorescence with distinctively different FWHMs. PMID:22629987

Li, Xiaochuan; Son, Young-A; Kim, Young-Sung; Kim, Sung-Hoon; Kun, Jun; Shin, Jong-Il

2012-02-01

55

Nonequilibrium polymer chains induced by conformational transitions in densely interfacial layers  

NASA Astrophysics Data System (ADS)

Nonequilibrium poly(N-isopropylacrylamide) (PNIPAM) chains are generated by temperature-induced conformational transitions in the densely interfacial PNIPAM layer at high adsorbed amounts in aqueous solution. The interleaving chains relax in a spatially heterogeneous space of adsorbed layer which is filled with the domains via the hydrogen bonding and hydrophobic interactions. The relaxation dynamics of interleaving chains is changed from the weekly stretched exponential behaviour at the lower adsorbed amount to the strongly stretched exponential behaviour at the higher adsorbed amount. The kinetic constraints for the relaxation dynamics depend on the segment density of the adsorbed layer which is controlled by the temperature. The stretched exponential relaxation is related to an ensemble of relaxations confined in the domains with different physical origins for the heterogeneous dynamics. The range of energy barriers for the relaxation is estimated from the stretched exponent based on the random first order transition theory.

Zhu, Peng-Wei

2012-09-01

56

Nonequilibrium polymer chains induced by conformational transitions in densely interfacial layers.  

PubMed

Nonequilibrium poly(N-isopropylacrylamide) (PNIPAM) chains are generated by temperature-induced conformational transitions in the densely interfacial PNIPAM layer at high adsorbed amounts in aqueous solution. The interleaving chains relax in a spatially heterogeneous space of adsorbed layer which is filled with the domains via the hydrogen bonding and hydrophobic interactions. The relaxation dynamics of interleaving chains is changed from the weekly stretched exponential behaviour at the lower adsorbed amount to the strongly stretched exponential behaviour at the higher adsorbed amount. The kinetic constraints for the relaxation dynamics depend on the segment density of the adsorbed layer which is controlled by the temperature. The stretched exponential relaxation is related to an ensemble of relaxations confined in the domains with different physical origins for the heterogeneous dynamics. The range of energy barriers for the relaxation is estimated from the stretched exponent based on the random first order transition theory. PMID:22979886

Zhu, Peng-Wei

2012-09-14

57

Conformational and phase transitions in DNA-photosensitive surfactant solutions: Experiment and modeling.  

PubMed

DNA binding to trans- and cis-isomers of azobenzene containing cationic surfactant in 5 mM NaCl solution was investigated by the methods of dynamic light scattering (DLS), low-gradient viscometry (LGV), atomic force microscopy (AFM), circular dichroism (CD), gel electrophoresis (GE), flow birefringence (FB), UV-Vis spectrophotometry. Light-responsive conformational transitions of DNA in complex with photosensitive surfactant, changes in DNA optical anisotropy and persistent length, phase transition of DNA into nanoparticles induced by high surfactant concentration, as well as transformation of surfactant conformation under its binding to macromolecule were studied. Computer simulations of micelles formation for cis- and trans-isomers of azobenzene containing surfactant, as well as DNA-surfactant interaction, were carried out. Phase diagram for DNA-surfactant solutions was designed. The possibility to reverse the DNA packaging induced by surfactant binding with the dilution and light irradiation was shown. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 109-122, 2015. PMID:25302479

Kasyanenko, N; Lysyakova, L; Ramazanov, R; Nesterenko, A; Yaroshevich, I; Titov, E; Alexeev, G; Lezov, A; Unksov, I

2015-02-01

58

The Role of Conserved Waters in Conformational Transitions of Q61H K-ras  

PubMed Central

To investigate the stability and functional role of long-residence water molecules in the Q61H variant of the signaling protein K-ras, we analyzed all available Ras crystal structures and conformers derived from a series of independent explicit solvent molecular dynamics (MD) simulations totaling 1.76 µs. We show that the protein samples a different region of phase space in the presence and absence of several crystallographically conserved and buried water molecules. The dynamics of these waters is coupled with the local as well as the global motions of the protein, in contrast to less buried waters whose exchange with bulk is only loosely coupled with the motion of loops in their vicinity. Aided by two novel reaction coordinates involving the distance (d) between the C? atoms of G60 at switch 2 and G10 at the P-loop and the N-C?-C-O dihedral (?) of G60, we further show that three water molecules located in lobe1, at the interface between the lobes and at lobe2, are involved in the relative motion of residues at the two lobes of Q61H K-ras. Moreover, a d/? plot classifies the available Ras x-ray structures and MD-derived K-ras conformers into active GTP-, intermediate GTP-, inactive GDP-bound, and nucleotide-free conformational states. The population of these states and the transition between them is modulated by water-mediated correlated motions involving the functionally critical switch 2, P-loop and helix 3. These results suggest that water molecules act as allosteric ligands to induce a population shift among distinct switch 2 conformations that differ in effector recognition. PMID:22359497

Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Gorfe, Alemayehu A.

2012-01-01

59

Thermal stability and conformational transitions of scrapie amyloid (prion) protein correlate with infectivity.  

PubMed Central

The scrapie amyloid (prion) protein (PrP27-30) is the protease-resistant core of a larger precursor (PrPSc) and a component of the infectious scrapie agent; the potential to form amyloid is a result of posttranslational event or conformational abnormality. The conformation, heat stability, and solvent-induced conformational transitions of PrP27-30 were studied in the solid state in films by CD spectroscopy and correlated with the infectivity of rehydrated and equilibrated films. The exposure of PrP27-30 in films to 60 degrees C, 100 degrees C, and 132 degrees C for 30 min did not change the beta-sheet secondary structure; the infectivity slightly diminished at 132 degrees C and correlated with a decreased solubility of PrP27-30 in sodium dodecyl sulfate (SDS), probably due to cross-linking. Exposing PrP27-30 films to formic acid (FA), trifluoroacetic acid (TFA), trifluoroethanol (TFE), hexafluoro-2-propanol (HFIP), and SDS transformed the amide CD band, diminished the mean residue ellipticity of aromatic bands, and inactivated scrapie infectivity. The convex constraint algorithm (CAA) deconvolution of the CD spectra of the solvent-exposed and rehydrated solid state PrP27-30 identified five common spectral components. The loss of infectivity quantitatively correlated with a decreasing proportion of native, beta-pleated sheet-like secondary structure component, an increasing amount of alpha-helical component, and an increasingly disordered tertiary structure. The results demonstrate the unusual thermal stability of the beta-sheet secondary structure of PrP27-30 protein in the solid state. The conformational perturbations of PrP27-30 parallel the changes in infectivity and suggest that the beta-sheet structure plays a key role in the physical stability of scrapie amyloid and in the ability to propagate and replicate scrapie. PMID:7905316

Safar, J.; Roller, P. P.; Gajdusek, D. C.; Gibbs, C. J.

1993-01-01

60

Electron Transfer to Ferricytochrome c: Reaction with Hydrated Electrons and Conformational Transitions Involved  

PubMed Central

The reaction of horse-heart cytochrome c with hydrated electrons has been studied by the pulseradiolysis technique. In neutral solution, the ferriheme group was reduced in a bimolecular reaction that takes place at a rate equal to that of the decay of the e-aq, and approaches the diffusion-controlled limit. This reduction is assigned mainly to a direct reaction, proceeding via the exposed edge of the porphyrin projecting into the cytochrome c crevice. The reaction absorption spectrum observed 20 ?sec after an electron pulse was very similar, yet blue-shifted relative to, the difference spectrum between the reduced and oxidized forms of cytochrome c. However, this shift vanishes in a slow monomolecular reaction, which seems to reflect the conformational relaxation of the protein to the final equilibrium state of its reduced form. In alkaline solutions, the transition of cytochrome c molecules into an irreducible conformation causes a proportionate decrease in the amount of ferricytochrome c reduced in the direct reaction. The rate of conformational transition of the protein into the reactive form is now the limiting step for a substantial part of the reduction that takes place via this slow monomolecular reaction. Pseudomonas cytochrome c 551 which, in contrast to horse-heart cytochrome c, is a negatively charged protein at neutral pH reacts with e-aq at a rate lower than does the horse-heart protein. The reduction of the heme group follows that of the e-aq decay with a small, yet significant, delay. Images PMID:4623664

Pecht, Israel; Faraggi, Moshe

1972-01-01

61

Distinguishing Unfolding and Functional Conformational Transitions of Calmodulin Using Ultraviolet Resonance Raman Spectroscopy  

SciTech Connect

Calmodulin (CaM) is a ubiquitous moderator protein for calcium signaling in all eukaryotic cells. This small calcium-binding protein exhibits a broad range of structural transitions, including domain opening and folding-unfolding, that allow it to recognize a wide variety of binding partners in vivo. While the static structures of CaM associated with its various binding activities are fairly well known, it has been challenging to examine the dynamics of transition between these structures in real-time, due to a lack of suitable spectroscopic probes of CaM structure. In this paper, we examine the potential of ultraviolet resonance Raman (UVRR) spectroscopy for clarifying the nature of structural transitions in CaM. We find that the UVRR spectral change (with 229 nm excitation) due to thermal unfolding of CaM is qualitatively different from that associated with opening of the C-terminal domain in response to Ca2+ binding. This spectral difference is entirely due to differences in teritary contacts at the inter-domain tyrosine residue Tyr138, toward which other spectroscopic methods are not sensitive. We conclude that UVRR is ideally suited to identifying the different types of structural transitions in CaM and other proteins with conformation-sensitive tyrosine residues, opening a path to time-resolved studies of CaM dynamics using Raman spectroscopy.

Jones, Eric M.; Balakrishnan, G.; Squier, Thomas C.; Spiro, Thomas

2014-06-14

62

Conformational transitions of cinnamoyl CoA reductase 1 from Leucaena leucocephala.  

PubMed

Conformational transitions of cinnamoyl CoA reductase, a key regulatory enzyme in lignin biosynthesis, from Leucaena leucocephala (Ll-CCRH1) were studied using fluorescence and circular dichroism spectroscopy. The native protein possesses four trp residues exposed on the surface and 66% of helical structure, undergoes rapid structural transitions at and above 45 °C and starts forming aggregates at 55 °C. Ll-CCRH1 was transformed into acid induced (pH 2.0) molten globule like structure, exhibiting altered secondary structure, diminished tertiary structure and exposed hydrophobic residues. The molten globule like structure was examined for the thermal and chemical stability. The altered secondary structure of L1-CCRH1 at pH 2.0 was stable up to 90 °C. Also, in presence of 0.25 M guanidine hydrochloride (GdnHCl), it got transformed into different structure which was stable in the vicinity of 2M GdnHCl (as compared to drastic loss of native structure in 2M GdnHCl) as seen in far UV-CD spectra. The structural transition of Ll-CCRH1 at pH 2.0 followed another transition after readjusting the pH to 8.0, forming a structure with hardly any similarity to that of native protein. PMID:24309513

Sonawane, Prashant D; Khan, Bashir M; Gaikwad, Sushama M

2014-03-01

63

Stability of the primary organization of nucleosome core particles upon some conformational transitions.  

PubMed Central

The sequential arrangement of histones along DNA in nucleosome core particles was determined between 0.5 and 600 mM salt and from 0 to 8 M urea. These concentrations of salt and urea up to 6 M had no significant effect on the linear order of histones along DNA but 8 M urea caused the rearrangement of histones. Conformational changes in cores have been identified within these ranges of conditions by several laboratories 8-21. Also, abrupt structural changes in the cores, apparently their unfolding, were found by gel electrophoresis to occur at urea concentration, between 4 and 5 M. 600 mM salt and 6 M urea were shown to relax the binding of histones to DNA in cores but do not however release histones or some part of their molecules from DNA. It appears therefore that nucleosomal cores can undergo some conformational transitions and unfolding whereas their primary organization remains essentially unaffected. These results are consistent with a model of the core particles in which the histone octamer forms something like a helical "rim" along the superhelical DNA and histone-histone interactions beyond the "rim" are rather weak in comparison with those within the "rim". Images PMID:7232210

Zayetz, V W; Bavykin, S G; Karpov, V L; Mirzabekov, A D

1981-01-01

64

Stability of the primary organization of nucleosome core particles upon some conformational transitions.  

PubMed

The sequential arrangement of histones along DNA in nucleosome core particles was determined between 0.5 and 600 mM salt and from 0 to 8 M urea. These concentrations of salt and urea up to 6 M had no significant effect on the linear order of histones along DNA but 8 M urea caused the rearrangement of histones. Conformational changes in cores have been identified within these ranges of conditions by several laboratories 8-21. Also, abrupt structural changes in the cores, apparently their unfolding, were found by gel electrophoresis to occur at urea concentration, between 4 and 5 M. 600 mM salt and 6 M urea were shown to relax the binding of histones to DNA in cores but do not however release histones or some part of their molecules from DNA. It appears therefore that nucleosomal cores can undergo some conformational transitions and unfolding whereas their primary organization remains essentially unaffected. These results are consistent with a model of the core particles in which the histone octamer forms something like a helical "rim" along the superhelical DNA and histone-histone interactions beyond the "rim" are rather weak in comparison with those within the "rim". PMID:7232210

Zayetz, V W; Bavykin, S G; Karpov, V L; Mirzabekov, A D

1981-03-11

65

Conformational transitions of macromolecules in an eluent flow and their manifestation in the chromatography of polymers  

NASA Astrophysics Data System (ADS)

The behaviour of macromolecules in a free eluent flow, in a confined space, and in a flow passing through a pore system is considered. It is shown that the behaviour of macromolecules can be described by different theories such as the De Gennes theory and the theory of A DiMarzio and C M Guttman. Specific features of chromatographic fractionation and separation processes with the use of membranes formed from ultrahigh-molecular-mass polymers, which are widely used as constructional materials, are discussed. To account for these features, theoretical models considering conformational transitions of macromolecules in the eluent flow and taking into account possible degradation of macromolecules under the influence of the flow are applied. The current state of theoretical and experimental studies of the behaviour of macromolecules in a fluid flow is surveyed. The bibliography includes 152 references.

Kurganov, A. A.; Kanateva, A. Yu; Orekhov, V. A.

2014-07-01

66

Conformational transition of membrane-associated terminally-acylated HIV-1 Nef  

PubMed Central

Many proteins are post-translationally modified by acylation targetting them to lipid membranes. While methods such as X-ray crystallography and NMR are available to determine the structure of folded proteins in solution, the precise position of folded domains relative to a membrane remains largely unknown. We used neutron and X-ray reflection methods to measure the displacement of the core domain of HIV Nef from lipid membranes upon insertion of the N-terminal myristate group. Nef is one of several HIV-1 accessory proteins and an essential factor in AIDS progression. Upon insertion of the myristate and residues from the N-terminal arm, Nef transitions from a closed to open conformation that positions the core domain 70 Å from the lipid headgroups. This work rules out speculation that the Nef core remains closely associated with the membrane to optimize interactions with the cytoplasmic domain of MHC-1. PMID:24035710

Akgun, Bulent; Satija, Sushil; Nanda, Hirsh; Pirrone, Gregory F.; Shi, Xiaomeng; Engen, John R.; Kent, Michael S.

2013-01-01

67

Particular behavior of the adenine and guanine ring-breathing modes upon the DNA conformational transitions.  

PubMed

Harmonic dynamics calculations performed on the deoxyguanosine (dG) and deoxyadenosine (dA) residues, based on a reliable force field, show that the breathing motions of both guanine and adenine residues are involved in two different vibration modes (750-500 cm-1 spectral region). The calculated results reveal a strong coupling of these modes with the sugar pucker motions. This effect has been verified for the dG residue by the Raman spectra of polyd(G-C). As far as the dA residue is concerned, the particular behavior of the adenine residue breathing mode predicted by these calculations, has been confirmed by Raman spectra of polyd(A-T) undergoing a B----Z conformational transition. PMID:3139101

Ghomi, M; Letellier, R; Taillandier, E

1988-06-01

68

Nucleotide-free MalK drives the transition of the maltose transporter to the inward-facing conformation.  

PubMed

The complex MalFGK2 hydrolyzes ATP and alternates between inward- and outward-facing conformations during maltose transport. It has been shown that ATP promotes closure of MalK2 and opening of MalFG toward the periplasm. Yet, why the transporter rests in a conformation facing the cytosol in the absence of nucleotide and how it returns to this state after hydrolysis of ATP is unknown. The membrane domain MalFG may be naturally stable in the inward-facing conformation, or the ABC domain may catalyze the transition. We address this question by analyzing the conformation of MalFG in nanodiscs and in proteoliposomes. We find that MalFG alone exists in an intermediate state until MalK binds and converts the membrane domain to the inward-facing state. We also find that MalK, if overly-bound to MalFG, blocks the transition of the transporter, whereas suppressor mutations that weaken this association restore transport. MalK therefore exploits hydrolysis of ATP to reverse the conformation of MalFG to the inward-facing conformation, a step essential for release of maltose in the cytosol. PMID:24526688

Bao, Huan; Duong, Franck

2014-04-01

69

Detection of an en masse and reversible B- to A-DNA conformational transition in prokaryotes in response to desiccation  

PubMed Central

The role that DNA conformation plays in the biochemistry of cells has been the subject of intensive research since DNA polymorphism was discovered. B-DNA has long been considered the native form of DNA in cells although alternative conformations of DNA are thought to occur transiently and along short tracts. Here, we report the first direct observation of a fully reversible en masse conformational transition between B- and A-DNA within live bacterial cells using Fourier transform infrared (FTIR) spectroscopy. This biospectroscopic technique allows for non-invasive and reagent-free examination of the holistic biochemistry of samples. For this reason, we have been able to observe the previously unknown conformational transition in all four species of bacteria investigated. Detection of this transition is evidence of a previously unexplored biological significance for A-DNA and highlights the need for new research into the role that A-DNA plays as a cellular defence mechanism and in stabilizing the DNA conformation. Such studies are pivotal in understanding the role of A-DNA in the evolutionary pathway of nucleic acids. Furthermore, this discovery demonstrates the exquisite capabilities of FTIR spectroscopy and opens the door for further investigations of cell biochemistry with this under-used technique. PMID:24898023

Whelan, Donna R.; Hiscox, Thomas J.; Rood, Julian I.; Bambery, Keith R.; McNaughton, Don; Wood, Bayden R.

2014-01-01

70

Conformational transition pathway and free energy analyses of proteins by parallel cascade selection molecular dynamics (PaCS-MD)  

NASA Astrophysics Data System (ADS)

Parallel Cascade Selection Molecular Dynamics (PaCS-MD) was recently proposed to generate conformational transition pathways of proteins under the condition that a certain target quantity to be reached is introduced (R. Harada and A. Kitao, J. Chem. Phys., 139, 035103 2013). In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the target quantity for the next cycle are repeated until the simulated structures move sufficiently close to the target. Conformational sampling efficiency is demonstrated in the cases of mini-protein folding/unfolding and protein large conformational transitions. The result of PaCS-MD was further utilized to calculate free energy landscape by the combination with weighted-histogram analysis method or Markov state model.

Harada, Ryuhei; Nishihara, Yasutaka; Wakai, Nobuhiko; Kitao, Akio

2014-10-01

71

Gating Mechanisms of Mechanosensitive Channels of Large Conductance, II: Systematic Study of Conformational Transitions  

PubMed Central

Part II of this study is based on the continuum mechanics-based molecular dynamics-decorated finite element method (MDeFEM) framework established in Part I. In Part II, the gating pathways of Escherichia coli-MscL channels under various basic deformation modes are simulated. Upon equibiaxial tension (which is verified to be the most effective mode for gating), the MDeFEM results agree well with both experiments and all-atom simulations in literature, as well as the analytical continuum models and elastic network models developed in Part I. Different levels of model sophistication and effects of structural motifs are explored in detail, where the importance of mechanical roles of transmembrane helices, cytoplasmic helices, and loops are discussed. The conformation transitions under complex membrane deformations are predicted, including bending, torsion, cooperativity, patch clamp, and indentation. Compared to atom-based molecular dynamics simulations and elastic network models, the MDeFEM framework is unusually well-suited for simulating complex deformations at large length scales. The versatile hierarchical framework can be further applied to simulate the gating transition of other mechanosensitive channels and other biological processes where mechanical perturbation is important. PMID:18390625

Tang, Yuye; Yoo, Jejoong; Yethiraj, Arun; Cui, Qiang; Chen, Xi

2008-01-01

72

Expression of Mutant ?1 Na/K-ATPase Defective in Conformational Transition Attenuates Src-mediated Signal Transduction*  

PubMed Central

The ?1 Na/K-ATPase possesses both pumping and signaling functions. Using purified enzyme we found that the ?1 Na/K-ATPase might interact with and regulate Src activity in a conformation-dependent manner. Here we further explored the importance of the conformational transition capability of ?1 Na/K-ATPase in regulation of Src-related signal transduction in cell culture. We first rescued the ?1-knockdown cells by wild-type rat ?1 or ?1 mutants (I279A and F286A) that are known to be defective in conformational transition. Stable cell lines with comparable expression of wild type ?1, I279A, and F286A were characterized. As expected, the defects in conformation transition resulted in comparable degree of inhibition of pumping activity in the mutant-rescued cell lines. However, I279A was more effective in inhibiting basal Src activity than either the wild-type or the F286A. Although much higher ouabain concentration was required to stimulate Src in I279A-rescued cells, extracellular K+ was comparably effective in regulating Src in both control and I279A cells. In contrast, ouabain and extracellular K+ failed to produce detectable changes in Src activity in F286A-rescued cells. Furthermore, expression of either mutant inhibited integrin-induced activation of Src/FAK pathways and slowed cell spreading processes. Finally, the expression of these mutants inhibited cell growth, with I279A being more potent than that of F286A. Taken together, the new findings suggest that the ?1 Na/K-ATPase may be a key player in dynamic regulation of cellular Src activity and that the capability of normal conformation transition is essential for both pumping and signaling functions of ?1 Na/K-ATPase. PMID:23288841

Ye, Qiqi; Lai, Fangfang; Banerjee, Moumita; Duan, Qiming; Li, Zhichuan; Si, Shuyi; Xie, Zijian

2013-01-01

73

Indirect readout of the trp-repressor-operator complex by B-DNA's backbone conformation transitions.  

PubMed

Although the trp-repressor-operator complex is one of the best studied transcriptional controlling systems, some questions regarding the specific recognition of the operator by the repressor remain. We performed a 2.35 ns long molecular dynamics simulation to clarify the influence of the two B-DNA backbone conformational substates B(I) and B(II) on complexation. The trp-repressor-operator is an ideal biological system for this study because experimental results have already figured out that the interaction between the internucleotide phosphates and the protein is essential for the formation of the high affinity complex. Our simulation supports these results, but more important it shows a strong correlation between the B(I)/B(II) phosphate substate and the number of interactions with this phosphate. In particular the B(I) <==> B(II) transitions occur synchronous to hydrogen bond breaking or formation. To the best of our knowledge, this was observed for the first time. Thus, we conclude that the sequence specific B(I)/B(II) behavior contributes via indirect readout to sequence specific recognition. These results have implication for the design of transcription-controlling drugs in view of the recently published influence of minor groove binders on the B(I)/B(II) pattern. The simulation also agrees with crystallographically observed hydration sites. This is consistent with experimental results and indicates the correctness of the model used. PMID:11900552

Wellenzohn, Bernd; Flader, Wolfgang; Winger, Rudolf H; Hallbrucker, Andreas; Mayer, Erwin; Liedl, Klaus R

2002-03-26

74

Application of conductivity studies and polyelectrolyte theory to the conformation and order-disorder transition of xanthan polysaccharide  

Microsoft Academic Search

The conductivity of xanthan (extracellular polysaccharide from Xanthomonas campestris) in the potassium salt form has been studied over the temperature range 5–80°C spanning the order-disorder conformational transition. In salt-free solution data analysis using Manning's polyelectrolyte-conductivity theory gives a charge spacing, b, of 0.58±0.04 nm for the low temperature ordered form, consistent with a single rather than a double helix (b=0.58

S. A. Jones; D. M. Goodall; A. N. Cutler; I. T. Norton

1987-01-01

75

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI  

PubMed Central

A set of techniques developed under the umbrella of the string method is used in combination with all-atom molecular dynamics simulations to analyze the conformation change between the prepowerstroke (PPS) and rigor (R) structures of the converter domain of myosin VI. The challenges specific to the application of these techniques to such a large and complex biomolecule are addressed in detail. These challenges include (i) identifying a proper set of collective variables to apply the string method, (ii) finding a suitable initial string, (iii) obtaining converged profiles of the free energy along the transition path, (iv) validating and interpreting the free energy profiles, and (v) computing the mean first passage time of the transition. A detailed description of the PPS?R transition in the converter domain of myosin VI is obtained, including the transition path, the free energy along the path, and the rates of interconversion. The methodology developed here is expected to be useful more generally in studies of conformational transitions in complex biomolecules. PMID:21361558

Ovchinnikov, Victor; Karplus, Martin; Vanden-Eijnden, Eric

2011-01-01

76

?-Fluorophosphonates reveal how a phosphomutase conserves transition state conformation over hexose recognition in its two-step reaction.  

PubMed

?-Phosphoglucomutase (?PGM) catalyzes isomerization of ?-D-glucose 1-phosphate (?G1P) into D-glucose 6-phosphate (G6P) via sequential phosphoryl transfer steps using a ?-D-glucose 1,6-bisphosphate (?G16BP) intermediate. Synthetic fluoromethylenephosphonate and methylenephosphonate analogs of ?G1P deliver novel step 1 transition state analog (TSA) complexes for ?PGM, incorporating trifluoromagnesate and tetrafluoroaluminate surrogates of the phosphoryl group. Within an invariant protein conformation, the ?-D-glucopyranose ring in the ?G1P TSA complexes (step 1) is flipped over and shifted relative to the G6P TSA complexes (step 2). Its equatorial hydroxyl groups are hydrogen-bonded directly to the enzyme rather than indirectly via water molecules as in step 2. The (C)O-P bond orientation for binding the phosphate in the inert phosphate site differs by ? 30° between steps 1 and 2. By contrast, the orientations for the axial O-Mg-O alignment for the TSA of the phosphoryl group in the catalytic site differ by only ? 5°, and the atoms representing the five phosphorus-bonded oxygens in the two transition states (TSs) are virtually superimposable. The conformation of ?G16BP in step 1 does not fit into the same invariant active site for step 2 by simple positional interchange of the phosphates: the TS alignment is achieved by conformational change of the hexose rather than the protein. PMID:25104750

Jin, Yi; Bhattasali, Debabrata; Pellegrini, Erika; Forget, Stephanie M; Baxter, Nicola J; Cliff, Matthew J; Bowler, Matthew W; Jakeman, David L; Blackburn, G Michael; Waltho, Jonathan P

2014-08-26

77

A conformational transition in the myosin VI converter contributes to the variable step size.  

PubMed

Myosin VI (MVI) is a dimeric molecular motor that translocates backwards on actin filaments with a surprisingly large and variable step size, given its short lever arm. A recent x-ray structure of MVI indicates that the large step size can be explained in part by a novel conformation of the converter subdomain in the prepowerstroke state, in which a 53-residue insert, unique to MVI, reorients the lever arm nearly parallel to the actin filament. To determine whether the existence of the novel converter conformation could contribute to the step-size variability, we used a path-based free-energy simulation tool, the string method, to show that there is a small free-energy difference between the novel converter conformation and the conventional conformation found in other myosins. This result suggests that MVI can bind to actin with the converter in either conformation. Models of MVI/MV chimeric dimers show that the variability in the tilting angle of the lever arm that results from the two converter conformations can lead to step-size variations of ?12 nm. These variations, in combination with other proposed mechanisms, could explain the experimentally determined step-size variability of ?25 nm for wild-type MVI. Mutations to test the findings by experiment are suggested. PMID:22098742

Ovchinnikov, V; Cecchini, M; Vanden-Eijnden, E; Karplus, M

2011-11-16

78

New insights into the role of the N terminus in conformational transitions of the Na,K-ATPase.  

PubMed

The deletion of 32 residues from the N terminus of the alpha1 catalytic subunit of the rat Na,K-ATPase (mutant alpha1M32) shifts the E(1)/E(2) conformational equilibrium toward E(1), and the combination of this deletion with mutation E233K in the M2-M3 loop acts synergistically to shift the conformation further toward E(1) (Boxenbaum, N., Daly, S. E., Javaid, Z. Z., Lane, L. K., and Blostein, R. (1998) J. Biol. Chem. 273, 23086-23092). To delimit the region of the cytoplasmic N terminus involved in these interactions, the consequences of a series of N-terminal deletions of alpha1 beyond Delta32 were evaluated. Criteria to assess shifts in conformational equilibrium were based on effects of perturbation of the entire catalytic cycle ((i) sensitivity to vanadate inhibition, (ii) K(+) sensitivity of Na-ATPase measured at micromolar ATP, (iii) changes in K'(ATP), and (iv) catalytic turnover), as well as estimates of the rates of the conformational transitions of phospho- and dephosphoenzyme (E(1)P --> E(2)P and E(2)(K(+)) --> E(1) + K(+)). The results show that, compared with alpha1M32, the deletion of up to 40 residues (alpha1M40) further shifts the poise toward E(1). Remarkably, further deletions (mutants alpha1M46, alpha1M49, and alpha1M56) reverse the effect, such that these mutants increasingly resemble the wild type alpha1. These results suggest novel intramolecular interactions involving domains within the N terminus that impact the manner in which the N terminus/M2-M3 loop regulatory domain interacts with the M4-M5 catalytic loop to effect E(1) <--> E(2) transitions. PMID:12110690

Segall, Laura; Lane, Lois K; Blostein, Rhoda

2002-09-20

79

Direct visualization of flow-induced conformational transitions of single actin filaments in entangled solutions  

E-print Network

While semi-flexible polymers and fibers are an important class of material due to their rich mechanical properties, it remains unclear how these properties relate to the microscopic conformation of the polymers. Actin filaments constitute an ideal model polymer system due to their micron-sized length and relatively high stiffness that allow imaging at the single filament level. Here we study the effect of entanglements on the conformational dynamics of actin filaments in shear flow. We directly measure the full three-dimensional conformation of single actin filaments, using confocal microscopy in combination with a counter-rotating cone-plate shear cell. We show that initially entangled filaments form disentangled orientationally ordered hairpins, confined in the flow-vorticity plane. In addition, shear flow causes stretching and shear alignment of the hairpin tails, while the filament length distribution remains unchanged. These observations explain the strain-softening and shear-thinning behavior of entangl...

Kirchenbuechler, Inka; Kurniawan, Nicholas A; Koenderink, Gijsje H; Lettinga, M Paul

2015-01-01

80

Cooperative conformational transitions keep RecA filament active during ATPase cycle.  

PubMed

The active, stretched conformation of the RecA filament bound to single-stranded DNA is required for homologous recombination. During this process, the RecA filament mediates the homology search and base pair exchange with a complementary sequence. Subsequently, the RecA filament dissociates from DNA upon reaction completion. ATP binding and hydrolysis is critical throughout these processes. Little is known about the timescale, order of conversion between different cofactor bound forms during ATP hydrolysis, and the associated changes in filament conformation. We used single-molecule fluorescence techniques to investigate how ATP hydrolysis is coupled with filament dynamics. For the first time, we observed real-time cooperative structural changes within the RecA filament. This cooperativity between neighboring monomers provides a time window for nucleotide cofactor exchange, which keeps the filament in the active conformation amidst continuous cycles of ATP hydrolysis. PMID:25252114

Kim, Sung Hyun; Ragunathan, Kaushik; Park, Jeehae; Joo, Chirlmin; Kim, Doseok; Ha, Taekjip

2014-10-22

81

Thermodynamic and spectroscopic analysis of the conformational transition of poly(vinyl alcohol) by temperature-dependent FTIR.  

PubMed

The conformational change of poly(vinyl alcohol) has been studied by Fourier transform infrared spectroscopy at various temperatures in the 4000-400cm(-1) region. The molecular motion and the trans/gauche content are sensitive to the CH, CC stretching modes. FTIR spectra show that the I2920/I2849 decreases from 1.84 to 1.0 with increasing temperature, companying the decrease in I1047/I1095 from 0.78 to 0.58, implying the conformational transition from trans to gauche in alkyl chain. Based on the van't Hoff relation, the enthalpies and entropies have been calculated in different temperatures, which are 4.61kJmol(-1) and 15.23Jmol(-1)K(-1), respectively, in the region of 80-140°C. From the CO stretching mode and OH band, it can be concluded that the intermolecular hydrogen bonds decrease owing to elevating temperature, which leads to more gauche conformers. PMID:25554949

Han, Shan; Luan, Ye-Mei; Pang, Shu-Feng; Zhang, Yun-Hong

2015-03-15

82

Modulation of Calmodulin Lobes by Different Targets: An Allosteric Model with Hemiconcerted Conformational Transitions  

PubMed Central

Calmodulin is a calcium-binding protein ubiquitous in eukaryotic cells, involved in numerous calcium-regulated biological phenomena, such as synaptic plasticity, muscle contraction, cell cycle, and circadian rhythms. It exibits a characteristic dumbell shape, with two globular domains (N- and C-terminal lobe) joined by a linker region. Each lobe can take alternative conformations, affected by the binding of calcium and target proteins. Calmodulin displays considerable functional flexibility due to its capability to bind different targets, often in a tissue-specific fashion. In various specific physiological environments (e.g. skeletal muscle, neuron dendritic spines) several targets compete for the same calmodulin pool, regulating its availability and affinity for calcium. In this work, we sought to understand the general principles underlying calmodulin modulation by different target proteins, and to account for simultaneous effects of multiple competing targets, thus enabling a more realistic simulation of calmodulin-dependent pathways. We built a mechanistic allosteric model of calmodulin, based on an hemiconcerted framework: each calmodulin lobe can exist in two conformations in thermodynamic equilibrium, with different affinities for calcium and different affinities for each target. Each lobe was allowed to switch conformation on its own. The model was parameterised and validated against experimental data from the literature. In spite of its simplicity, a two-state allosteric model was able to satisfactorily represent several sets of experiments, in particular the binding of calcium on intact and truncated calmodulin and the effect of different skMLCK peptides on calmodulin’s saturation curve. The model can also be readily extended to include multiple targets. We show that some targets stabilise the low calcium affinity T state while others stabilise the high affinity R state. Most of the effects produced by calmodulin targets can be explained as modulation of a pre-existing dynamic equilibrium between different conformations of calmodulin’s lobes, in agreement with linkage theory and MWC-type models. PMID:25611683

Lai, Massimo; Brun, Denis; Edelstein, Stuart J.; Le Novère, Nicolas

2015-01-01

83

Direct visualization of flow-induced conformational transitions of single actin filaments in entangled solutions  

NASA Astrophysics Data System (ADS)

While semi-flexible polymers and fibres are an important class of material due to their rich mechanical properties, it remains unclear how these properties relate to the microscopic conformation of the polymers. Actin filaments constitute an ideal model polymer system due to their micron-sized length and relatively high stiffness that allow imaging at the single filament level. Here we study the effect of entanglements on the conformational dynamics of actin filaments in shear flow. We directly measure the full three-dimensional conformation of single actin filaments, using confocal microscopy in combination with a counter-rotating cone-plate shear cell. We show that initially entangled filaments form disentangled orientationally ordered hairpins, confined in the flow-vorticity plane. In addition, shear flow causes stretching and shear alignment of the hairpin tails, while the filament length distribution remains unchanged. These observations explain the strain-softening and shear-thinning behaviour of entangled F-actin solutions, which aids the understanding of the flow behaviour of complex fluids containing semi-flexible polymers.

Kirchenbuechler, Inka; Guu, Donald; Kurniawan, Nicholas A.; Koenderink, Gijsje H.; Lettinga, M. Paul

2014-10-01

84

Direct visualization of flow-induced conformational transitions of single actin filaments in entangled solutions.  

PubMed

While semi-flexible polymers and fibres are an important class of material due to their rich mechanical properties, it remains unclear how these properties relate to the microscopic conformation of the polymers. Actin filaments constitute an ideal model polymer system due to their micron-sized length and relatively high stiffness that allow imaging at the single filament level. Here we study the effect of entanglements on the conformational dynamics of actin filaments in shear flow. We directly measure the full three-dimensional conformation of single actin filaments, using confocal microscopy in combination with a counter-rotating cone-plate shear cell. We show that initially entangled filaments form disentangled orientationally ordered hairpins, confined in the flow-vorticity plane. In addition, shear flow causes stretching and shear alignment of the hairpin tails, while the filament length distribution remains unchanged. These observations explain the strain-softening and shear-thinning behaviour of entangled F-actin solutions, which aids the understanding of the flow behaviour of complex fluids containing semi-flexible polymers. PMID:25297898

Kirchenbuechler, Inka; Guu, Donald; Kurniawan, Nicholas A; Koenderink, Gijsje H; Lettinga, M Paul

2014-01-01

85

Conformational transitions driven by pyridoxal-5'-phosphate uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii.  

PubMed

Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme belonging to the fold type I superfamily, which catalyzes in vivo the reversible conversion of l-serine and tetrahydropteroylglutamate (H4 PteGlu) to glycine and 5,10-methylenetetrahydropteroylglutamate (5,10-CH(2) -H(4) PteGlu). The SHMT from the psychrophilic bacterium Psychromonas ingrahamii (piSHMT) had been recently purified and characterized. This enzyme was shown to display catalytic and stability properties typical of psychrophilic enzymes, namely high catalytic activity at low temperature and thermolability. To gain deeper insights into the structure-function relationship of piSHMT, the three-dimensional structure of its apo form was determined by X-ray crystallography. Homology modeling techniques were applied to build a model of the piSHMT holo form. Comparison of the two forms unraveled the conformation modifications that take place when the apo enzyme binds its cofactor. Our results show that the apo form is in an "open" conformation and possesses four (or five, in chain A) disordered loops whose electron density is not visible by X-ray crystallography. These loops contain residues that interact with the PLP cofactor and three of them are localized in the major domain that, along with the small domain, constitutes the single subunit of the SHMT homodimer. Cofactor binding triggers a rearrangement of the small domain that moves toward the large domain and screens the PLP binding site at the solvent side. Comparison to the mesophilic apo SHMT from Salmonella typhimurium suggests that the backbone conformational changes are wider in psychrophilic SHMT. PMID:25044250

Angelaccio, Sebastiana; Dworkowski, Florian; Di Bello, Angela; Milano, Teresa; Capitani, Guido; Pascarella, Stefano

2014-10-01

86

Conformation and dynamics of biopharmaceuticals: transition of mass spectrometry-based tools from academe to industry  

PubMed Central

Mass spectrometry plays a very visible role in biopharmaceutical industry, although its use in development, characterization and quality control of protein drugs is mostly limited to the analysis of covalent structure (amino acid sequence and post-translational modifications). Despite the centrality of protein conformation to biological activity, stability and safety of biopharmaceutical products, the expanding arsenal of mass spectrometry-based methods that are currently available to probe higher order structure and conformational dynamics of biopolymers did not enjoy until recently much attention in the industry. This is beginning to change as a result of recent work demonstrating the utility of these experimental tools for various aspects of biopharmaceutical product development and manufacturing. In this work we use a paradigmatic protein drug interferon ?-1a as an example to illustrate the utility of mass spectrometry as a powerful tool not only to assess the integrity of higher order structure of a protein drug, but also to predict consequences of its degradation at a variety of levels. PMID:19963397

Kaltashov, Igor A.; Bobst, Cedric E.; Abzalimov, Rinat R.; Berkowitz, Steven A.; Houde, Damian

2009-01-01

87

Understanding the conformation transition in the activation pathway of ?2 adrenergic receptor via a targeted molecular dynamics simulation.  

PubMed

G protein coupled receptors (GPCRs) play a crucial role in regulating signal recognition and transduction through their activation. The conformation transition in the activation pathway is of particular importance for their function. However, it has been poorly elucidated due to experimental difficulties in determining the conformations and the time limitation of conventional molecular dynamics (CMD) simulation. Thus, in this work, we employed a targeted molecular dynamic (TMD) simulation to study the activation process from an inactive structure to a fully active one for ?2 adrenergic receptor (?2AR). As a reference, 110 ns CMD simulations on wild ?2AR and its D130N mutant were also carried out. TMD results show that there is at least an intermediate conformation cluster in the activation process, evidenced by the principal component analysis and the structural and dynamic differences of some important motifs. It is noteworthy that the activation of the ligand binding site lags the G-protein binding site, displaying uncoupled correlation. Comparisons between the CMD and TMD results show that the D130N mutation significantly speeds up ICL2 and key ionic lock to enter into the intermediate state, which to some extent facilitates the activation involved in the NPxxY, DRY region and the separation between TM3 and TM6. However, the contribution from the D130N mutation to the activation of the ligand binding site could not be observed within the scale of 110 ns time. These observations could provide novel insights into previous studies for better understanding of the activation mechanism for ?2AR. PMID:25494239

Xiao, Xiuchan; Zeng, Xiaojun; Yuan, Yuan; Gao, Nan; Guo, Yanzhi; Pu, Xuemei; Li, Menglong

2015-01-28

88

Conformation transitions of blood proteins under influence of physical factors on microwave dielectric method  

NASA Astrophysics Data System (ADS)

In this article, the influence of ?-irradiation and temperature on albumin and fibrinogen conformation and dielectric properties of protein solutions have been studied by the microwave dielectric method. Both the values of the real part ?? (dielectric permittivity) and the imaginary part ?? (dielectric losses) of the complex dielectric permittivity of the aqueous solution of bovine serum albumin and human fibrinogen as functions of temperature and ?-irradiation dose have been obtained. The time of dielectric relaxation of water molecules in the protein solutions was calculated. The hydration of the albumin and fibrinogen molecules was determined. The temperature dependencies of hydration are non-monotonous and have a number of characteristic features at the temperatures 30 34 and 44 47 °C for serum albumin, and 24 and 32 °C for fibrinogen.

Gorobchenko, O. A.; Nikolov, O. T.; Gatash, S. V.

2006-11-01

89

A selective NMR probe to monitor the conformational transition from inactive to active kinase.  

PubMed

Kinases control many aspects of cellular signaling and are therefore therapeutic targets for numerous disease states. Monitoring the conformational changes that drive activation and inactivation of the catalytic kinase core is a challenging experimental problem due to the dynamic nature of these enzymes. We apply [(13)C] reductive methylation to chemically introduce NMR-active nuclei into unlabeled protein kinases. The results demonstrate that solution NMR spectroscopy can be used to monitor specific changes in the chemical environment of structurally important lysines in a [(13)C]-methylated kinase as it shifts from the inactive to active state. This approach provides a solution based method to complement X-ray crystallographic data and can be applied to nearly any kinase, regardless of size or method of production. PMID:25248068

Xie, Qian; Fulton, D Bruce; Andreotti, Amy H

2015-01-16

90

A Conformational Phase Transition in a Langmuir Film of an Amphiphilic Azacrown David Gidalevitz, Oksana Y. Mindyuk, MacKenzie R. Stetzer, and Paul A. Heiney*  

E-print Network

A Conformational Phase Transition in a Langmuir Film of an Amphiphilic Azacrown David Gidalevitz to study an amphiphilic azacrown derivative at the air-water interface. The compound studied has a ring with this rearrangement, the film develops long-range in-plane structural order. 1. Introduction Amphiphilic rod

Kurnaz, Levent

91

Characterization of the Ca(2+)-triggered conformational transition in troponin C.  

PubMed Central

Troponin C is the Ca(2+)-binding subunit of troponin in vertebrate striated muscle. Binding of Ca2+ to troponin C is thought to induce a conformational change that triggers subsequent events in the initiation of muscle contraction. A molecular modeling study has proposed that, when Ca2+ binds to the N-terminal triggering sites, helices B and C separate from the helices D and A, thereby exposing a crucial interaction site for troponin I, the inhibitory subunit of troponin [Herzberg, O., Moult, J., and James, M. N. G. (1986) J. Biol. Chem. 261, 2638-2644]. In the present study the question of whether this separation actually occurs is addressed directly. A mutant rabbit skeletal troponin C containing a pair of cysteines at position 12 in helix A and position 49 in the polypeptide segment linking helices B and C was created by site-directed mutagenesis. Pyrene excimer fluorescence and resonance energy transfer studies on the labeled mutant troponin C reveal a Ca(2+)-induced increase in distance between the two cysteines. Under certain assumptions, the distance increase could be estimated from the extent of energy transfer to be approximately 13 A, in good agreement with the distance increase predicted by molecular modeling. Our results provide further experimental support for the model proposed by Herzberg et al. (above). Images PMID:1465405

Wang, Z; Gergely, J; Tao, T

1992-01-01

92

The ?1 72-96 Loop Controls Conformational Transitions during Reovirus Cell Entry  

PubMed Central

The reovirus outer capsid protein ?1 forms a lattice surrounding the viral core. In the native state, ?1 determines the environmental stability of the viral capsid. Additionally, during cell entry, ?1 undergoes structural rearrangements that facilitate delivery of the viral cores across the membrane. To determine how the capsid-stabilizing functions of ?1 impinge on the capacity of ?1 to undergo conformational changes required for cell entry, we characterized viruses with mutations engineered at charged residues within the ?1 loop formed by residues 72 to 96 (72-96 loop). This loop is proposed to stabilize the capsid by mediating interactions between neighboring ?1 trimers and between trimers and the core. We found that mutations at Glu89 (E89) within this loop produced viruses with compromised efficiency for completing their replication cycle. ISVPs of E89 mutants converted to ISVP*s more readily than those of wild-type viruses. The E89 mutants yielded revertants with second-site substitutions within regions that mediate interaction between ?1 trimers at a site distinct from the 72-96 loop. These viruses also contained changes in regions that control interactions within ?1 trimers. Viruses containing these second-site changes displayed restored plaque phenotypes and were capable of undergoing ISVP-to-ISVP* conversion in a regulated manner. These findings highlight regions of ?1 that stabilize the reovirus capsid and demonstrate that an enhanced propensity to form ISVP*s in an unregulated manner compromises viral fitness. PMID:24089575

Sarkar, Payel

2013-01-01

93

Single-Molecule Analysis of Protein Large-Amplitude Conformational Transitions  

NASA Astrophysics Data System (ADS)

Proteins have evolved to harness thermal fluctuations, rather than frustrated by them, to carry out chemical transformations and mechanical work. What are, then, the operation and design principles of protein machines? To frame the problem in a tractable way, several basic questions have been formulated to guide the experimental design: (a) How many conformational states can a protein sample on the functionally important timescale? (b) What are the inter-conversion rates between states? (c) How do ligand binding or interactions with other proteins modulate the motions? (d) What are the structural basis of flexibility and its underlying molecular mechanics? Guided by this framework, we have studied protein tyrosine phosphatase B, PtpB, from M. tuberculosis (a virulence factor of tuberculosis and a potential drug target) and adenylate kinase, AK, from E. coli (a ubiquitous energy-balancing enzyme in cells). These domain movements have been followed in real time on their respective catalytic timescales using high-resolution single-molecule F"orster resonance energy transfer (FRET) spectroscopy. It is shown quantitatively that both PtpB and AK are capable of dynamically sampling two distinct states that correlate well with those observed by x-ray crystallography. Integrating these microscopic dynamics into macroscopic kinetics allows us to place the experimentally measured free-energy landscape in the context of enzymatic turnovers.

Yang, Haw

2011-03-01

94

pH-dependent conformational transitions in conalbumin (ovotransferrin), a metalloproteinase from hen egg white.  

PubMed

Acid unfolding pathway of conalbumin (CA), a monomeric glycoprotein from hen egg white, has been investigated using far- and near-UV CD spectroscopy, intrinsic fluorescence emission, extrinsic fluorescence probe 1-anilino-8-napthalene sulfonate (ANS) and dynamic light scattering (DLS). We observe pH-dependent changes in secondary and tertiary structure of CA. It has native-like ?-helical secondary structure at pH 4.0 but loss structure at pH 3.0. The CA existed exclusively as a pre-molten globule state and molten globule state in solution at pH 4.0 and pH 3.0, respectively. The effect of pH on the conformation and thermostability of CA points toward its heat resistance at neutral pH. DLS results show that MG state existed as compact form in aqueous solutions with hydrodynamic radii of 4.7 nm. Quenching of tryptophan fluorescence by acrylamide further confirmed the accumulation of an intermediate state, partly unfolded, in-between native and unfolded states. PMID:21833676

Rabbani, Gulam; Ahmad, Ejaz; Zaidi, Nida; Khan, Rizwan Hasan

2011-12-01

95

Protein conformational transitions at the liquid-gas interface as studied by dilational surface rheology.  

PubMed

Experimental results on the dynamic dilational surface elasticity of protein solutions are analyzed and compared. Short reviews of the protein behavior at the liquid-gas interface and the dilational surface rheology precede the main sections of this work. The kinetic dependencies of the surface elasticity differ strongly for the solutions of globular and non-globular proteins. In the latter case these dependencies are similar to those for solutions of non-ionic amphiphilic polymers and have local maxima corresponding to the formation of the distal region of the surface layer (type I). In the former case the dynamic surface elasticity is much higher (>60 mN/m) and the kinetic dependencies are monotonical and similar to the data for aqueous dispersions of solid nanoparticles (type II). The addition of strong denaturants to solutions of bovine serum albumin and ?-lactoglobulin results in an abrupt transition from the type II to type I dependencies if the denaturant concentration exceeds a certain critical value. These results give a strong argument in favor of the preservation of the protein globular structure in the course of adsorption without any denaturants. The addition of cationic surfactants also can lead to the non-monotonical kinetic dependencies of the dynamic surface elasticity indicating destruction of the protein tertiary and secondary structures. The addition of anionic surfactants gives similar results only for the protein solutions of high ionic strength. The influence of cationic surfactants on the local maxima of the kinetic dependencies of the dynamic surface elasticity for solutions of a non-globular protein (?-casein) differs from the influence of anionic surfactants due to the heterogeneity of the charge distribution along the protein chain. In this case one can use small admixtures of ionic surfactants as probes of the adsorption mechanism. The effect of polyelectrolytes on the kinetic dependencies of the dynamic surface elasticity of protein solutions is weaker than the effect of conventional surfactants but exceeds the error limits. PMID:24238394

Noskov, Boris A

2014-04-01

96

Glass transition phenomenon due to freezing-in of conformational disorder of ethylenediamine framework in crystalline [Ni(acac)(tmen)(H 2O) 2]CIO 4  

NASA Astrophysics Data System (ADS)

Heat capacities of crystalline [Ni(acac)(tmen)(H 2O) 2]ClO 4 were measured with an adiabatic calorimeter in the range 10-300 K, where acac and tmen are acetylacetonate and N, N, N', N' -tetramethylethylenendiamine, respectively. A glass transition was found at 107.2 K with the accompanied heat capacity jump of 2.6J K -1 mol -1, and interpreted as due to the freezing-in of disorder between the two, ? and ?, conformations of a ligand tmen. The energy difference between the two conformations and the activation energy for the conformational change were determined by analyses of the calorimetric data to be 1.26 kJ mol -1 and 31.0 kJ mol -1, respectively.

Fukuda, Yutaka; Yoshida, Tomoko; Oguni, Masaharu

1994-03-01

97

Conformation Transition in Silk Protein Films Monitored by Time-Resolved Fourier Transform Infrared Spectroscopy:  Effect of Potassium Ions on Nephila Spidroin Films †  

Microsoft Academic Search

We used time-resolved Fourier transform infrared spectroscopy (FTIR) to follow a conformation transition in Nephila spidroin film from random coil and\\/or helical structures to ‚-sheet induced by the addition of KCl from 0.01 to 1.0 mol\\/L in D2O. Time series difference spectra showed parallel increases in absorption at 1620 and 1691 cm-1, indicating formation of ‚-sheet, together with a coincident

Xin Chen; David P. Knight; Zhengzhong Shao; Fritz Vollrath

2002-01-01

98

Salt induced transitions between multiple conformations of poly (rG-m5dC).poly (rG-m5dC).  

PubMed Central

Salt induced transitions between four conformations of the methylated ribo-deoxyribo co-polymer poly (rG-m5dC).poly (rG-m5dC) have been studied using phosphorous-NMR, Raman spectroscopy, and circular dichroism. A high salt A-Z transition is observed for the polymer. However, the methylated polymer does not enter the high salt Z form more readily than the analogous unmethylated polymer, unlike the effect of methylation on the fully deoxy polymer poly (dG-dC).poly (dG-dC). The methylated polymer fails to undergo a low salt A-Z transition in 5 mM Tris buffer, unlike the unmethylated poly (rG-dC).poly (rG-dC). However, if the counterion is changed to triethanolamine buffer, an A-Z transition does take place. In 5 mM Tris buffer the phosphorous-NMR spectrum of poly (rG-m5dC).poly (rG-m5dC) shows one resonance in the absence of NaCl that splits into two closely spaced resonances as the NaCl level is increased to 30 mM. The Raman spectrum of poly (rG-m5dC).poly (rG-m5dC) shows that it is in the A conformation at intermediate salt concentrations. From this we conclude that poly (rG-m5dC).poly (rG-m5dC) is in a regular A conformation in Tris buffer at low Na+ levels, shifting to an alternating A conformation with a dinucleotide repeat at intermediate salt concentrations. PMID:3892484

Wu, H Y; Behe, M J

1985-01-01

99

Solvent-dependent cage dynamics of small nonpolar radicals: lessons from the photodissociation and geminate recombination of alkylcobalamins.  

PubMed

Time-resolved transient absorption spectroscopy was used to investigate the primary geminate recombination and cage escape of alkyl radicals in solution over a temperature range from 0 to 80 degrees C. Radical pairs were produced by photoexcitation of methyl, ethyl, propyl, hexylnitrile, and adenosylcobalamin in water, ethylene glycol, mixtures of water and ethylene glycol, and sucrose solutions. In contrast to previous studies of cage escape and geminate recombination, these experiments demonstrate that cage escape for these radical pairs occurs on time scales ranging from a hundred picoseconds to over a nanosecond as a function of solvent fluidity and radical size. Ultrafast cage escape (<100 ps) is only observed for the methyl radical where the radical pair is produced through excitation to a directly dissociative electronic state. The data are interpreted using a unimolecular model with competition between geminate recombination and cage escape. The escape rate constant, k(e), is not a simple function of the solvent fluidity (T/eta) but depends on the nature of the solvent as well. The slope of k(e) as a function of T/eta for the adenosyl radical in water is in near quantitative agreement with the slope calculated using a hydrodynamic model and the Stokes-Einstein equation for the diffusion coefficients. The solvent dependence is reproduced when diffusion constants are calculated taking into account the relative volume and mass of both solvent and solute using the expression proposed by Akgerman (Akgerman, A.; Gainer, J. L. Ind. Eng. Chem. Fundam. 1972, 11, 373-379). Rate constants for cage escape of the other radicals investigated are consistently smaller than the calculated values suggesting a systematic correction for radical size or coupled radical pair motion. PMID:19585970

Stickrath, Andrew B; Carroll, Elizabeth C; Dai, Xiaochuan; Harris, D Ahmasi; Rury, Aaron; Smith, Broc; Tang, Kuo-Chun; Wert, Jonathan; Sension, Roseanne J

2009-07-30

100

Solvent-dependent excited-state hydrogen transfer and intersystem crossing in 2-(2'-hydroxyphenyl)-benzothiazole.  

PubMed

The excited-state intramolecular hydrogen transfer (ESIHT) of 2-(2'-hydroxyphenyl) benzothiazole (HBT) has been investigated in a series of nonpolar, polar aprotic, and polar protic solvents. A variety of state-of-the-art experimental methods were employed, including femto- and nanosecond transient absorption and fluorescence upconversion spectroscopy with broadband capabilities. We show that the dynamics and mechanism of ESIHT of the singlet excited HBT are strongly solvent-dependent. In nonpolar solvents, the data demonstrate that HBT molecules adopt a closed form stabilized by O-H···N chelated hydrogen bonds with no twisting angle, and the photoinduced H transfer occurs within 120 fs, leading to the formation of a keto tautomer. In polar solvents, owing to dipole-dipole cross talk and hydrogen bonding interactions, the H transfer process is followed by ultrafast nonradiative deactivation channels, including ultrafast internal conversion (IC) and intersystem crossing (ISC). This is likely to be driven by the twisting motion around the C-C bond between the hydroxyphenyl and thiazole moieties, facilitating the IC back to the enol ground state or to the keto triplet state. In addition, our femtosecond time-resolved fluorescence experiments indicate, for the first time, that the lifetime of the enol form in ACN is approximately 280 fs. This observation indicates that the solvent plays a crucial role in breaking the H bond and deactivating the excited state of the HBT. Interestingly, the broadband transient absorption and fluorescence up-conversion data clearly demonstrate that the intermolecular proton transfer from the excited HBT to the DMSO solvent is about 190 fs, forming the HBT anion excited state. PMID:25325788

Aly, Shawkat M; Usman, Anwar; AlZayer, Maytham; Hamdi, Ghada A; Alarousu, Erkki; Mohammed, Omar F

2015-02-12

101

Structure Transition in PSS/Lysozyme Complexes: A Chain-Conformation-Driven Process, as Directly Seen by Small Angle Neutron Scattering  

E-print Network

Measurements of chain conformation in proteins/polyelectrolytes complexes (lysozyme and PSSNa) show that the crossover observed between an open structure -a chain network crosslinked by the proteins, and a globular one - dense globules of ~ 10 nm aggregated in a fractal way, results from a conformation modification prior to the transition. Before showing this, we have widened the parameters range for the observation of the transition. We had shown before that the two structures can be formed depending on chain length (for a given [PSS]/[lysozyme] ratio): gel for large chains, globules for short chains. We show here that the crossover between these two regimes can also be reached as a function of chains concentration or salinity of the buffer. Since all these crossover parameters act on chains overlapping concentration c*, we reinforce the idea of a transition from the dilute to the semi-dilute regime, but c* is shifted compared to pure PSS solutions. In order to understand this, we have measured by SANS the conformation of a single chain of PSS in presence of proteins within the complexes. This is achieved by a specific labeling trick where we take advantage of the fact that lysozyme and hydrogenated PSS chains have the same neutron scattering length density. In the gel structure, the PSS chains keep a wormlike structure as in pure solutions, but their persistence length is strongly reduced, from 50 {\\AA} without proteins to 20 {\\AA} in average with lysozyme. With this value of 20 {\\AA}, we calculate new overlapping thresholds (concentration, mass, ionic strength) in agreement with observed ones. In a second stage, after the globular structure is formed, the PSS chains get a third conformation, no longer wormlike, but more collapsed, within the globules.

Jérémie Gummel; Fabrice Cousin; François Boué

2009-03-30

102

Unusual solvent-dependent photophysical and self-assembly properties of NO2 substituted T-shaped phenazines.  

PubMed

This paper investigates the importance of substituent placement when designing low-molecular mass ?-organogelators. The electron-deficient NO2 substituent was systematically added to novel T-shaped phenazines to examine electronic as well as assembly properties. This T-shaped molecular platform promotes selective electronic tuning, which can be theoretically analyzed by examining the system's frontier molecular orbitals. Electronic properties were characterized by UV-vis spectroscopy and cyclic voltammetry, and comparisons were made based on number and placement of the NO2 group. Computational chemistry (B3LYP/6-31G*) was employed for geometry optimizations, and to generate molecular orbital diagrams for all systems. The most noticeable influence of NO2 position was found for two molecules with four NO2 groups placed at different locations about the molecule (T-34dNT and T-35dNT). A 0.13 eV difference in ELUMO was observed while EHOMO was not significantly impacted by this change only in NO2 placement. Interestingly and unexpectedly, the photophysical properties and solvent-dependent gelation properties were considerably different for T-34dNT and T-35dNT. T-34dNT exhibited a unique fluorescence (FL) solvatochromism, with FL intensity and maxima dependent on solvent polarity. This result is indicative of intramolecular charge transfer. In addition, long tailing at the solid-state absorption of T-34dNT suggests the presence of intermolecular charge transfer. The gelation of T-34dNT produced chromism ranging from red to orange to yellow when the solvents changed from acetonitrile to ethyl acetate to cyclohexane, respectively. T-35dNT gels in these solvents did not exhibit any of the same properties. Xerogel morphology characterizations were carried out using three different solvents for both T-34dNT and T-35dNT. In the case of T-34dNT, striking differences in the morphology were detected by field-emission scanning electron microscopy (FE-SEM). We conclude that numbers of substituents are not the only consideration in effective molecular design for organogelators, but that substituent position plays a critical role in certain fundamental properties of these systems. PMID:25491727

Lee, Dong-Chan; Brownell, Lacie V; Jang, Kyoungmi; Han, Seung Ju; Robins, Kathleen A

2015-01-28

103

Insights into the potential functionality of single-chain force-induced conformational transitions in polymer networks: Implications for polysaccharide signaling in the plant cell wall  

NASA Astrophysics Data System (ADS)

The behavior of biopolymer networks comprised of clickable polysaccharide chains that can undergo force-induced conformational transitions was investigated during straining using a simulation technique. The simulation was carried out both using an affine deformation field and alternatively using Lees-Edwards boundary conditions as an example of a nonaffine case. In the affine situation the simulated stress-strain curves were found to be consistent with results obtained by evaluating the molecular force-extension curve at a single average extension and calculating the bulk modulus as an average over all possible orientations with respect to the deformation. While in all cases examined the macroscopic mechanical responses of networks of randomly oriented chains, consisting either of simple extensible wormlike chains or their clickable analogs, were found to be indistinguishable, the simulation additionally allowed the number of chains containing sugar rings in different conformational states to be monitored, and this was found to change significantly during straining. This supports the hypothesis that in networks of randomly oriented clickable polysaccharide chains, such conformational transitions could have biological significance as stress switches in signaling processes but that they are unlikely to affect the bulk rheological properties of tissue.

Schuster, E.; Lundin, L.; Williams, M. A. K.

2010-11-01

104

Effects of solvents on the intrinsic propensity of peptide backbone conformations  

NASA Astrophysics Data System (ADS)

We investigated the effects of solvents on the intrinsic propensity of peptide backbone conformations based on molecular dynamics simulations. The results show that compared with pure water, aqueous urea decreases the helix propensity. In comparison, methanol decreases the polyproline II (PPII) propensity. Such a solvent dependence of the intrinsic propensity of the backbone conformation is correlated with the solvent dependence of the hydration of the backbone groups and the formation probability of the local intrapeptide hydrogen bonds. Aqueous urea which has low ability to stabilize the local intrapeptide hydrogen bonds disfavors the helical conformation. Whereas, methanol which has low ability to hydrate the backbone groups disfavors the polyproline II conformation. In addition, the solvent effects can be further modulated by the side chains of the peptides. The solvent effects of the intrinsic propensity of peptide backbone conformations observed in this work suggest that changing the intrinsic propensity of the protein backbone conformations can partly contribute to the solvent-induced protein structure and dynamics variations. These results will be useful in understanding the solvent dependence of the conformational distributions of the unfolded proteins or peptides (or intrinsically disordered proteins) in which the global tertiary interactions are less important than that in the well-folded proteins.

Li, Wenfei; Qin, Meng; Tie, Zuoxiu; Wang, Wei

2011-10-01

105

Solvent-dependent host guest complexation of two homologous merocyanines by a water-soluble calix[8]arene: Spectroscopic analysis and structural calculations  

NASA Astrophysics Data System (ADS)

The sulfonated calixarene I 8C 12 acts as a host for homologous merocyanines Mc1 and Mc2 in organic solvents, exhibiting neither selectivity towards the guest dyes nor solvent dependence of the complexation equilibria. In water, on the contrary, only the lower homologue, Mc1, is solubilized in the presence of the calixarene. A combination of UV-visible and fluorescence spectroscopic and photophysical analysis and MD structural simulation of the calixarene-dye complexes was employed to account for the observations, and suggests that a radical change in the complexation mode occurs upon moving from an organic to an aqueous environment.

Lodi, Andrea; Caselli, Monica; Casnati, Alessandro; Momicchioli, Fabio; Sansone, Francesco; Vanossi, Davide; Ponterini, Glauco

2007-11-01

106

Solvent dependent competition between fluorescence resonance energy transfer and through bond energy transfer in rhodamine appended hexaphenylbenzene derivatives for sensing of Hg(2+) ions.  

PubMed

Hexaphenylbenzene (HPB) derivatives 5 and 7 having rhodamine B moieties have been designed and synthesized, and have been shown to display solvent dependent. Fluorescence resonance energy transfer (FRET) and through bond energy transfer (TBET) in the presence of Hg(2+) ions among the various cations (Cu(2+), Pb(2+), Zn(2+), Ni(2+), Cd(2+), Ag(+), Ba(2+), Mg(2+), K(+), Na(+), and Li(+)) have been tested. Derivative 5 displays quite high through bond energy transfer efficiency in the presence of Hg(2+) ions in methanol whereas derivative 7 exhibits better FRET efficiency in the presence of Hg(2+) ions in THF and CH(3)CN than derivative 5. PMID:23385981

Bhalla, Vandana; Vij, Varun; Tejpal, Ruchi; Singh, Gopal; Kumar, Manoj

2013-04-01

107

A conformational transition at the N terminus of the prion protein features in formation of the scrapie isoform.  

PubMed

The scrapie prion protein (PrPSc) is formed from the cellular isoform (PrPC) by a post-translational process that involves a profound conformational change. Linear epitopes for recombinant antibody Fab fragments (Fabs) on PrPC and on the protease-resistant core of PrPSc, designated PrP 27-30, were identified using ELISA and immunoprecipitation. An epitope region at the C terminus was accessible in both PrPC and PrP 27-30; in contrast, epitopes towards the N-terminal region (residues 90 to 120) were accessible in PrPC but largely cryptic in PrP 27-30. Denaturation of PrP 27-30 exposed the epitopes of the N-terminal domain. We argue from our findings that the major conformational change underlying PrPSc formation occurs within the N-terminal segment of PrP 27-30. PMID:9356250

Peretz, D; Williamson, R A; Matsunaga, Y; Serban, H; Pinilla, C; Bastidas, R B; Rozenshteyn, R; James, T L; Houghten, R A; Cohen, F E; Prusiner, S B; Burton, D R

1997-10-31

108

A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution  

SciTech Connect

Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.

Pallan, Pradeep S.; Prakash, Thazha P.; Li, Feng; Eoff, Robert L.; Manoharan, Muthiah; Egli, Martin; (Isis Pharm.); (Alnylam Pharm.); (Vanderbilt)

2009-06-17

109

All hierarchical levels are involved in conformational transitions of the 4×6-meric tarantula hemocyanin upon oxygenation  

Microsoft Academic Search

The respiratory protein of the tarantula Eurypelma californicum is a 4×6-meric hemocyanin that binds oxygen with high cooperativity. This requires the existence of different conformations which have been confirmed by small angle X-ray scattering (SAXS). Here we present reconstructed 3D-models of the oxy- and deoxy-forms of tarantula hemocyanins, as obtained by fitting small angle X-rays scattering curves on the basis

Hermann Hartmann; Heinz Decker

2002-01-01

110

FTIR/PCA study of propanol in argon matrix: The initial stage of clustering and conformational transitions  

NASA Astrophysics Data System (ADS)

FTIR spectra of 1-propanol in an argon matrix were studied in the range 11-30 K. Principal component analysis of dynamic FTIR spectra and nonlinear band shape fitting has been carried out. The peaks of monomer, open dimer, mixed propanol-water dimer and those of higher H-bond clusters have been resolved and analyzed. The attribution of certain FTIR peaks has been supported by proper density functional theory calculations. Analyzing dependences of the integral band intensities of various aggregates on temperature it has been deduced that in the initial stage of clustering monomers and dimers are the basic building blocks forming higher H-bond clusters. The peaks assigned to two conformers of monomers and mixed propanol-water dimers were investigated processing the temperature dependences of their integral intensities in Arrhenius plot. The obtained values of 0.18 kJ.mol-1 for propanol monomer and 0.26 kJ.mol-1 for mixed dimer are well comparable with the energy differences between the global minimum conformation of 1-propanol (Gt) and some other energetically higher structures (Tt or Tg).

Doroshenko, Iryna; Balevicius, Vytautas; Pitsevich, George; Aidas, Kestutis; Sablinskas, Valdas; Pogorelov, Valeriy

2014-12-01

111

Structural basis of conformational transitions in the active site and 80?s loop in the FK506-binding protein FKBP12  

PubMed Central

The extensive set of NMR doublings exhibited by the immunophilin FKBP12 (FK506-binding protein 12) arose from a slow transition to the cis-peptide configuration at Gly89 near the tip of the 80?s loop, the site for numerous protein-recognition interactions for both FKBP12 and other FKBP domain proteins. The 80?s loop also exhibited linebroadening, indicative of microsecond to millisecond conformational dynamics, but only in the trans-peptide state. The G89A variant shifted the trans–cis peptide equilibrium from 88:12 to 33:67, whereas a proline residue substitution induced fully the cis-peptide configuration. The 80?s loop conformation in the G89P crystal structure at 1.50 Å resolution differed from wild-type FKBP12 primarily at residues 88, 89 and 90, and it closely resembled that reported for FKBP52. Structure-based chemical-shift predictions indicated that the microsecond to millisecond dynamics in the 80?s loop probably arose from a concerted main chain (?88 and ?89) torsion angle transition. The indole side chain of Trp59 at the base of the active-site cleft was reoriented ~90o and the adjacent backbone was shifted in the G89P crystal structure. NOE analysis of wild-type FKBP12 demonstrated that this indole populates the perpendicular orientation at 20%. The 15N relaxation analysis was consistent with the indole reorientation occurring in the nanosecond timeframe. Recollection of the G89P crystal data at 1.20 Å resolution revealed a weaker wild-type-like orientation for the indole ring. Differences in the residues that underlie the Trp59 indole ring and altered interactions linking the 50?s loop to the active site suggested that reorientation of this ring may be disfavoured in the other six members of the FKBP domain family that bear this active-site tryptophan residue. PMID:24405377

Mustafi, Sourajit M.; Brecher, Matthew; Zhang, Jing; Li, Hongmin; Lemaster, David M.; Hernández, Griselda

2014-01-01

112

Structure Analysis and Conformational Transitions of the Cell Penetrating Peptide Transportan 10 in the Membrane-Bound State  

PubMed Central

Structure analysis of the cell-penetrating peptide transportan 10 (TP10) revealed an exemplary range of different conformations in the membrane-bound state. The bipartite peptide (derived N-terminally from galanin and C-terminally from mastoparan) was found to exhibit prominent characteristics of (i) amphiphilic ?-helices, (ii) intrinsically disordered peptides, as well as (iii) ?-pleated amyloid fibrils, and these conformational states become interconverted as a function of concentration. We used a complementary approach of solid-state 19F-NMR and circular dichroism in oriented membrane samples to characterize the structural and dynamical behaviour of TP10 in its monomeric and aggregated forms. Nine different positions in the peptide were selectively substituted with either the L- or D-enantiomer of 3-(trifluoromethyl)-bicyclopent-[1.1.1]-1-ylglycine (CF3-Bpg) as a reporter group for 19F-NMR. Using the L-epimeric analogs, a comprehensive three-dimensional structure analysis was carried out in lipid bilayers at low peptide concentration, where TP10 is monomeric. While the N-terminal region is flexible and intrinsically unstructured within the plane of the lipid bilayer, the C-terminal ?-helix is embedded in the membrane with an oblique tilt angle of ?55° and in accordance with its amphiphilic profile. Incorporation of the sterically obstructive D-CF3-Bpg reporter group into the helical region leads to a local unfolding of the membrane-bound peptide. At high concentration, these helix-destabilizing C-terminal substitutions promote aggregation into immobile ?-sheets, which resemble amyloid fibrils. On the other hand, the obstructive D-CF3-Bpg substitutions can be accommodated in the flexible N-terminus of TP10 where they do not promote aggregation at high concentration. The cross-talk between the two regions of TP10 thus exerts a delicate balance on its conformational switch, as the presence of the ?-helix counteracts the tendency of the unfolded N-terminus to self-assemble into ?-pleated fibrils. PMID:24937132

Strandberg, Erik; Verdurmen, Wouter P. R.; Bürck, Jochen; Ehni, Sebastian; Mykhailiuk, Pavel K.; Afonin, Sergii; Gerthsen, Dagmar; Komarov, Igor V.; Brock, Roland; Ulrich, Anne S.

2014-01-01

113

Nonequilibrium phase transitions and a nonequilibrium critical point from anti-de Sitter space and conformal field theory correspondence.  

PubMed

We find novel phase transitions and critical phenomena that occur only outside the linear-response regime of current-driven nonequilibrium states. We consider the strongly interacting (3+1)-dimensional N = 4 large-N(c) SU(N(c)) supersymmetric Yang-Mills theory with a single flavor of fundamental N = 2 hypermultiplet as a microscopic theory. We compute its nonlinear nonballistic quark-charge conductivity by using the AdS/CFT correspondence. We find that the system exhibits a novel nonequilibrium first-order phase transition where the conductivity jumps and the sign of the differential conductivity flips at finite current density. A nonequilibrium critical point is discovered at the end point of the first-order regime. We propose a nonequilibrium steady-state analogue of thermodynamic potential in terms of the gravity-dual theory in order to define the transition point. Nonequilibrium analogues of critical exponents are proposed as well. The critical behavior of the conductivity is numerically confirmed on the basis of these proposals. The present work provides a new example of nonequilibrium phase transitions and nonequilibrium critical points. PMID:23005930

Nakamura, Shin

2012-09-21

114

Accounting for conformational flexibility and torsional anharmonicity in the H + CH{sub 3}CH{sub 2}OH hydrogen abstraction reactions: A multi-path variational transition state theory study  

SciTech Connect

This work reports a detailed theoretical study of the hydrogen abstraction reactions from ethanol by atomic hydrogen. The calculated thermal rate constants take into account torsional anharmonicity and conformational flexibility, in addition to the variational and tunneling effects. Specifically, the kinetics calculations were performed by using multi-path canonical variational transition state theory with least-action path tunneling corrections, to which we have added the two-dimensional non-separable method to take into account torsional anharmonicity. The multi-path thermal rate constant is expressed as a sum over conformational reaction channels. Each of these channels includes all the transition states that can be reached by internal rotations. The results show that, in the interval of temperatures between 250 and 2500 K, the account for multiple paths leads to higher thermal rate constants with respect to the single path approach, mainly at low and at high temperatures. In addition, torsional anharmonicity enhances the slope of the Arrhenius plot in this range of temperatures. Finally, we show that the incorporation of tunneling into the hydrogen abstraction reactions substantially changes the contribution of each of the transition states to the conformational reaction channel.

Meana-Pañeda, Rubén; Fernández-Ramos, Antonio, E-mail: qf.ramos@usc.es [Department of Physical Chemistry and Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, 15706 Santiago de Compostela (Spain)] [Department of Physical Chemistry and Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, 15706 Santiago de Compostela (Spain)

2014-05-07

115

Sequence Preference for BI/BII Conformations in DNA: MD and Crystal Structure Data Analysis  

E-print Network

- conformation. Non-canonical conformations in B-DNA involve correlated transitions in backbone torsion angles (OSequence Preference for BI/BII Conformations in DNA: MD and Crystal Structure Data Analysis http the conformational substates of DNA. BII conformation, one of the conformational sub- states of B-DNA, is known

Bansal, Manju

116

Redox-dependent conformational transition of catalytic domain of protein disulfide isomerase indicated by crystal structure-based molecular dynamics simulation  

NASA Astrophysics Data System (ADS)

Protein disulfide isomerase is a multidomain protein operating as an essential folding catalyst. The b? and a? domains of this enzyme exhibit a domain rearrangement depending on the redox states of the a? domain, which is coupled with an open-closed conformational change of substrate-binding hydrophobic surface. Here we performed crystallographic analysis along with molecular dynamics simulations to study the structural mechanisms underlying this domain rearrangement. Based on our data, we propose that oxidization of the a? active site induces conformational changes in its b?-interacting segments, which is concealed by crystal packing, resulting in segregation of these two domains.

Inagaki, Koya; Satoh, Tadashi; Itoh, Satoru G.; Okumura, Hisashi; Kato, Koichi

2015-01-01

117

Targeting conformational plasticity of protein kinases.  

PubMed

The quest for ever more selective kinase inhibitors as potential future drugs has yielded a large repertoire of chemical probes that are selective for specific kinase conformations. These probes have been useful tools to obtain structural snapshots of kinase conformational plasticity. Similarly, kinetic and thermodynamic inhibitor binding experiments provide glimpses at the time scales and energetics of conformational interconversions. These experimental insights are complemented by computational predictions of conformational energy landscapes and simulations of conformational transitions and of the process of inhibitors binding to the protein kinase domain. A picture emerges in which highly selective inhibitors capitalize on the dynamic nature of kinases. PMID:25486330

Tong, Michael; Seeliger, Markus A

2015-01-16

118

Conformable seal  

DOEpatents

Sealing apparatus and method, comprising first and second surfaces or membranes, at least one of which surfaces is deformable, placed in proximity to one another. Urging means cause these surfaces to contact one another in a manner such that the deformable surface deforms to conform to the geometry of the other surface, thereby creating a seal. The seal is capable of undergoing multiple cycles of sealing and unsealing.

Neef, W.S.; Lambert, D.R.

1982-08-10

119

Conformation analysis and computation of energy barrier to rotation about Csbnd N bond in para-methylphenyl carbamate and its solvent dependence in comparison with tertiary carbamates and tertiary amides  

NASA Astrophysics Data System (ADS)

Barrier to rotation about conjugated Csbnd N bond in p-Methyl phenyl carbamate (PMPC) was computed 14-16 kcal/mol at three levels of HF, B3LYP and MP2 using 6-311++G?? basis set. The solvent effect and energy barriers about Csbnd N bond in PMPC were compared to the case of tertiary carbamates and tertiary amides. Moreover, it is shown that in primary carbamates such as PMPC and tertiary amides isomerisation process passes through TS2 and TS1 respectively, while in tertiary carbamates goes through a combination of both TSs. Furthermore, X-ray analysis which is reported for the first time for primary aryl carbamates demonstrated that the inclusive plane of carbamate functional group is perpendicular to the plane of phenyl ring. The results of computations are completely in agreement with the X-ray data.

Modarresi-Alam, Ali Reza; Nowroozi, Alireza; Najafi, Parisa; Movahedifar, Fahimeh; Hajiabadi, Hossein

2014-11-01

120

Single Polymer Molecules: Chain Conformation after Adsorption  

NASA Astrophysics Data System (ADS)

Single Polymer Molecules: Chain Conformation after Adsorption Manfred Stamm 1, Anton Kiriy 1, Ganna Gorodyska 1, Sergiy Minko 2, Werner Jaeger 3, Petr Stepanek 4 1 Institut fuer Polymerforschung Dresden, Germany, 2 Clarkson University, New York, USA, 3 Fraunhofer-Institut fuer Angewandte Polymerforschung, Golm, Germany 4 Institute of Macromolecular Chemistry, Prague, Czech Republic, Single polyelectrolyte molecules can be adsorbed on a charged solid substrate from dilute solution. Scanning force microscopy then offers the possibility to determine the chain conformation in detail. Several polymer molecules have been adsorbed, where the chain conformation in the adsorbed state is believed to reflect the conformation in solution. We observe different states depending on pH and solvent quality. In particular we observe coil-like, pearl necklace-globule conformations and compact globule, and can follow the transition of chain conformation from coil to globular one. The transition appears not to be simple first order but a cascade of abrupt conformational transitions where in the transition regime different conformations can coexist at different amounts.

Stamm, Manfred

2004-03-01

121

Combined Use of Residual Dipolar Couplings and Solution X-ray Scattering To Rapidly Probe Rigid-Body Conformational Transitions in a Non-phosphorylatable Active-Site Mutant of the 128 kDa Enzyme I Dimer  

SciTech Connect

The first component of the bacterial phosphotransferase system, enzyme I (EI), is a multidomain 128 kDa dimer that undergoes large rigid-body conformational transitions during the course of its catalytic cycle. Here we investigate the solution structure of a non-phosphorylatable active-site mutant in which the active-site histidine is substituted by glutamine. We show that perturbations in the relative orientations and positions of the domains and subdomains can be rapidly and reliably determined by conjoined rigid-body/torsion angle/Cartesian simulated annealing calculations driven by orientational restraints from residual dipolar couplings and shape and translation information afforded by small- and wide-angle X-ray scattering. Although histidine and glutamine are isosteric, the conformational space available to a Gln side chain is larger than that for the imidazole ring of His. An additional hydrogen bond between the side chain of Gln189 located on the EIN{sup {alpha}/{beta}} subdomain and an aspartate (Asp129) on the EIN{sup {alpha}} subdomain results in a small ({approx}9{sup o}) reorientation of the EIN{sup {alpha}} and EIN{sup {alpha}/{beta}} subdomains that is in turn propagated to a larger reorientation ({approx}26{sup o}) of the EIN domain relative to the EIC dimerization domain, illustrating the positional sensitivity of the EIN domain and its constituent subdomains to small structural perturbations.

Takayama, Yuki; Schwieters, Charles D.; Grishaev, Alexander; Ghirlando, Rodolfo; Clore, G. Marius (NIH)

2012-10-23

122

Effects of pH and Calcium Ions on the Conformational Transitions in Silk Fibroin Using 2D Raman Correlation Spectroscopy and 13 C Solid-State NMR †  

Microsoft Academic Search

Silk fibroin exists in a number of different states, such as silk I and silk II, with different properties largely defined by differences in secondary structure composition. Numerous attempts have been made to control the transitions from silk I to silk II in vitro to produce high-performance materials. Of all the factors influencing the structural compositions, pH and some metal

Ping Zhou; Xun Xie; David P. Knight; Xiao-Hong Zong; Feng Deng; Wen-Hua Yao

2004-01-01

123

Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: Explicit treatment of the vibronic transitions  

SciTech Connect

Here, we extend a recently introduced theoretical-computational procedure [M. D’Alessandro, M. Aschi, C. Mazzuca, A. Palleschi, and A. Amadei, J. Chem. Phys. 139, 114102 (2013)] to include quantum vibrational transitions in modelling electronic spectra of atomic molecular systems in condensed phase. The method is based on the combination of Molecular Dynamics simulations and quantum chemical calculations within the Perturbed Matrix Method approach. The main aim of the presented approach is to reproduce as much as possible the spectral line shape which results from a subtle combination of environmental and intrinsic (chromophore) mechanical-dynamical features. As a case study, we were able to model the low energy UV-vis transitions of pyrene in liquid acetonitrile in good agreement with the experimental data.

D’Abramo, Marco [Supercomputing Applications and Innovation, CINECA, Via dei Tizii, 6, 00185 Rome (Italy) [Supercomputing Applications and Innovation, CINECA, Via dei Tizii, 6, 00185 Rome (Italy); Dipartimento di Chimica, Universitá Sapienza, P.le Aldo Moro, 5, 00185, Rome (Italy); Aschi, Massimiliano [Department of Physical and Chemical Sciences, University of Aquila, via Vetoio (Coppito 1), 67010 Aquila (Italy)] [Department of Physical and Chemical Sciences, University of Aquila, via Vetoio (Coppito 1), 67010 Aquila (Italy); Amadei, Andrea, E-mail: andrea.amadei@uniroma2.it [Dipartimento di Scienze e Tecnologie Chimiche Universita’ di Roma, Tor Vergata, via della Ricerca Scientifica 1, I-00133 Roma (Italy)] [Dipartimento di Scienze e Tecnologie Chimiche Universita’ di Roma, Tor Vergata, via della Ricerca Scientifica 1, I-00133 Roma (Italy)

2014-04-28

124

Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: Explicit treatment of the vibronic transitions  

NASA Astrophysics Data System (ADS)

Here, we extend a recently introduced theoretical-computational procedure [M. D'Alessandro, M. Aschi, C. Mazzuca, A. Palleschi, and A. Amadei, J. Chem. Phys. 139, 114102 (2013)] to include quantum vibrational transitions in modelling electronic spectra of atomic molecular systems in condensed phase. The method is based on the combination of Molecular Dynamics simulations and quantum chemical calculations within the Perturbed Matrix Method approach. The main aim of the presented approach is to reproduce as much as possible the spectral line shape which results from a subtle combination of environmental and intrinsic (chromophore) mechanical-dynamical features. As a case study, we were able to model the low energy UV-vis transitions of pyrene in liquid acetonitrile in good agreement with the experimental data.

D'Abramo, Marco; Aschi, Massimiliano; Amadei, Andrea

2014-04-01

125

Solvent dependent branching between C-I and C-Br bond cleavage following 266 nm excitation of CH{sub 2}BrI  

SciTech Connect

It is well known that ultraviolet photoexcitation of halomethanes results in halogen-carbon bond cleavage. Each halogen-carbon bond has a dominant ultraviolet (UV) absorption that promotes an electron from a nonbonding halogen orbital (n{sub X}) to a carbon-halogen antibonding orbital (?*{sub C-X}). UV absorption into specific transitions in the gas phase results primarily in selective cleavage of the corresponding carbon-halogen bond. In the present work, broadband ultrafast UV-visible transient absorption studies of CH{sub 2}BrI reveal a more complex photochemistry in solution. Transient absorption spectra are reported spanning the range from 275 nm to 750 nm and 300 fs to 3 ns following excitation of CH{sub 2}BrI at 266 nm in acetonitrile, 2-butanol, and cyclohexane. Channels involving formation of CH{sub 2}Br + I radical pairs, iso-CH{sub 2}Br-I, and iso-CH{sub 2}I-Br are identified. The solvent environment has a significant influence on the branching ratios, and on the formation and stability of iso-CH{sub 2}Br-I. Both iso-CH{sub 2}Br-I and iso-CH{sub 2}I-Br are observed in cyclohexane with a ratio of ?2.8:1. In acetonitrile this ratio is 7:1 or larger. The observation of formation of iso-CH{sub 2}I-Br photoproduct as well as iso-CH{sub 2}Br-I following 266 nm excitation is a novel result that suggests complexity in the dissociation mechanism. We also report a solvent and concentration dependent lifetime of iso-CH{sub 2}Br-I. At low concentrations the lifetime is >4 ns in acetonitrile, 1.9 ns in 2-butanol and ?1.4 ns in cyclohexane. These lifetimes decrease with higher initial concentrations of CH{sub 2}BrI. The concentration dependence highlights the role that intermolecular interactions can play in the quenching of unstable isomers of dihalomethanes.

Anderson, Christopher P.; Spears, Kenneth G.; Wilson, Kaitlynn R.; Sension, Roseanne J. [Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States)] [Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States)

2013-11-21

126

Crystal Structures of Progressive Ca2+ Binding States of the Ca2+ Sensor Ca2+ Binding Domain 1 (CBD1) from the CALX Na+/Ca2+ Exchanger Reveal Incremental Conformational Transitions*  

PubMed Central

Na+/Ca2+ exchangers (NCX) constitute a major Ca2+ export system that facilitates the re-establishment of cytosolic Ca2+ levels in many tissues. Ca2+ interactions at its Ca2+ binding domains (CBD1 and CBD2) are essential for the allosteric regulation of Na+/Ca2+ exchange activity. The structure of the Ca2+-bound form of CBD1, the primary Ca2+ sensor from canine NCX1, but not the Ca2+-free form, has been reported, although the molecular mechanism of Ca2+ regulation remains unclear. Here, we report crystal structures for three distinct Ca2+ binding states of CBD1 from CALX, a Na+/Ca2+ exchanger found in Drosophila sensory neurons. The fully Ca2+-bound CALX-CBD1 structure shows that four Ca2+ atoms bind at identical Ca2+ binding sites as those found in NCX1 and that the partial Ca2+ occupancy and apoform structures exhibit progressive conformational transitions, indicating incremental regulation of CALX exchange by successive Ca2+ binding at CBD1. The structures also predict that the primary Ca2+ pair plays the main role in triggering functional conformational changes. Confirming this prediction, mutagenesis of Glu455, which coordinates the primary Ca2+ pair, produces dramatic reductions of the regulatory Ca2+ affinity for exchange current, whereas mutagenesis of Glu520, which coordinates the secondary Ca2+ pair, has much smaller effects. Furthermore, our structures indicate that Ca2+ binding only enhances the stability of the Ca2+ binding site of CBD1 near the hinge region while the overall structure of CBD1 remains largely unaffected, implying that the Ca2+ regulatory function of CBD1, and possibly that for the entire NCX family, is mediated through domain interactions between CBD1 and the adjacent CBD2 at this hinge. PMID:19815561

Wu, Mousheng; Le, Hoa Dinh; Wang, Meitian; Yurkov, Vladimir; Omelchenko, Alexander; Hnatowich, Mark; Nix, Jay; Hryshko, Larry V.; Zheng, Lei

2010-01-01

127

Side-Chain Conformational Changes upon Protein-Protein Association  

PubMed Central

Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short and long side chains have different propensities for the conformational changes. Long side chains with three or more dihedral angles are often subject to large conformational transition. Shorter residues with one or two dihedral angles typically undergo local conformational changes not leading to a conformational transition. The relationship between the local readjustments and the equilibrium fluctuations of a side chain around its unbound conformation is suggested. Most of the side chains undergo larger changes in the dihedral angle most distant from the backbone. The frequencies of the core-to-surface interface transitions of six nonpolar residues and Tyr are larger than the frequencies of the opposite, surface-to-core transitions. The binding increases both polar and nonpolar interface areas. However, the increase of the nonpolar area is larger for all considered classes of protein complexes, suggesting that the protein association perturbs the unbound interfaces to increase the hydrophobic contribution to the binding free energy. To test modeling approaches to side-chain flexibility in protein docking, conformational changes in the X-ray set were compared with those in the docking decoys sets. The results lead to a better understanding of the conformational changes in proteins and suggest directions for efficient conformational sampling in docking protocols. PMID:21354429

Ruvinsky, Anatoly M.; Kirys, Tatsiana; Tuzikov, Alexander V.; Vakser, Ilya A.

2011-01-01

128

Solvent dependent photophysical properties of dimethoxy curcumin  

NASA Astrophysics Data System (ADS)

Dimethoxy curcumin (DMC) is a methylated derivative of curcumin. In order to know the effect of ring substitution on photophysical properties of curcumin, steady state absorption and fluorescence spectra of DMC were recorded in organic solvents with different polarity and compared with those of curcumin. The absorption and fluorescence spectra of DMC, like curcumin, are strongly dependent on solvent polarity and the maxima of DMC showed red shift with increase in solvent polarity function (?f), but the above effect is prominently observed in case of fluorescence maxima. From the dependence of Stokes' shift on solvent polarity function the difference between the excited state and ground state dipole moment was estimated as 4.9 D. Fluorescence quantum yield (?f) and fluorescence lifetime (?f) of DMC were also measured in different solvents at room temperature. The results indicated that with increasing solvent polarity, ?f increased linearly, which has been accounted for the decrease in non-radiative rate by intersystem crossing (ISC) processes.

Barik, Atanu; Indira Priyadarsini, K.

2013-03-01

129

Solvent dependent photophysical properties of dimethoxy curcumin.  

PubMed

Dimethoxy curcumin (DMC) is a methylated derivative of curcumin. In order to know the effect of ring substitution on photophysical properties of curcumin, steady state absorption and fluorescence spectra of DMC were recorded in organic solvents with different polarity and compared with those of curcumin. The absorption and fluorescence spectra of DMC, like curcumin, are strongly dependent on solvent polarity and the maxima of DMC showed red shift with increase in solvent polarity function (?f), but the above effect is prominently observed in case of fluorescence maxima. From the dependence of Stokes' shift on solvent polarity function the difference between the excited state and ground state dipole moment was estimated as 4.9 D. Fluorescence quantum yield (?(f)) and fluorescence lifetime (?(f)) of DMC were also measured in different solvents at room temperature. The results indicated that with increasing solvent polarity, ?(f) increased linearly, which has been accounted for the decrease in non-radiative rate by intersystem crossing (ISC) processes. PMID:23314392

Barik, Atanu; Indira Priyadarsini, K

2013-03-15

130

Solvent dependence of 7-azaindole dimerization.  

PubMed

We have investigated 7-azaindole (AI) in a variety of solvents including CCl4, CHCl3, CH2Cl2, acetone, CH3CN, and DMSO by femtosecond Raman-induced Kerr effect spectroscopy. In differential low-frequency Kerr spectra between the solutions and the respective neat solvents, vibrational bands of the AI hydrogen-bonding (HB) dimer have been observed at ca. 90 and 105 cm(-1) in CHCl3 and CH2Cl2, as well as CCl4: the standard solvent for the AI dimer. In contrast, a broad monomodal band at ca. 80 cm(-1) characterizes an HB mode between the AI monomer and solvent in acetone, CH3CN, and DMSO. The overdamped Kerr transients in the picosecond region show evidence of both the AI monomer and dimer reorientations in CHCl3, CH2Cl2, acetone, and CH3CN, but only the monomer reorientation has been confirmed in DMSO. The clear intermolecular HB bands have not been observed in acetone, CH3CN, and DMSO because these solvents are sufficiently strong HB acceptors, which form HB AI-solvent complexes, thus preventing quantitative AI dimerization. In addition, it is plausible that the HB band of between AI and solvent obscures the intermolecular bands of the AI dimer when the concentration of the AI dimer is much lower than the AI monomer. For comparison, we have employed NMR to study the concentration-dependent chemical shift of the proton attached to the N at the 7-position of AI and to estimate the dimerization constant: 356, 13.3, 14.7, 0.727, and 0.910 M(-1) in CCl4, CHCl3, CH2Cl2, acetone, and CH3CN, respectively. The femtosecond Raman-induced Kerr effect spectroscopy and NMR results are in good agreement. PMID:24191715

Shirota, Hideaki; Fukuda, Takao; Kato, Tatsuya

2013-12-19

131

The conformational basis of thrombosis.  

PubMed

Antithrombin readily undergoes a spontaneous transition from its active five-stranded form to a six-stranded inactive latent form. The recognition of this change in plasma has been obscured by the immediate linkage of newly formed latent antithrombin to a molecule of active antithrombin to give a dimer with an electrophoretic mobility readily confused with that of native active antithrombin. A new micromethod now allows unequivocal identification of latent antithrombin in whole plasma. This shows that at 37 degrees C some 10% of plasma antithrombin is converted to the latent form in 24 h. The rate of conversion is greatly accelerated at increased temperatures, as occurs in the pasteurisation of plasma concentrates that should now be checked for efficacy. But increased transition also occurs in the plasma at the slightly increased temperatures that accompany incidental infections. This is of particular significance if there is a conformationally unstable variant of antithrombin; here fever can provoke a sudden transition with the onset of a characteristically severe episode of thromboembolism. Such variants are not rare and include those previously classified as pleiotropic. The precise structural pathway, now known with antithrombin, provides a model of the changes occurring in other conformational diseases, including Alzheimer's and the prion dementias. PMID:11487000

Carrell, R W; Huntington, J A; Mushunje, A; Zhou, A

2001-07-01

132

Local conformal symmetry in physics and cosmology  

NASA Astrophysics Data System (ADS)

We show how to lift a generic non-scale-invariant action in Einstein frame into a locally conformally invariant (or Weyl-invariant) theory and present a new general form for Lagrangians consistent with Weyl symmetry. Advantages of such a conformally invariant formulation of particle physics and gravity include the possibility of constructing geodesically complete cosmologies. We present a conformal-invariant version of the standard model coupled to gravity, and show how Weyl symmetry may be used to obtain unprecedented analytic control over its cosmological solutions. Within this new framework, generic Friedmann-Robertson-Walker cosmologies are geodesically complete through a series of big crunch-big bang transitions. We discuss a new scenario of cosmic evolution driven by the Higgs field in a "minimal" conformal standard model, in which there is no new physics beyond the standard model at low energies, and the current Higgs vacuum is metastable as indicated by the latest LHC data.

Bars, Itzhak; Steinhardt, Paul; Turok, Neil

2014-02-01

133

Toward TeV Conformality  

SciTech Connect

We study the chiral condensate <{bar {psi}}{psi}> for an SU(3) gauge theory with N{sub f} massless Dirac fermions in the fundamental representation when N{sub f} is increased from 2 to 6. For N{sub f} = 2, our lattice simulations of <{bar {psi}}{psi}>/F{sup 3}, where F is the Nambu-Goldstone-boson decay constant, agree with the measured QCD value. For N{sub f} = 6, this ratio shows significant enhancement, presaging an even larger enhancement anticipated as N{sub f} increases further, toward the critical value for transition from confinement to infrared conformality.

Appelquist, T; Avakian, A; Babich, R; Brower, R C; Cheng, M; Clark, M A; Cohen, S D; Fleming, G T; Kiskis, J; Neil, E T; Osborn, J C; Rebbi, C; Schaich, D; Soltz, R; Vranas, P

2009-11-30

134

Conformational isomers of linear rotaxanes.  

PubMed

We examine a simple model of rotaxane structure, with 3 asymmetric rings interacting via repulsive power-law forces. This interlocked molecule exhibits conformational isomerisation which is different from that of molecules whose connectedness is through covalent bonds. The rings are free to translate along and rotate around the axle, and hence weak interaction forces between the rings can lead to distinct rotamer states. We use energy minimisation to determine these states exactly, and show that there can be transitions from asymmetric to symmetric states by varying the bond lengths. We also use classical statistical mechanics to show the effect of thermal noise. PMID:25240369

Sevick, Edith M; Williams, David R M

2014-09-21

135

New massive conformal gravity  

E-print Network

We investigate the new massive conformal gravity which is not invariant under conformal transformations, in comparison to the massive conformal gravity. We find five polarization modes of gravitational waves propagating on the Minkowski spacetimes. The stability of Minkowski spacetimes is guaranteed if the mass squared is not negative and the linearized Ricci tenor is employed to describe a massive spin-2 graviton. However, the small Schwarzschild black hole is unstable against the $s$-mode massive graviton perturbations.

Yun Soo Myung

2014-02-09

136

Galilean conformal electrodynamics  

NASA Astrophysics Data System (ADS)

Maxwell's Electrodynamics admits two distinct Galilean limits called the Electric and Magnetic limits. We show that the equations of motion in both these limits are invariant under the Galilean Conformal Algebra in D = 4, thereby exhibiting non-relativistic conformal symmetries. Remarkably, the symmetries are infinite dimensional and thus Galilean Electrodynamics give us the first example of an infinitely extended Galilean Conformal Field Theory in D > 2. We examine details of the theory by looking at purely non-relativistic conformal methods and also use input from the limit of the relativistic theory.

Bagchi, Arjun; Basu, Rudranil; Mehra, Aditya

2014-11-01

137

Discovering Conformational Sub-States Relevant to Protein Function  

PubMed Central

Background Internal motions enable proteins to explore a range of conformations, even in the vicinity of native state. The role of conformational fluctuations in the designated function of a protein is widely debated. Emerging evidence suggests that sub-groups within the range of conformations (or sub-states) contain properties that may be functionally relevant. However, low populations in these sub-states and the transient nature of conformational transitions between these sub-states present significant challenges for their identification and characterization. Methods and Findings To overcome these challenges we have developed a new computational technique, quasi-anharmonic analysis (QAA). QAA utilizes higher-order statistics of protein motions to identify sub-states in the conformational landscape. Further, the focus on anharmonicity allows identification of conformational fluctuations that enable transitions between sub-states. QAA applied to equilibrium simulations of human ubiquitin and T4 lysozyme reveals functionally relevant sub-states and protein motions involved in molecular recognition. In combination with a reaction pathway sampling method, QAA characterizes conformational sub-states associated with cis/trans peptidyl-prolyl isomerization catalyzed by the enzyme cyclophilin A. In these three proteins, QAA allows identification of conformational sub-states, with critical structural and dynamical features relevant to protein function. Conclusions Overall, QAA provides a novel framework to intuitively understand the biophysical basis of conformational diversity and its relevance to protein function. PMID:21297978

Ramanathan, Arvind; Savol, Andrej J.; Langmead, Christopher J.; Agarwal, Pratul K.; Chennubhotla, Chakra S.

2011-01-01

138

Folded Conformations of Maitotoxin  

Microsoft Academic Search

We used classical molecular mechanics and dynamics simulations to sample the conformational space of maitotoxin, the largest and most lethal natural product. Among the set of minima obtained, the five conformers with the lowest energies show folded structures with an intramolecular hole. We found the folding mainly due to hydrogen bonds that fasten the mobile zones of the molecule. The

Myrna H. Matus; Laura Escobar; Marcelo Galván

2008-01-01

139

Fusion of conformal interfaces  

Microsoft Academic Search

We study the fusion of conformal interfaces in the c = 1 conformal field theory. We uncover an elegant structure reminiscent of that of black holes in supersymmetric theories. The role of the BPS black holes is played by topological interfaces, which (a) minimize the entropy function, (b) fix through an attractor mechanism one or both of the bulk radii,

C. Bachas; I. Brunner

2008-01-01

140

Conformations of Substituted Ethanes.  

ERIC Educational Resources Information Center

Reviews state-of-the-art of conformational analysis and factors which affect it. Emphasizes sp-3 hybridized acrylic molecules. Provides examples on the importance of certain factors in determining conformation. Purpose, is to provide examples for examination questions. (Author/SA)

Kingsbury, Charles A.

1979-01-01

141

Conformity index: A review  

SciTech Connect

We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear.

Feuvret, Loic [Institut Curie, Orsay (France)]. E-mail: loic.feuvret@cpo.curie.net; Noel, Georges [Institut Curie, Orsay (France); Mazeron, Jean-Jacques [Institut Curie, Orsay (France); Pitie Salpetriere Hospital, Paris (France); Bey, Pierre [Institut Curie, Orsay (France); Institut Curie, Paris (France)

2006-02-01

142

Influence of tetraalkyl ammonium ions on the structure of poly (rG-dC).poly (rG-dC): unexpected transitions among the Z, A and B conformations.  

PubMed Central

The conformation of the double-stranded, mixed ribodeoxyribo polynucleotide, poly (rG-dC).poly (rG-dC), has been examined in the presence of tetraalkyl ammonium ions. Tetramethyl ammonium ion stabilizes the "low salt" Z conformation (1) of the polymer from submillimolar to molar concentrations of the counterion. In the presence of tetraethyl and tetrapropyl ammonium ions the polymer exists in the low salt Z form up to 2 mM concentration of the counterions and then flips to the right hand helical A form. With tetrabutyl ammonium counterions the polymer is in an A conformation at low ion concentrations and converts to a B form at concentrations greater than thirty millimolar. These results are interpreted in terms of electrostatic and solvent interactions of the polynucleotide. PMID:3588312

Jayasena, S D; Behe, M J

1987-01-01

143

Infrared study on annealing effect on conformation of zinc stearate  

Microsoft Academic Search

The molecular conformation and thermal transition behavior of two zinc stearate specimens, unannealed one and annealed one, were compared. The unannealed specimen has one thermal transition at 134°C. Annealing was made by increasing temperature to 150°C and cooling to room temperature slowly. This annealed specimen has an exothermic peak at 103°C, and endothermic shoulders and a peak at 118, 124

Tsutomu Ishioka; Atsushi Kiritani; Takuya Kojima

2007-01-01

144

Conformal Carroll groups  

NASA Astrophysics Data System (ADS)

Conformal extensions of Lévy-Leblond's Carroll group, based on geometric properties analogous to those of Newton-Cartan space-time are proposed. The extensions are labeled by an integer k. This framework includes and extends our recent study of the Bondi-Metzner-Sachs (BMS) and Newman-Unti (NU) groups. The relation to conformal Galilei groups is clarified. Conformal Carroll symmetry is illustrated by ‘Carrollian photons’. Motion both in the Newton-Cartan and Carroll spaces may be related to that of strings in the Bargmann space.

Duval, C.; Gibbons, G. W.; Horvathy, P. A.

2014-08-01

145

Vibrational Spectroscopic Investigation and Conformational Analysis of 1-HEPTYLAMINE: a Comparative Density Functional Study  

NASA Astrophysics Data System (ADS)

FT-IR and Raman spectra of 1-heptylamine (1-ha) were experimentally reported in the region of 4000-10 cm-1 and 4000-100 cm-1, respectively. The conformational analysis, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of 1-ha (C7H17N) were theoretically examined by means of Becke-3-Lee-Yang-Parr (B3-LYP) density functional theory (DFT) method together with 6-31++G(d,p) basis set. Furthermore, reliable vibrational assignments were made on the basis of potential energy distribution (PED) calculated and the thermodynamics functions, highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO) of 1-ha were predicted. Calculations were carried out with the possible ten conformational isomers (TT, TG, GT, GT1, GG1, GG2, GG3, GG4, GG5, GG6; T and G denote trans and gauge) of 1-ha, both in gas phase and in solution. Solvent effects were investigated using benzene and methanol. All results indicates that B3-LYP method provides satisfactory results for the prediction vibrational wavenumbers, TT isomer is the most stable form of 1-ha and the conformational energy barrier is independent of the solvent whereas the vibrational frequencies and assignments, IR and Raman intensities of 1-ha are solvent dependent.

Tursun, Mahir; Kesan, Gurkan; Parlak, Cemal; Senyel, Mustafa

2013-06-01

146

Studies of (-)-pironetin binding to ?-tubulin: conformation, docking, and molecular dynamics.  

PubMed

A comprehensive conformational analysis for the anticancer agent pironetin (1) was achieved by molecular modeling using density functional theory calculations at the B3PW91/DGTZVP level in combination with calculated and experimental (1)H-(1)H coupling constants comparison. Two solvent-dependent conformational families (L and M) were revealed for the optimum conformations. Docking studies of the pironetin-tubulin complex determined a quantitative model for the hydrogen-bond interactions of pironetin through the ?Asn249, ?Asn258, and ?Lys352 amino groups in ?-tubulin, which supported the formation of a covalent adduct between the ?Lys352 and the ? carbon atom of the ?,?-unsaturated lactone. Saturation-transfer difference NMR spectroscopy confirmed that pironetin binds to tubulin, while molecular dynamics exposed a distortion of the tubulin secondary structure at the H8 and H10 ?-helices as well as at the S9 ?-sheet, where ?Lys352 is located. A large structural perturbation in the M-loop geometry between the ?Ile274 and ?Leu285 residues, an essential region for molecular recognition between ?-? and ?-? units of protofilaments, was also identified and provided a rationale for the pironetin inhibitory activity. PMID:24761989

Bañuelos-Hernández, Angel E; Mendoza-Espinoza, José Alberto; Pereda-Miranda, Rogelio; Cerda-García-Rojas, Carlos M

2014-05-01

147

Logarithmic conformal field theory  

NASA Astrophysics Data System (ADS)

Conformal field theory (CFT) has proven to be one of the richest and deepest subjects of modern theoretical and mathematical physics research, especially as regards statistical mechanics and string theory. It has also stimulated an enormous amount of activity in mathematics, shaping and building bridges between seemingly disparate fields through the study of vertex operator algebras, a (partial) axiomatisation of a chiral CFT. One can add to this that the successes of CFT, particularly when applied to statistical lattice models, have also served as an inspiration for mathematicians to develop entirely new fields: the Schramm-Loewner evolution and Smirnov's discrete complex analysis being notable examples. When the energy operator fails to be diagonalisable on the quantum state space, the CFT is said to be logarithmic. Consequently, a logarithmic CFT is one whose quantum space of states is constructed from a collection of representations which includes reducible but indecomposable ones. This qualifier arises because of the consequence that certain correlation functions will possess logarithmic singularities, something that contrasts with the familiar case of power law singularities. While such logarithmic singularities and reducible representations were noted by Rozansky and Saleur in their study of the U (1|1) Wess-Zumino-Witten model in 1992, the link between the non-diagonalisability of the energy operator and logarithmic singularities in correlators is usually ascribed to Gurarie's 1993 article (his paper also contains the first usage of the term 'logarithmic conformal field theory'). The class of CFTs that were under control at this time was quite small. In particular, an enormous amount of work from the statistical mechanics and string theory communities had produced a fairly detailed understanding of the (so-called) rational CFTs. However, physicists from both camps were well aware that applications from many diverse fields required significantly more complicated non-rational theories. Examples include critical percolation, supersymmetric string backgrounds, disordered electronic systems, sandpile models describing avalanche processes, and so on. In each case, the non-rationality and non-unitarity of the CFT suggested that a more general theoretical framework was needed. Driven by the desire to better understand these applications, the mid-1990s saw significant theoretical advances aiming to generalise the constructs of rational CFT to a more general class. In 1994, Nahm introduced an algorithm for computing the fusion product of representations which was significantly generalised two years later by Gaberdiel and Kausch who applied it to explicitly construct (chiral) representations upon which the energy operator acts non-diagonalisably. Their work made it clear that underlying the physically relevant correlation functions are classes of reducible but indecomposable representations that can be investigated mathematically to the benefit of applications. In another direction, Flohr had meanwhile initiated the study of modular properties of the characters of logarithmic CFTs, a topic which had already evoked much mathematical interest in the rational case. Since these seminal theoretical papers appeared, the field has undergone rapid development, both theoretically and with regard to applications. Logarithmic CFTs are now known to describe non-local observables in the scaling limit of critical lattice models, for example percolation and polymers, and are an integral part of our understanding of quantum strings propagating on supermanifolds. They are also believed to arise as duals of three-dimensional chiral gravity models, fill out hidden sectors in non-rational theories with non-compact target spaces, and describe certain transitions in various incarnations of the quantum Hall effect. Other physical applications range from two-dimensional turbulence and non-equilibrium systems to aspects of the AdS/CFT correspondence and describing supersymmetric sigma models beyond the topological sector. We refer the reader to the

Gainutdinov, Azat; Ridout, David; Runkel, Ingo

2013-12-01

148

Conformal and non conformal dilaton gravity  

NASA Astrophysics Data System (ADS)

The quantum dynamics of the gravitational field non-minimally coupled to an (also dynamical) scalar field is studied in the broken phase. For a particular value of the coupling the system is classically conformal, and can actually be understood as the group averaging of Einstein-Hilbert's action under conformal transformations. Conformal invariance implies a simple Ward identity asserting that the trace of the equation of motion for the graviton is the equation of motion of the scalar field. We perform an explicit one-loop computation to show that the DeWitt effective action is not UV divergent on shell and to find that the Weyl symmetry Ward identity is preserved on shell at that level. We also discuss the fate of this Ward identity at the two-loop level — under the assumption that the two-loop UV divergent part of the effective action can be retrieved from the Goroff-Sagnotti counterterm — and show that its preservation in the renormalized theory requires the introduction of counterterms which exhibit a logarithmic dependence on the dilaton field.

Alvarez, Enrique; Herrero-Valea, Mario; Martín, C. P.

2014-10-01

149

Characterizing Protein Conformation Space  

E-print Network

In this work, we propose a radical approach for exploring the space of all possible protein structures. We present techniques to explore the clash-free conformation space, which comprises all protein structures whose atoms ...

Nigham, Anshul

150

Assemblies of Conformal Tanks  

NASA Technical Reports Server (NTRS)

Assemblies of tanks having shapes that conform to each other and/or conform to other proximate objects have been investigated for use in storing fuels and oxidizers in small available spaces in upper stages of spacecraft. Such assemblies might also prove useful in aircraft, automobiles, boats, and other terrestrial vehicles in which space available for tanks is limited. The basic concept of using conformal tanks to maximize the utilization of limited space is not new in itself: for example, conformal tanks are used in some automobiles to store windshield -washer liquid and coolant that overflows from radiators. The novelty of the present development lies in the concept of an assembly of smaller conformal tanks, as distinguished from a single larger conformal tank. In an assembly of smaller tanks, it would be possible to store different liquids in different tanks. Even if the same liquid were stored in all the tanks, the assembly would offer an advantage by reducing the mechanical disturbance caused by sloshing of fuel in a single larger tank: indeed, the requirement to reduce sloshing is critical in some applications. The figure shows a prototype assembly of conformal tanks. Each tank was fabricated by (1) copper plating a wax tank mandrel to form a liner and (2) wrapping and curing layers of graphite/epoxy composite to form a shell supporting the liner. In this case, the conformal tank surfaces are flat ones where they come in contact with the adjacent tanks. A band of fibers around the outside binds the tanks together tightly in the assembly, which has a quasi-toroidal shape. For proper functioning, it would be necessary to maintain equal pressure in all the tanks.

DeLay, Tom

2009-01-01

151

Population shuffling of protein conformations.  

PubMed

Motions play a vital role in the functions of many proteins. Discrete conformational transitions to excited states, happening on timescales of hundreds of microseconds, have been extensively characterized. On the other hand, the dynamics of the ground state are widely unexplored. Newly developed high-power relaxation dispersion experiments allow the detection of motions up to a one-digit microsecond timescale. These experiments showed that side chains in the hydrophobic core as well as at protein-protein interaction surfaces of both ubiquitin and the third immunoglobulin binding domain of protein?G move on the microsecond timescale. Both proteins exhibit plasticity to this microsecond motion through redistribution of the populations of their side-chain rotamers, which interconvert on the picosecond to nanosecond timescale, making it likely that this "population shuffling" process is a general mechanism. PMID:25377083

Smith, Colin A; Ban, David; Pratihar, Supriya; Giller, Karin; Schwiegk, Claudia; de Groot, Bert L; Becker, Stefan; Griesinger, Christian; Lee, Donghan

2015-01-01

152

Two-Dimensional Heterospectral Correlation Analysis of the Redox-Induced Conformational Transition in Cytochrome c Using Surface-Enhanced Raman and Infrared Absorption Spectroscopies on a Two-Layer Gold Surface  

PubMed Central

The heme protein cytochrome c adsorbed to a two-layer gold surface modified with a self-assembled monolayer of 2-mercaptoethanol was analyzed using a two-dimensional (2D) heterospectral correlation analysis that combined surface-enhanced infrared absorption spectroscopy (SEIRAS) and surface-enhanced Raman spectroscopy (SERS). Stepwise increasing electric potentials were applied to alter the redox state of the protein and to induce conformational changes within the protein backbone. We demonstrate herein that 2D heterospectral correlation analysis is a particularly suitable and useful technique for the study of heme-containing proteins as the two spectroscopies address different portions of the protein. Thus, by correlating SERS and SEIRAS data in a 2D plot, we can obtain a deeper understanding of the conformational changes occurring at the redox center and in the supporting protein backbone during the electron transfer process. The correlation analyses are complemented by molecular dynamics calculations to explore the intramolecular interactions. PMID:23930980

2013-01-01

153

Infrared study on annealing effect on conformation of zinc stearate.  

PubMed

The molecular conformation and thermal transition behavior of two zinc stearate specimens, unannealed one and annealed one, were compared. The unannealed specimen has one thermal transition at 134 degrees C. Annealing was made by increasing temperature to 150 degrees C and cooling to room temperature slowly. This annealed specimen has an exothermic peak at 103 degrees C, and endothermic shoulders and a peak at 118, 124 and 131 degrees C, respectively. The observed frequencies of all bands of the unannealed specimen at room temperature are assigned to the all-trans conformation. We found new bands at 858, 823, 793, 766, 688, and 604 cm-1 for the annealed specimen. Based on the normal mode analyses, these bands are assigned to the TGT conformation at the COO end, where T means trans and G means gauche. The annealed specimen consists of almost all-trans molecule but partial molecules have the TGT conformation. PMID:16875870

Ishioka, Tsutomu; Kiritani, Atsushi; Kojima, Takuya

2007-04-01

154

Infrared study on annealing effect on conformation of zinc stearate  

NASA Astrophysics Data System (ADS)

The molecular conformation and thermal transition behavior of two zinc stearate specimens, unannealed one and annealed one, were compared. The unannealed specimen has one thermal transition at 134 °C. Annealing was made by increasing temperature to 150 °C and cooling to room temperature slowly. This annealed specimen has an exothermic peak at 103 °C, and endothermic shoulders and a peak at 118, 124 and 131 °C, respectively. The observed frequencies of all bands of the unannealed specimen at room temperature are assigned to the all-trans conformation. We found new bands at 858, 823, 793, 766, 688, and 604 cm -1 for the annealed specimen. Based on the normal mode analyses, these bands are assigned to the TGT conformation at the COO end, where T means trans and G means gauche. The annealed specimen consists of almost all-trans molecule but partial molecules have the TGT conformation.

Ishioka, Tsutomu; Kiritani, Atsushi; Kojima, Takuya

2007-04-01

155

An extensive galactic search for conformer II glycine  

NASA Technical Reports Server (NTRS)

The most extensive galactic search reported to date for conformer II glycine, a higher energy form of the simplest amino acid has been conducted. The search utilized four glycine transitions at centimeter wavelengths and 21 at millimeter wavelengths to observe 18 galactic molecular sources and one comet. No conformer II glycine lines were detected, and measurements of representative sources were used to compute upper limits on total column densities. Several unidentified lines were detected and are reported here with some suggested possible identifications.

Snyder, L. E.; Hollis, J. M.; Brown, L. W.; Buhl, D.; Suenram, R. D.; Lovas, F. J.

1983-01-01

156

Conformal supermultiplets without superpartners  

E-print Network

We consider polynomial deformations of Lie superalgebras and their representations. For the class A(n-1,0) ~ sl(n/1), we identify families of superalgebras of quadratic and cubic type, consistent with Jacobi identities. For such deformed superalgebras we point out the possibility of zero step supermultiplets, carried on a single, irreducible representation of the even (Lie) subalgebra. For the conformal group SU(2,2) in 1+3-dimensional spacetime, such irreducible (unitary) representations correspond to standard conformal fields (j_1,j_2;d), where (j_1,j_2) is the spin and d the conformal dimension; in the massless class j_1 j_2=0, and d=j_1+j_2+1. We show that these repesentations are zero step supermultiplets for the superalgebra SU_(2)(2,2/1), the quadratic deformation of conformal supersymmetry SU(2,2/1). We propose to elevate SU_(2)(2,2/1) to a symmetry of the S-matrix. Under this scenario, low-energy standard model matter fields (leptons, quarks, Higgs scalars and gauge fields) descended from such conformal supermultiplets are not accompanied by superpartners.

Peter Jarvis

2011-06-24

157

Protein Conformational Populations and Functionally Relevant Sub-states  

SciTech Connect

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 the 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.

Agarwal, Pratul K [ORNL; Burger, Virginia [University of Pittsburgh School of Medicine, Pittsburgh PA; Savol, Andrej [University of Pittsburgh School of Medicine, Pittsburgh PA; Ramanathan, Arvind [ORNL; Chennubhotla, Chakra [University of Pittsburgh School of Medicine, Pittsburgh PA

2013-01-01

158

Conformal Random Geometry  

E-print Network

In these Notes, a comprehensive description of the universal fractal geometry of conformally-invariant scaling curves or interfaces, in the plane or half-plane, is given. The present approach focuses on deriving critical exponents associated with interacting random paths, by exploiting their underlying quantum gravity structure. The latter relates exponents in the plane to those on a random lattice, i.e., in a fluctuating metric, using the so-called Knizhnik, Polyakov and Zamolodchikov (KPZ) map. This is accomplished within the framework of random matrix theory and conformal field theory, with applications to geometrical critical models, like Brownian paths, self-avoiding walks, percolation, and more generally, the O(N) or Q-state Potts models and, last but not least, Schramm's Stochastic Loewner Evolution (SLE_kappa). These Notes can be considered as complementary to those by Wendelin Werner (2006 Fields Medalist!), ``Some Recent Aspects of Random Conformally Invariant Systems,'' arXiv:math.PR/0511268.

Bertrand Duplantier

2006-08-23

159

Compact conformal manifolds  

NASA Astrophysics Data System (ADS)

In this note we begin a systematic study of compact conformal manifolds of SCFTs in four dimensions (our notion of compactness is with respect to the topology induced by the Zamolodchikov metric). Supersymmetry guarantees that such manifolds are Kähler, and so the simplest possible non-trivial compact conformal manifold in this set of geometries is a complex one-dimensional projective space. We show that such a manifold is indeed realized and give a general prescription for constructing complex N-dimensional projective space conformal manifolds as certain small breaking deformations of strongly interacting SCFTs. In many cases, our prescription reduces the construction of such spaces to a study of the chiral ring. We also give an algorithm for constructing more general compact spaces of SCFTs.

Buican, Matthew; Nishinaka, Takahiro

2015-01-01

160

Random Conformal Weldings  

E-print Network

We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle. The homeomorphism is constructed using the exponential of $\\beta X$ where $X$ is the restriction of the two dimensional free field on the circle and the parameter $\\beta$ is in the "high temperature" regime $\\betawelding problem is solved by studying a non-uniformly elliptic Beltrami equation with a random complex dilatation. For the existence a method of Lehto is used. This requires sharp probabilistic estimates to control conformal moduli of annuli and they are proven by decomposing the free field as a sum of independent fixed scale fields and controlling the correlations of the complex dilation restricted to dyadic cells of various scales. For uniqueness we invoke a result by Jones and Smirnov on conformal removability of H\\"older curves. We conjecture that our curves are locally related to SLE$(\\kappa)$ for $\\kappa<4$.

K. Astala; P. Jones; A. Kupiainen; E. Saksman

2009-09-07

161

Random Conformal Weldings  

E-print Network

We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle. The homeomorphism is constructed using the exponential of $\\beta X$ where $X$ is the restriction of the two dimensional free field on the circle and the parameter $\\beta$ is in the "high temperature" regime $\\betawelding problem is solved by studying a non-uniformly elliptic Beltrami equation with a random complex dilatation. For the existence a method of Lehto is used. This requires sharp probabilistic estimates to control conformal moduli of annuli and they are proven by decomposing the free field as a sum of independent fixed scale fields and controlling the correlations of the complex dilation restricted to dyadic cells of various scales. For uniqueness we invoke a result by Jones and Smirnov on conformal removability of H\\"older curves. We conjecture that our curves are locally related to SLE$(\\kappa)$ for $\\kappa<4$.

Astala, K; Kupiainen, A; Saksman, E

2009-01-01

162

Holography of the Conformal Window  

E-print Network

Inspired by the model of Jarvinen and Kiritsis, we present a simple holographic model for the on set of chiral symmetry breaking at the edge of the conformal window in QCD in the Veneziano limit. Our most naive model enforces the QCD two loop running coupling on a D3/D7 holographic brane system. The mass of the holographic field, describing the chiral condensate in the model, is driven below the BF bound when the running is sufficiently strong, triggering chiral symmetry breaking for N_f/N_c<2.9. This model though contains too great a remnant of supersymmetry and does not correctly encode the perturbative anomalous dimensions of QCD. In a second model we impose the QCD anomalous dimension result and find chiral symmetry breaking sets in for N_f/N_c=4 at a BKT-type phase transition. In this case the transition is triggered when the anomalous dimension of the mass operator \\gamma_m=1.

Raul Alvares; Nick Evans; Keun-Young Kim

2012-04-11

163

Charged conformal Killing spinors  

NASA Astrophysics Data System (ADS)

We study the twistor equation on pseudo-Riemannian Spinc-manifolds whose solutions we call charged conformal Killing spinors (CCKSs). We derive several integrability conditions for the existence of CCKS and study their relations to spinor bilinears. A construction principle for Lorentzian manifolds admitting CCKS with nontrivial charge starting from CR-geometry is presented. We obtain a partial classification result in the Lorentzian case under the additional assumption that the associated Dirac current is normal conformal and complete the classification of manifolds admitting CCKS in all dimensions and signatures ?5 which has recently been initiated in the study of supersymmetric field theories on curved space.

Lischewski, Andree

2015-01-01

164

Ethyl anion preferred conformation  

NASA Astrophysics Data System (ADS)

Ab initio architecture and torsional barrier for ethyl anion, C2H -5 are analyzed using natural bond orbital methodology. The B3LYP/6-311++G(3df,2p) 2-kcal/mol torsional barrier between the preferred staggered and higher-energy eclipsed conformer is calculated to be one-third lower than for ethane. This decrease is largely attributed to reduced hyperconjugative stabilization of the equilibrium anion conformer compared to that for ethane. Proton removal is also predicted to cause opening of the ethane central CCH angle by 7°, attributed to decreased steric repulsion and to increased hyperconjugative stabilization accompanying angle widening in the ion.

Goodman, Lionel; Sauers, Ronald R.

165

Galilean conformal and superconformal symmetries  

SciTech Connect

Firstly we discuss briefly three different algebras named as nonrelativistic (NR) conformal: Schroedinger, Galilean conformal, and infinite algebra of local NR conformal isometries. Further we shall consider in some detail Galilean conformal algebra (GCA) obtained in the limit c{yields}{infinity} from relativistic conformal algebraO(d+1, 2) (d-number of space dimensions). Two different contraction limits providing GCA and some recently considered realizations will be briefly discussed. Finally by considering NR contraction of D = 4 superconformal algebra the Galilei conformal superalgebra (GCSA) is obtained, in the formulation using complexWeyl supercharges.

Lukierski, J., E-mail: lukier@ift.uni.wroc.pl [University of Wroclaw, Institute for Theoretical Physics (Poland)

2012-10-15

166

Galilean conformal and superconformal symmetries  

NASA Astrophysics Data System (ADS)

Firstly we discuss briefly three different algebras named as nonrelativistic (NR) conformal: Schrödinger, Galilean conformal, and infinite algebra of local NR conformal isometries. Further we shall consider in some detail Galilean conformal algebra (GCA) obtained in the limit c?? from relativistic conformal algebra O( d+1, 2) ( d-number of space dimensions). Two different contraction limits providing GCA and some recently considered realizations will be briefly discussed. Finally by considering NR contraction of D = 4 superconformal algebra the Galilei conformal superalgebra (GCSA) is obtained, in the formulation using complexWeyl supercharges.

Lukierski, J.

2012-10-01

167

Conformal cloak for waves  

SciTech Connect

Conformal invisibility devices are only supposed to work within the valid range of geometrical optics. Here, we show by numerical simulations and analytical arguments that for certain quantized frequencies, they are nearly perfect even in a regime that clearly violates geometrical optics. The quantization condition follows from the analogy between the Helmholtz equation and the stationary Schroedinger equation.

Chen Huanyang [School of Physical Science and Technology, Soochow University, Suzhou, 215006 Jiangsu (China); Leonhardt, Ulf [School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS (United Kingdom); Tyc, Tomas [Faculty of Science, Kotlarska 2, and Faculty of Informatics, Botanicka 68a, Masaryk University, CZ-61137 Brno (Czech Republic)

2011-05-15

168

Massive conformal gravity  

E-print Network

In this article we construct a massive theory of gravity that is invariant under conformal transformations. The massive action of the theory depend on the metric tensor and a scalar field, which are considered as the only field variables. We find the vacuum field equations of the theory and the solution of its Newtonian limit.

F. F. Faria

2013-12-19

169

Conformal transformation optics  

NASA Astrophysics Data System (ADS)

The field of transformation optics shows that media containing gradients in optical properties are equivalent to curved geometries of spacetime for the propagation of light. Conformal transformation optics -- a particular variant of this feature -- can be used to design devices with novel functionalities from inhomogeneous, isotropic dielectric media.

Xu, Lin; Chen, Huanyang

2015-01-01

170

Metamaterials with conformational nonlinearity  

E-print Network

Metamaterials with conformational nonlinearity Mikhail Lapine1,2 , Ilya V. Shadrivov1,2 , David A development, metamaterials became a prominent area of research, bridging theoretical and applied electrodynamics, electrical engineering and material science. Being man-made structures, metamaterials offer

171

Conforming polygonal finite elements  

Microsoft Academic Search

SUMMARY In this paper, conforming finite elements on polygon meshes are developed. Polygonal finite elements provide greater flexibility in mesh generation and are better-suited for applications in solid mechanics which involve a significant change in the topology of the material domain. In this study, recent advances in meshfree approximations, computational geometry, and computer graphics are used to construct different trial

N. Sukumar; A. Tabarraei

2004-01-01

172

Conforming quadrilaterals meshes on the cubed sphere.  

SciTech Connect

The cubed sphere geometry, obtained by inscribing a cube in a sphere and mapping points between the two surfaces using a gnomonic (central) projection, is commonly used in atmospheric models because it is free of polar singularities and is well-suited for parallel computing. Global meshes on the cubed-sphere typically project uniform (square) grids from each face of the cube onto the sphere, and if refinement is desired then it is done with non-conforming meshes - overlaying the area of interest with a finer uniform mesh, which introduces so-called hanging nodes on edges along the boundary of the fine resolution area. An alternate technique is to tile each face of the cube with quadrilaterals without requiring the quads to be rectangular. These meshes allow for refinement in areas of interest with a conforming mesh, providing a smoother transition between high and low resolution portions of the grid than non-conforming refinement. The conforming meshes are demonstrated in HOMME, NCAR's High Order Method Modeling Environment, where two modifications have been made: the dependence on uniform meshes has been removed, and the ability to read arbitrary quadrilateral meshes from a previously-generated file has been added. Numerical results come from a conservative spectral element method modeling a selection of the standard shallow water test cases.

Taylor, Mark A.; Levy, Michael Nathan; Overfelt, James Robert

2010-08-01

173

Electronically Rich N-Substituted Tetrahydroisoquinoline 3-Carboxylic Acid Esters: Concise Synthesis and Conformational Studies  

PubMed Central

Recent work in our laboratory has shown that the highly substituted, electronically rich 1,2,3,4–tetrahydroisoquinoline–3–carboxylic acid (THIQ3CA) scaffold is a key building block for a novel class of promising anticoagulants (Al-Horani et al. J. Med. Chem. 2011, 54, 6125–6138). The synthesis of THIQ3CA analogs, especially containing specific, electronically rich substituents, has been a challenge and essentially no efficient methods have been reported in the literature. We describe three complementary, glycine donor-based strategies for high yielding synthesis of highly substituted, electronically rich THIQ3CA esters. Three glycine donors studied herein include hydantoin 1, (±)-Boc-?-phosphonoglycine trimethyl ester 2 and (±)-Z-?-phosphonoglycine trimethyl ester 3. Although the synthesis of THIQ3CA analogs could be achieved using either of the three, an optimal, high yielding approach for the desired THIQ3CA esters was best achieved using 3 in three mild, efficient steps. Using this approach, a focused library of advanced N-arylacyl, N-arylalkyl, and bis-THIQ3CA analogs was synthesized. Variable temperature and solvent-dependent NMR chemical shift studies indicated the presence of two major conformational rotamers in 3:1 proportion for N–arylacyl–THIQ3CA analogs, which were separated by a high kinetic barrier of ~17 kcal/mol. In contrast, N–arylalkyl and bis–THIQ3CA variants displayed no rotamerism, which implicates restricted rotation around the amide bond as the origin for high-barrier conformational interconversion. This phenomenon is of major significance because structure-based drug design typically utilizes only one conformation. Overall, the work presents fundamental studies on the synthesis and conformational properties of highly substituted, electronically rich THIQ3CA analogs. PMID:22665943

Al-Horani, Rami A.; Desai, Umesh R.

2012-01-01

174

Loop Virasoro Lie conformal algebra  

SciTech Connect

The Lie conformal algebra of loop Virasoro algebra, denoted by CW, is introduced in this paper. Explicitly, CW is a Lie conformal algebra with C[?]-basis (L{sub i} | i?Z) and ?-brackets [L{sub i}?{sub ?}?L{sub j}] = (???2?)L{sub i+j}. Then conformal derivations of CW are determined. Finally, rank one conformal modules and Z-graded free intermediate series modules over CW are classified.

Wu, Henan, E-mail: wuhenanby@163.com; Chen, Qiufan; Yue, Xiaoqing [Department of Mathematics, Tongji University, Shanghai 200092 (China)] [Department of Mathematics, Tongji University, Shanghai 200092 (China)

2014-01-15

175

Conformal Relativity: Theory and Observations  

Microsoft Academic Search

Theoretical and observational arguments are listed in favor of a new principle of relativity of units of measurements as the basis of a conformal-invariant unification of General Relativity and Standard Model by replacement of all masses with a scalar (dilaton) field. The relative units mean conformal observables: the coordinate distance, conformal time, running masses, and constant temperature. They reveal to

V. Pervushin; V. Zinchuk; A. Zorin

2004-01-01

176

CONFORMATIONS OF ALKANES AND CYCLOALKANES  

E-print Network

89 CHAPTER 3 CONFORMATIONS OF ALKANES AND CYCLOALKANES H ydrogen peroxide is formed in the cells this chapter we'll examine the conformations of various alkanes and cycloal- kanes, focusing most of our that are placed symmetrically around it. 90 CHAPTER THREE Conformations of Alkanes and Cycloalkanes Eclipsed

Ferreira, Márcia M. C.

177

Movement of Elongation Factor G between Compact and Extended Conformations.  

PubMed

Previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor G (EF-G). Here, we follow the movement of domain IV of EF-G relative to domain II of EF-G using ensemble and single-molecule Förster resonance energy transfer. Our results indicate that ribosome-free EF-G predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain IV moves away from domain II. By contrast, ribosome-bound EF-G predominantly adopts an extended conformation regardless of whether it is interacting with pretranslocation ribosomes or with posttranslocation ribosomes. Our data suggest that ribosome-bound EF-G may also occasionally sample at least one more compact conformation. GTP hydrolysis catalyzed by EF-G does not affect the relative stability of the observed conformations in ribosome-free and ribosome-bound EF-G. Our data support a model suggesting that, upon binding to a pretranslocation ribosome, EF-G moves from a compact to a more extended conformation. This transition is not coupled to but likely precedes both GTP hydrolysis and mRNA/tRNA translocation. PMID:25463439

Salsi, Enea; Farah, Elie; Netter, Zoe; Dann, Jillian; Ermolenko, Dmitri N

2015-01-30

178

Conformal gripping device  

NASA Technical Reports Server (NTRS)

The present invention relates to a conformal gripping device. In an embodiment of the present invention a conformal gripper device may be disclosed comprising a frame that includes an array of movable pins. The device may also include a roller locking and unlocking system within the frame. The system may comprise a pair of locking rollers for each row of gripper pins to facilitate locking and unlocking the array of gripper pins on a column-by-column basis. The system may also include a striker element that may force the locking rollers to roll along an angled roll surface to facilitate unlocking of the array of pins on a column-by-column basis. The system may further include an electromagnetic actuator or solenoid and permanent magnets to facilitate movement of the striker element and the locking rollers.

Vranish, John M. (Inventor)

2009-01-01

179

Conformal higher spin theory  

NASA Astrophysics Data System (ADS)

We construct gauge theory of interacting symmetric traceless tensors of all ranks s=0,1,2,3,… which generalizes Weyl-invariant dilaton gravity to the higher spin case, in any dimension d>2. The action is given by the trace of the projector to the subspace with positive eigenvalues of an arbitrary Hermitian differential operator overlineH, and the symmetric tensors emerge after expansion of the latter in power series in derivatives. After decomposition in perturbative series around conformally flat point overlineH=? with Euclidean metric, the action functional describes conformal higher spin theory. Namely, the linear in fluctuation term cancels, while the one quadratic in fluctuation breaks up as a sum of conformal higher spin theories, the latter being free gauge theories of symmetric traceless tensors of rank s with actions of d-4+2 s order in derivatives (in odd dimensions they are boundary terms), for all integer s, introduced in 4d case by Fradkin and Tseytlin and studied at the cubic order level by Fradkin and Linetsky. Higher orders in interaction are well-defined. The action appears to be the unique functional invariant w.r.t. general similarity transformations overlineH'=e ??<†overlineHe ??, the latter invariance plays the role of gauge symmetry group of the model. In the framework of the perturbative decomposition, the Hermitian part of ? gauges away the trace parts of the symmetric tensors parameterizing the fluctuation, while the anti-Hermitian one provides standard linearized gauge transformations of conformal higher spin fields. The action can be calculated as a semiclassical series in ? which counts the number of space-time derivatives and thereby exhibits itself as a parameter of low-energy expansion, like ?' in string theory, in so doing the classical term is given by the volume of the domain H( x, p)>0 (where H( x, p) is the Weyl symbol of overlineH), it does not contain derivatives and is interpreted as a cosmological term. At the same time, further terms of the ?-expansion are given by integrals of distributions localized on the constraint surface H( x, p)=0, and the conformal higher spin- s action arises from the ? d-4+2 s-correction. The full gauge invariance of the model is interpreted as covariance algebra of generalized Klein-Gordon equation overlineH|?>=0 for complex scalar field ?.

Segal, Arkady Y.

2003-08-01

180

Dissecting conformational contributions to glycosidase catalysis and inhibition  

PubMed Central

Glycoside hydrolases (GHs) are classified into >100 sequence-based families. These enzymes process a wide variety of complex carbohydrates with varying stereochemistry at the anomeric and other ring positions. The shapes that these sugars adopt upon binding to their cognate GHs, and the conformational changes that occur along the catalysis reaction coordinate is termed the conformational itinerary. Efforts to define the conformational itineraries of GHs have focussed upon the critical points of the reaction: substrate-bound (Michaelis), transition state, intermediate (if relevant) and product-bound. Recent approaches to defining conformational itineraries that marry X-ray crystallography of enzymes bound to ligands that mimic the critical points, along with advanced computational methods and kinetic isotope effects are discussed. PMID:25016573

Speciale, Gaetano; Thompson, Andrew J; Davies, Gideon J; Williams, Spencer J

2014-01-01

181

Conformal superalgebras via tractor calculus  

NASA Astrophysics Data System (ADS)

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.

Lischewski, Andree

2015-01-01

182

Conformers and photochemistry of propyl nitrites: a matrix isolation study.  

PubMed

The infrared spectra of both constitutional isomers (n and i) of propyl nitrite have been recorded in an Ar matrix. Conformational analysis and assignments of the vibrational transitions have been carried out on the basis of quantum chemical calculations. Assignment of spectral lines to different conformers was also aided experimentally, by utilizing the different rate of photodecomposition of the conformers, as well as by employing conformational cooling using a supersonic jet as the inlet source for matrix deposition. The rate of photodecomposition is primarily determined by the steric alignment of the nitrite group, whereas jet cooling affects mainly the conformation of the alkyl tail. On the basis of these experimental observations and computational predictions two to three conformers of isopropyl nitrite and eight conformers of n-propyl nitrite were identified. After broadband ultraviolet-visible (UV-vis) photolysis of isopropyl nitrite in the matrix, HNO, acetone, HNO.acetone complex, acetaldehyde, and nitrosomethane were identified as the main products. Furthermore, in a small amount, NO and possibly the isopropoxy radical were also present in the matrix. Photolysis of n-propyl nitrite yielded HNO, propanal, and their 1:1 complex as the main products together with a small amount of NO and cis-1-nitrosopropanol. PMID:17228893

Matyus, Edit; Magyarfalvi, Gabor; Tarczay, György

2007-01-25

183

Conformations of amphiphilic polyelectrolyte stars with diblock copolymer arms  

E-print Network

We consider conformations and intra-molecular conformational transitions in amphiphilic starlike polymers formed by diblock copolymer arms with inner hydrophobic and outer polyelectrolyte blocks. A combination of an analytical mean-field theory with the assumption-free numerical self-consistent field (SCF) modeling approach is applied. It is demonstrated that unimolecular micelles with collapsed hydrophobic cores and swollen polyelectrolyte coronae are formed in dilute aqueous solutions at high ionic strength or/and low degree of ionization of the outer hydrophilic block. An intra-molecular conformational transition related to the unfolding of the hydrophobic core of the unimolecular micelles can be triggered by a decrease in the ionic strength of the solution or/and increase in the degree of ionization of the coronal blocks. In the stars with large number of diblock copolymer arms the transition between conformations with collapsed or stretched core-forming blocks occurs continuously by progressive unfolding of the core domain. By contrast, in the stars with relatively small number of arms the continuous unfolding of the core is interrupted by an abrupt unravelling transition. A detailed SCF analysis indicates that under both unfolding scenario the arms of the star are extended fairly equally, i.e., no intra-molecular disproportionation occurs.

Alexey A. Polotsky; Tatiana M. Birshtein; Mohamed Daoud; Oleg V. Borisov

2012-05-12

184

40 CFR 93.106 - Content of transportation plans and timeframe of conformity determinations.  

Code of Federal Regulations, 2012 CFR

...2012-07-01 false Content of transportation plans and timeframe of conformity...or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed...Transit Laws § 93.106 Content of transportation plans and timeframe of...

2012-07-01

185

40 CFR 93.106 - Content of transportation plans and timeframe of conformity determinations.  

Code of Federal Regulations, 2013 CFR

...2013-07-01 false Content of transportation plans and timeframe of conformity...or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed...Transit Laws § 93.106 Content of transportation plans and timeframe of...

2013-07-01

186

40 CFR 93.106 - Content of transportation plans and timeframe of conformity determinations.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 false Content of transportation plans and timeframe of conformity...or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed...Transit Laws § 93.106 Content of transportation plans and timeframe of...

2010-07-01

187

40 CFR 93.106 - Content of transportation plans and timeframe of conformity determinations.  

...2013-07-01 true Content of transportation plans and timeframe of conformity...or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed...Transit Laws § 93.106 Content of transportation plans and timeframe of...

2014-07-01

188

40 CFR 93.106 - Content of transportation plans and timeframe of conformity determinations.  

Code of Federal Regulations, 2011 CFR

...2011-07-01 false Content of transportation plans and timeframe of conformity...or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed...Transit Laws § 93.106 Content of transportation plans and timeframe of...

2011-07-01

189

Metamaterials with conformational nonlinearity.  

PubMed

Within a decade of fruitful development, metamaterials became a prominent area of research, bridging theoretical and applied electrodynamics, electrical engineering and material science. Being man-made structures, metamaterials offer a particularly useful playground to develop interdisciplinary concepts. Here we demonstrate a novel principle in metamaterial assembly which integrates electromagnetic, mechanical, and thermal responses within their elements. Through these mechanisms, the conformation of the meta-molecules changes, providing a dual mechanism for nonlinearity and offering nonlinear chirality. Our proposal opens a wide road towards further developments of nonlinear metamaterials and photonic structures, adding extra flexibility to their design and control. PMID:22355655

Lapine, Mikhail; Shadrivov, Ilya V; Powell, David A; Kivshar, Yuri S

2011-01-01

190

Metamaterials with conformational nonlinearity  

PubMed Central

Within a decade of fruitful development, metamaterials became a prominent area of research, bridging theoretical and applied electrodynamics, electrical engineering and material science. Being man-made structures, metamaterials offer a particularly useful playground to develop interdisciplinary concepts. Here we demonstrate a novel principle in metamaterial assembly which integrates electromagnetic, mechanical, and thermal responses within their elements. Through these mechanisms, the conformation of the meta-molecules changes, providing a dual mechanism for nonlinearity and offering nonlinear chirality. Our proposal opens a wide road towards further developments of nonlinear metamaterials and photonic structures, adding extra flexibility to their design and control. PMID:22355655

Lapine, Mikhail; Shadrivov, Ilya V.; Powell, David A.; Kivshar, Yuri S.

2011-01-01

191

Metamaterials with conformational nonlinearity  

NASA Astrophysics Data System (ADS)

Within a decade of fruitful development, metamaterials became a prominent area of research, bridging theoretical and applied electrodynamics, electrical engineering and material science. Being man-made structures, metamaterials offer a particularly useful playground to develop interdisciplinary concepts. Here we demonstrate a novel principle in metamaterial assembly which integrates electromagnetic, mechanical, and thermal responses within their elements. Through these mechanisms, the conformation of the meta-molecules changes, providing a dual mechanism for nonlinearity and offering nonlinear chirality. Our proposal opens a wide road towards further developments of nonlinear metamaterials and photonic structures, adding extra flexibility to their design and control.

Lapine, Mikhail; Shadrivov, Ilya V.; Powell, David A.; Kivshar, Yuri S.

2011-11-01

192

A Conformational Intermediate in Glutamate Receptor Activation  

PubMed Central

SUMMARY Ionotropic glutamate receptors (iGluRs) transduce the chemical signal of neurotransmitter release into membrane depolarization at excitatory synapses in the brain. The opening of the transmembrane ion channel of these ligand-gated receptors is driven by conformational transitions that are induced by the association of glutamate molecules to the ligand-binding domains (LBDs). Here, we describe the crystal structure of a GluA2 LBD tetramer in a configuration that involves an ~30° rotation of the LBD dimers relative to the crystal structure of the full-length receptor. The configuration is stabilized by an engineered disulfide crosslink. Biochemical and electrophysiological studies on full-length receptors incorporating either this crosslink or an engineered metal bridge show that this LBD configuration corresponds to an intermediate state of receptor activation. GluA2 activation therefore involves a combination of both intra-LBD (cleft closure) and inter-LBD dimer conformational transitions. Overall, these results provide a comprehensive structural characterization of an iGluR intermediate state. PMID:23931998

Lau, Albert Y.; Salazar, Héctor; Blachowicz, Lydia; Ghisi, Valentina; Plested, Andrew J.R.; Roux, Benoît

2013-01-01

193

Fe-heme conformations in ferric myoglobin.  

PubMed Central

X-ray absorption near-edge structure (XANES) spectra of ferric myoglobin from horse heart have been acquired as a function of pH (between 5.3 and 11.3). At pH = 11.3 temperature-dependent spectra (between 20 and 293 K) have been collected as well. Experimental data solve three main conformations of the Fe-heme: the first, at low pH, is related to high-spin aquomet-myoglobin (Mb+OH2). The other two, at pH 11.3, are related to hydroxymet-myoglobin (Mb+OH-), and are in thermal equilibrium, corresponding to high- and low-spin Mb+OH-. The structure of the three Fe-heme conformations has been assigned according to spin-resolved multiple scattering simulations and fitting of the XANES data. The chemical transition between Mb+OH2 and high-spin Mb+OH-, and the spin transition of Mb+OH-, are accompanied by changes of the Fe coordination sphere due to its movement toward the heme plane, coupled to an increase of the axial asymmetry. PMID:9826636

Longa, S D; Pin, S; Cortès, R; Soldatov, A V; Alpert, B

1998-01-01

194

Conformational analysis and circular dichroism of bilirubin, the yellow pigment of jaundice  

NASA Astrophysics Data System (ADS)

Conformational analysis of (4Z, 15Z)-bilirubin-IX(alpha) by molecular mechanics computations reveals a global energy minimum folded conformation. Powerful added stabilization is achieved through intramolecular hydrogen bonding. Theoretical treatment of bilirubin as a molecular exciton predicts an intense bisignate circular dichroism spectrum for the folded conformation: (Delta) (epsilon) is congruent to 270 L (DOT) mole-1 (DOT) cm-1 for the $OM450 nm electronic transition(s). Synthesis of bilirubin analogs with propionic acid groups methylated at the (alpha) or (beta) position introduces an allosteric effect that allows for an optical resolution of the pigments, with enantiomers exhibiting the theoretically predicted circular dichroism.

Lightner, David A.; Person, Richard; Peterson, Blake; Puzicha, Gisbert; Pu, Yu-Ming; Bojadziev, Stefan

1991-06-01

195

Synthesis, molecular conformation, vibrational and electronic transition, isometric chemical shift, polarizability and hyperpolarizability analysis of 3-(4-methoxy-phenyl)-2-(4-nitro-phenyl)-acrylonitrile: a combined experimental and theoretical analysis.  

PubMed

This work presents the synthesis and characterization of a novel compound, 3-(4-methoxy-phenyl)-2-(4-nitro-phenyl)-acrylonitrile (abbreviated as 3-(4MP)-2-(4-NP)-AN, C(16)H(12)N(2)O(3)). The spectroscopic properties of the compound were examined by FT-IR, UV-vis and NMR ((1)H and (13)C) techniques. FT-IR spectrum in solid state was observed in the region 4000-400 cm(-1). The UV-vis absorption spectrum of the compound which dissolved in chloroform was recorded in the range of 200-800 nm. The (1)H and (13)C NMR spectra were recorded in CDCl(3) solution. To determine lowest-energy molecular conformation of the title molecule, the selected torsion angle is varied every 10° and molecular energy profile is calculated from 0° to 360°. The structural and spectroscopic data of the molecule in the ground state were calculated using density functional theory (DFT) employing B3LYP/6-31G(d,p) basis set. The dipole moment, linear polarizability and first hyperpolarizability values were also computed using the same basis set. A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The HOMO and LUMO analysis were used to elucidate information regarding charge transfer within the molecule. The vibrational wavenumbers were calculated and scaled values were compared with experimental FT-IR spectrum. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Isotropic chemical shifts were calculated using the gauge-invariant atomic orbital (GIAO) method. Comparison of the calculated frequencies, NMR chemical shifts, absorption wavelengths with the experimental values revealed that DFT and TD-DFT method produce good results. The linear polarizabilities and first hyperpolarizabilities of the studied molecule indicate that the title compound can be used as a good nonlinear optical material. The thermodynamic properties of the studied compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures. PMID:21856218

Asiri, Abdullah Mohamed; Karabacak, Mehmet; Kurt, Mustafa; Alamry, Khalid A

2011-11-01

196

Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions.  

PubMed

A combination of conformational search, energy minimization, and energetic evaluation using a continuum solvent treatment has been employed to study the stability of various conformations of the DNA fragment d(CGCAGAA)/d(TTCGCG) containing a single adenine bulge. The extra-helical (looped-out) bulge conformation derived from a published x-ray structure and intra-helical (stacked bulge base) model structures partially based on nuclear magnetic resonance (NMR) data were used as start structures for the conformational search. Solvent-dependent contributions to the stability of the conformations were calculated from the solvent exposed molecular surface area and by using the finite difference Poisson-Boltzmann approach. Three classes (I-III) of bulge conformations with calculated low energies can be distinguished. The lowest-energy conformations were found in class I, corresponding to structures with the bulge base stacked between flanking helices, and class II, composed of structures forming a triplet of the bulge base and a flanking base pair. All extra-helical bulge structures, forming class III, were found to be less stable compared with the lowest energy structures of class I and II. The results are consistent with NMR data on an adenine bulge in the same sequence context indicating an intra-helical or triplet bulge conformation in solution. Although the total energies and total electrostatic energies of the low-energy conformations show only relatively modest variations, the energetic contributions to the stability were found to vary significantly among the classes of bulge structures. All intra-helical bulge structures are stabilized by a more favorable Coulomb charge-charge interaction but destabilized by a larger electrostatic reaction field contribution compared with all extra-helical and most triplet bulge structures. Van der Waals packing interactions and nonpolar surface-area-dependent contributions appear to favor triplet class II structures and to a lesser degree also the intra-helical stacked bulge conformations. The large conformational variation found for class III conformers might add a favorable entropic contribution to the stability of the extra-helical bulge form. PMID:9414214

Zacharias, M; Sklenar, H

1997-12-01

197

Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions.  

PubMed Central

A combination of conformational search, energy minimization, and energetic evaluation using a continuum solvent treatment has been employed to study the stability of various conformations of the DNA fragment d(CGCAGAA)/d(TTCGCG) containing a single adenine bulge. The extra-helical (looped-out) bulge conformation derived from a published x-ray structure and intra-helical (stacked bulge base) model structures partially based on nuclear magnetic resonance (NMR) data were used as start structures for the conformational search. Solvent-dependent contributions to the stability of the conformations were calculated from the solvent exposed molecular surface area and by using the finite difference Poisson-Boltzmann approach. Three classes (I-III) of bulge conformations with calculated low energies can be distinguished. The lowest-energy conformations were found in class I, corresponding to structures with the bulge base stacked between flanking helices, and class II, composed of structures forming a triplet of the bulge base and a flanking base pair. All extra-helical bulge structures, forming class III, were found to be less stable compared with the lowest energy structures of class I and II. The results are consistent with NMR data on an adenine bulge in the same sequence context indicating an intra-helical or triplet bulge conformation in solution. Although the total energies and total electrostatic energies of the low-energy conformations show only relatively modest variations, the energetic contributions to the stability were found to vary significantly among the classes of bulge structures. All intra-helical bulge structures are stabilized by a more favorable Coulomb charge-charge interaction but destabilized by a larger electrostatic reaction field contribution compared with all extra-helical and most triplet bulge structures. Van der Waals packing interactions and nonpolar surface-area-dependent contributions appear to favor triplet class II structures and to a lesser degree also the intra-helical stacked bulge conformations. The large conformational variation found for class III conformers might add a favorable entropic contribution to the stability of the extra-helical bulge form. PMID:9414214

Zacharias, M; Sklenar, H

1997-01-01

198

Conformational Dynamics of a Ligand-Free Adenylate Kinase  

PubMed Central

Adenylate kinase (AdK) is a phosphoryl-transfer enzyme with important physiological functions. Based on a ligand-free open structure and a ligand-bound closed structure solved by crystallography, here we use molecular dynamics simulations to examine the stability and dynamics of AdK conformations in the absence of ligands. We first perform multiple simulations starting from the open or the closed structure, and observe their free evolutions during a simulation time of 100 or 200 nanoseconds. In all seven simulations starting from the open structure, AdK remained stable near the initial conformation. The eight simulations initiated from the closed structure, in contrast, exhibited large variation in the subsequent evolutions, with most (seven) undergoing large-scale spontaneous conformational changes and approaching or reaching the open state. To characterize the thermodynamics of the transition, we propose and apply a new sampling method that employs a series of restrained simulations to calculate a one-dimensional free energy along a curved pathway in the high-dimensional conformational space. Our calculated free energy profile features a single minimum at the open conformation, and indicates that the closed state, with a high (?13 kcal/mol) free energy, is not metastable, consistent with the observed behaviors of the unrestrained simulations. Collectively, our simulations suggest that it is energetically unfavorable for the ligand-free AdK to access the closed conformation, and imply that ligand binding may precede the closure of the enzyme. PMID:23861846

Song, Hyun Deok; Zhu, Fangqiang

2013-01-01

199

Dendrites and conformal symmetry  

E-print Network

Progress toward characterization of structural and biophysical properties of neural dendrites together with recent findings emphasizing their role in neural computation, has propelled growing interest in refining existing theoretical models of electrical propagation in dendrites while advocating novel analytic tools. In this paper we focus on the cable equation describing electric propagation in dendrites with different geometry. When the geometry is cylindrical we show that the cable equation is invariant under the Schr\\"odinger group and by using the dendrite parameters, a representation of the Schr\\"odinger algebra is provided. Furthermore, when the geometry profile is parabolic we show that the cable equation is equivalent to the Schr\\"odinger equation for the 1-dimensional free particle, which is invariant under the Schr\\"odinger group. Moreover, we show that there is a family of dendrite geometries for which the cable equation is equivalent to the Schr\\"odinger equation for the 1-dimensional conformal quantum mechanics.

Juan M. Romero; Carlos Trenado

2014-05-11

200

Capturing Chromosome Conformation  

NASA Astrophysics Data System (ADS)

We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G1 stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.

Dekker, Job; Rippe, Karsten; Dekker, Martijn; Kleckner, Nancy

2002-02-01

201

Thermal insulating conformal blanket  

NASA Technical Reports Server (NTRS)

The conformal thermal insulating blanket may have generally rigid batting material covered by an outer insulating layer formed of a high temperature resistant woven ceramic material and an inner insulating layer formed of a woven ceramic fiber material. The batting and insulating layers may be fastened together by sewing or stitching using an outer mold layer thread fabricated of a high temperature resistant material and an inner mold layer thread of a ceramic fiber material. The batting may be formed to a composite structure that may have a firmness factor sufficient to inhibit a pillowing effect after the stitching to not more than 0.03 inch. The outer insulating layer and an upper portion of the batting adjacent the outer insulating layer may be impregnated with a ceramic coating material.

Barney, Andrea (Inventor); Whittington, Charles A (Inventor); Eilertson, Bryan (Inventor); Siminski, Zenon (Inventor)

2003-01-01

202

Conformal Fermi Coordinates  

E-print Network

Fermi Normal Coordinates (FNC) are a useful frame for isolating the locally observable, physical effects of a long-wavelength spacetime perturbation. Their cosmological application, however, is hampered by the fact that they are only valid on scales much smaller than the horizon. We introduce a generalization that we call Conformal Fermi Coordinates (CFC). CFC preserve all the advantages of FNC, but in addition are valid outside the horizon. They allow us to calculate the coupling of long- and short-wavelength modes on all scales larger than the sound horizon of the cosmological fluid, starting from the epoch of inflation until today, by removing the complications of the second order Einstein equations to a large extent, and eliminating all gauge ambiguities. As an application, we present a calculation of the effect of long-wavelength tensor modes on small scale density fluctuations. We recover previous results, but clarify the physical content of the individual contributions in terms of locally measurable ef...

Dai, Liang; Schmidt, Fabian

2015-01-01

203

Holographic Dual of a Boundary Conformal Field Theory  

SciTech Connect

We propose a holographic dual of a conformal field theory defined on a manifold with boundaries, i.e., boundary conformal field theory (BCFT). Our new holography, which may be called anti-de Sitter BCFT, successfully calculates the boundary entropy or g function in two-dimensional BCFTs and it agrees with the finite part of the holographic entanglement entropy. Moreover, we can naturally derive a holographic g theorem. We also analyze the holographic dual of an interval at finite temperature and show that there is a first order phase transition.

Takayanagi, Tadashi [Institute for the Physics and Mathematics of the Universe (IPMU), University of Tokyo, Kashiwa, Chiba 277-8582 (Japan)

2011-09-02

204

Counselor Identity: Conformity or Distinction?  

ERIC Educational Resources Information Center

The authors explore 3 debates in other disciplines similar to counseling's identity debate in order to learn about common themes and outcomes. Conformity, distinction, and cohesion emerged as common themes. They conclude that counselors should retain their distinctive, humanistic approach rather than conforming to the dominant, medical approach.

McLaughlin, Jerry E.; Boettcher, Kathryn

2009-01-01

205

Algebraic orbifold conformal field theories  

Microsoft Academic Search

The unitary rational orbifold conformal field theories in the algebraic quantum field theory and subfactor theory framework are formulated. Under general conditions, it is shown that the orbifold of a given unitary rational conformal field theory generates a unitary modular category. Many new unitary modular categories are obtained. It is also shown that the irreducible representations of orbifolds of rank

Feng Xu

2000-01-01

206

Conformations of immunoglobulin hypervariable regions  

Microsoft Academic Search

On the basis of comparative studies of known antibody structures and sequences it has been argued that there is a small repertoire of main-chain conformations for at least five of the six hypervariable regions of antibodies, and that the particular conformation adopted is determined by a few key conserved residues. These hypotheses are now supported by reasonably successful predictions of

Cyrus Chothia; Arthur M. Lesk; Anna Tramontano; Michael Levitt; Sandra J. Smith-Gill; Gillian Air; Steven Sheriff; Eduardo A. Padlan; David Davies; William R. Tulip; Peter M. Colman; Silvia Spinelli; Pedro M. Alzari; Roberto J. Poljak

1989-01-01

207

Conformal Transformations and Space Travel  

Microsoft Academic Search

Conformal transformations are applied to the motion of a space ship experiencing a constant acceleration. The role of proper time is interpreted in terms of atomic periods, and the relationship between the conformal transformations and the general theory of relativity is clarified.

Suraj N. Gupta

1961-01-01

208

Projectors, shadows, and conformal blocks  

NASA Astrophysics Data System (ADS)

We introduce a method for computing conformal blocks of operators in arbitrary Lorentz representations in any spacetime dimension, making it possible to apply bootstrap techniques to operators with spin. The key idea is to implement the "shadow formalism" of Ferrara, Gatto, Grillo, and Parisi in a setting where conformal invariance is manifest. Conformal blocks in d-dimensions can be expressed as integrals over the projective null-cone in the "embedding space" d+1,1. Taking care with their analytic structure, these integrals can be evaluated in great generality, reducing the computation of conformal blocks to a bookkeeping exercise. To facilitate calculations in four-dimensional CFTs, we introduce techniques for writing down conformally-invariant correlators using auxiliary twistor variables, and demonstrate their use in some simple examples.

Simmons-Duffin, David

2014-04-01

209

Molecular insight into conformational transmission of human P-glycoprotein.  

PubMed

P-glycoprotein (P-gp), a kind of ATP-binding cassette transporter, can export candidates through a channel at the two transmembrane domains (TMDs) across the cell membranes using the energy released from ATP hydrolysis at the two nucleotide-binding domains (NBDs). Considerable evidence has indicated that human P-gp undergoes large-scale conformational changes to export a wide variety of anti-cancer drugs out of the cancer cells. However, molecular mechanism of the conformational transmission of human P-gp from the NBDs to the TMDs is still unclear. Herein, targeted molecular dynamics simulations were performed to explore the atomic detail of the conformational transmission of human P-gp. It is confirmed that the conformational transition from the inward- to outward-facing is initiated by the movement of the NBDs. It is found that the two NBDs move both on the two directions (x and y). The movement on the x direction leads to the closure of the NBDs, while the movement on the y direction adjusts the conformations of the NBDs to form the correct ATP binding pockets. Six key segments (KSs) protruding from the TMDs to interact with the NBDs are identified. The relative movement of the KSs along the y axis driven by the NBDs can be transmitted through ?-helices to the rest of the TMDs, rendering the TMDs to open towards periplasm in the outward-facing conformation. Twenty eight key residue pairs are identified to participate in the interaction network that contributes to the conformational transmission from the NBDs to the TMDs of human P-gp. In addition, 9 key residues in each NBD are also identified. The studies have thus provided clear insight into the conformational transmission from the NBDs to the TMDs in human P-gp. PMID:24329094

Chang, Shan-Yan; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

2013-12-14

210

Molecular insight into conformational transmission of human P-glycoprotein  

NASA Astrophysics Data System (ADS)

P-glycoprotein (P-gp), a kind of ATP-binding cassette transporter, can export candidates through a channel at the two transmembrane domains (TMDs) across the cell membranes using the energy released from ATP hydrolysis at the two nucleotide-binding domains (NBDs). Considerable evidence has indicated that human P-gp undergoes large-scale conformational changes to export a wide variety of anti-cancer drugs out of the cancer cells. However, molecular mechanism of the conformational transmission of human P-gp from the NBDs to the TMDs is still unclear. Herein, targeted molecular dynamics simulations were performed to explore the atomic detail of the conformational transmission of human P-gp. It is confirmed that the conformational transition from the inward- to outward-facing is initiated by the movement of the NBDs. It is found that the two NBDs move both on the two directions (x and y). The movement on the x direction leads to the closure of the NBDs, while the movement on the y direction adjusts the conformations of the NBDs to form the correct ATP binding pockets. Six key segments (KSs) protruding from the TMDs to interact with the NBDs are identified. The relative movement of the KSs along the y axis driven by the NBDs can be transmitted through ?-helices to the rest of the TMDs, rendering the TMDs to open towards periplasm in the outward-facing conformation. Twenty eight key residue pairs are identified to participate in the interaction network that contributes to the conformational transmission from the NBDs to the TMDs of human P-gp. In addition, 9 key residues in each NBD are also identified. The studies have thus provided clear insight into the conformational transmission from the NBDs to the TMDs in human P-gp.

Chang, Shan-Yan; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

2013-12-01

211

A Threaded Loop Conformation Adopted by a Family of Peptoid Nonamers  

PubMed Central

Non-natural polymers with well-defined three-dimensional folds offer considerable potential for engineering novel functions that are outside the scope of biological polymers. Here we describe a family of N-substituted glycine or ‘peptoid’ nonamers that folds into an unusual ‘threaded loop’ structure of exceptional thermal stability and conformational homogeneity in acetonitrile. The structure is chain length-specific and relies on bulky, chiral side chains and chain-terminating functional groups for stability. Notable elements of the structure include the engagement of the positively charged amino-terminus by carbonyl groups of the backbone through hydrogen bonding interactions, and shielding of polar groups from and near-complete exposure of hydrophobic groups to solvent, in a manner resembling a folded polypeptide globular domain turned ‘inside-out’. The structure is stable in a variety of organic solvents but is readily denatured in any solvent/cosolvent milieu with hydrogen bonding potential. The structure could serve as a scaffold for the elaboration of novel functions and could be used to test methodologies for predicting solvent-dependent polymer folding. PMID:16448149

Huang, Kai; Wu, Cindy W.; Sanborn, Tracy J.; Patch, James A.; Kirshenbaum, Kent; Zuckermann, Ronald N.; Barron, Annelise E.; Radhakrishnan, Ishwar

2008-01-01

212

Computational Investigation of Conformational Changes in Proteins upon Adsorption  

NASA Astrophysics Data System (ADS)

Amyloidogenic diseases, such as, Alzheimer's, are caused by adsorption and aggregation of partially unfolded proteins. Protein adsorption is often accompanied by conformational rearrangements, which are thought to affect many properties such as their adhesion strength to the surface, biological activity, and aggregation tendency. Experiments have shown that many proteins, upon adsorption to hydrophobic surfaces, undergo a helix to sheet or random coil secondary structural rearrangement. To better understand the equilibrium structural complexities of this phenomenon, we have performed Monte Carlo (MC) simulations and Single Chain Mean Field calculations of adsorption of different proteins, modeled as lattice chains, to study the adsorption behavior and equilibrium protein conformations at different temperatures, protein concentration and surface hydrophobicity. Free energy and entropic effects on adsorption have been studied by determining density of states using Weighted Histogram Analysis Method. Conformational transitions of proteins on surfaces will be discussed as a function of surface hydrophobicity.

Sharma, Sumit; Anand, Gaurav; Belfort, Georges; Kumar, Sanat K.

2009-03-01

213

Conformational Dynamics of Insulin  

PubMed Central

We have exploited a prandial insulin analog to elucidate the underlying structure and dynamics of insulin as a monomer in solution. A model was provided by insulin lispro (the active component of Humalog®; Eli Lilly and Co.). Whereas NMR-based modeling recapitulated structural relationships of insulin crystals (T-state protomers), dynamic anomalies were revealed by amide-proton exchange kinetics in D2O. Surprisingly, the majority of hydrogen bonds observed in crystal structures are only transiently maintained in solution, including key T-state-specific inter-chain contacts. Long-lived hydrogen bonds (as defined by global exchange kinetics) exist only at a subset of four ?-helical sites (two per chain) flanking an internal disulfide bridge (cystine A20–B19); these sites map within the proposed folding nucleus of proinsulin. The anomalous flexibility of insulin otherwise spans its active surface and may facilitate receptor binding. Because conformational fluctuations promote the degradation of pharmaceutical formulations, we envisage that “dynamic re-engineering” of insulin may enable design of ultra-stable formulations for humanitarian use in the developing world. PMID:22649374

Hua, Qing-Xin; Jia, Wenhua; Weiss, Michael A.

2011-01-01

214

Conformal Fermi Coordinates  

E-print Network

Fermi Normal Coordinates (FNC) are a useful frame for isolating the locally observable, physical effects of a long-wavelength spacetime perturbation. Their cosmological application, however, is hampered by the fact that they are only valid on scales much smaller than the horizon. We introduce a generalization that we call Conformal Fermi Coordinates (CFC). CFC preserve all the advantages of FNC, but in addition are valid outside the horizon. They allow us to calculate the coupling of long- and short-wavelength modes on all scales larger than the sound horizon of the cosmological fluid, starting from the epoch of inflation until today, by removing the complications of the second order Einstein equations to a large extent, and eliminating all gauge ambiguities. As an application, we present a calculation of the effect of long-wavelength tensor modes on small scale density fluctuations. We recover previous results, but clarify the physical content of the individual contributions in terms of locally measurable effects and "projection" terms.

Liang Dai; Enrico Pajer; Fabian Schmidt

2015-02-06

215

Dynamics of protein conformations  

NASA Astrophysics Data System (ADS)

A novel theoretical methodology is introduced to identify dynamic structural domains and analyze local flexibility in proteins. The methodology employs a multiscale approach combining identification of essential collective coordinates based on the covariance analysis of molecular dynamics trajectories, construction of the Mori projection operator with these essential coordinates, and analysis of the corresponding generalized Langevin equations [M.Stepanova, Phys.Rev.E 76(2007)051918]. Because the approach employs a rigorous theory, the outcomes are physically transparent: the dynamic domains are associated with regions of relative rigidity in the protein, whereas off-domain regions are relatively soft. This also allows scoring the flexibility in the macromolecule with atomic-level resolution [N.Blinov, M.Berjanskii, D.S.Wishart, and M.Stepanova, Biochemistry, 48(2009)1488]. The applications include the domain coarse-graining and characterization of conformational stability in protein G and prion proteins. The results are compared with published NMR experiments. Potential applications for structural biology, bioinformatics, and drug design are discussed.

Stepanova, Maria

2010-10-01

216

Conformationally resolved spectra of acetaminophen by UV-UV hole burning and IR dip spectroscopy in the gas phase.  

PubMed

Electronic and vibrational spectra of acetaminophen were measured by using UV-UV hole burning (HB) and IR dip spectroscopy. HB spectra show the coexistence of 4 different species, which include two new ones. Low-frequency transitions in the spectra are reproduced by a one-dimensional periodic potential with a free-rotor basis set for the methyl group. From the analysis, we concluded that acetaminophen has two conformers and each conformer gives two independent transitions starting from the most stable 0a(1) and the hot 1e internal rotational levels. It is also found that the HB spectrum of the trans-conformer in the previous report is that from the 1e excited level, while the HB spectrum of the cis-conformer is contaminated by the transitions of the trans-conformer. Potential curves of the methyl rotational motion are determined both in S(0) and S(1). PMID:23207427

Sohn, Woon Yong; Ishiuchi, Shun-ichi; Miyazaki, Mitsuhiko; Kang, Jeongseok; Lee, Soyoung; Min, Ahreum; Choi, Myong Yong; Kang, Hyuk; Fujii, Masaaki

2013-01-21

217

Conformal Tensors via Lovelock Gravity  

E-print Network

Constructs from conformal geometry are important in low dimensional gravity models, while in higher dimensions the higher curvature interactions of Lovelock gravity are similarly prominent. Considering conformal invariance in the context of Lovelock gravity leads to natural, higher-curvature generalizations of the Weyl, Schouten, Cotton and Bach tensors, with properties that straightforwardly extend those of their familiar counterparts. As a first application, we introduce a new set of conformally invariant gravity theories in D=4k dimensions, based on the squares of the higher curvature Weyl tensors.

David Kastor

2013-06-24

218

Conformal Tensors via Lovelock Gravity  

E-print Network

Constructs from conformal geometry are important in low dimensional gravity models, while in higher dimensions the higher curvature interactions of Lovelock gravity are similarly prominent. Considering conformal invariance in the context of Lovelock gravity leads to natural, higher-curvature generalizations of the Weyl, Schouten, Cotton and Bach tensors, with properties that straightforwardly extend those of their familiar counterparts. As a first application, we introduce a new set of conformally invariant gravity theories in D=4k dimensions, based on the squares of the higher curvature Weyl tensors.

Kastor, David

2013-01-01

219

Conformal tensors via Lovelock gravity  

NASA Astrophysics Data System (ADS)

Constructs from conformal geometry are important in low dimensional gravity models, while in higher dimensions the higher curvature interactions of Lovelock gravity are similarly prominent. Considering conformal invariance in the context of Lovelock gravity leads to natural, higher curvature generalizations of the Weyl, Schouten, Cotton and Bach tensors, with properties that straightforwardly extend those of their familiar counterparts. As a first application, we introduce a new set of conformally invariant gravity theories in D = 4k dimensions, based on the squares of the higher curvature Weyl tensors.

Kastor, David

2013-10-01

220

Conformational switching at cytochrome a during steady-state turnover of cytochrome c oxidase.  

PubMed Central

As an electron transfer-driven proton pump, cytochrome c oxidase (ferrocytochrome-c:oxygen oxidoreductase, EC 1.9.3.1) must alternate between two conformations in each valence state of the redox element associated with ion translocation. Using second derivative absorption spectroscopy, the conformation of the cytochrome a cofactor has been investigated during steady-state turnover of this enzyme. Resting cytochrome c oxidase displays a transition for ferric cytochrome a at 430 nm. During aerobic steady-state turnover, this band is replaced by a ferrous cytochrome a transition at 450 nm. When anaerobicity is achieved, the transition occurs at 444 nm. The 450-nm-absorbing species is thus the dominant form during turnover, suggesting that conformational transitions of cytochrome a direct electron transfer during catalysis and may direct as well proton translocation in the last step of the respiratory electron transfer chain. PMID:1651500

Copeland, R A

1991-01-01

221

Parameterization of 3D Conformal Transformations in Conformal Geometric Algebra  

NASA Astrophysics Data System (ADS)

Conformal geometric algebra is a powerful mathematical language for describing and manipulating geometric configurations and their conformal transformations. By providing a 5D algebraic representation of 3D geometric configurations, conformal geometric algebra proves to be very helpful in pose estimation, motion design, and neuron-based machine learning (Bayro-Corrochano et al., J. Math. Imaging Vis. 24(1):55-81, 2006; Dorst et al., Geometric Algebra for Computer Science, Morgan Kaufmann, San Mateo, 2007; Hildenbrand, Comput. Graph. 29(5):795-803, 2005; Lasenby, Computer Algebra and Geometric Algebra with Applications, LNCS, vol. 3519, pp. 298-328, Springer, Berlin, 2005; Li et al., Geometric Computing with Clifford Algebras, pp. 27-60, Springer, Heidelberg, 2001; Mourrain and Stolfi, Invariant Methods in Discrete and Computational Geometry, pp. 107-139, Reidel, Dordrecht, 1995; Rosenhahn and Sommer, J. Math. Imaging Vis. 22:27-70, 2005; Sommer et al., Computer Algebra and Geometric Algebra with Applications, pp. 278-297, Springer, Berlin, 2005). In this chapter, we present some theoretical results on conformal geometric algebra which should prove to be useful in computer applications. The focus is on parameterizing 3D conformal transformations with either quaternionic Vahlen matrices or polynomial Cayley transform from the Lie algebra to the Lie group of conformal transformations in space.

Li, Hongbo

222

Solvent-dependent cation exchange in metal-organic frameworks.  

PubMed

We investigated which factors govern the critical steps of cation exchange in metal-organic frameworks by studying the effect of various solvents on the insertion of Ni(2+) into MOF-5 and Co(2+) into MFU-4l. After plotting the extent of cation insertion versus different solvent parameters, trends emerge that offer insight into the exchange processes for both systems. This approach establishes a method for understanding critical aspects of cation exchange in different MOFs and other materials. PMID:24782420

Brozek, Carl K; Bellarosa, Luca; Soejima, Tomohiro; Clark, Talia V; López, Núria; Dinc?, Mircea

2014-06-01

223

Solution NMR conformation of glycosaminoglycans.  

PubMed

Nuclear magnetic resonance (NMR) spectroscopy has been giving a pivotal contribution to the progress of glycomics, mostly by elucidating the structural, dynamical, conformational and intermolecular binding aspects of carbohydrates. Particularly in the field of conformation, NOE resonances, scalar couplings, residual dipolar couplings, and chemical shift anisotropy offsets have been the principal NMR parameters utilized. Molecular dynamics calculations restrained by NMR-data input are usually employed in conjunction to generate glycosidic bond dihedral angles. Glycosaminoglycans (GAGs) are a special class of sulfated polysaccharides extensively studied worldwide. Besides regulating innumerous physiological processes, these glycans are also widely explored in the global market as either clinical or nutraceutical agents. The conformational aspects of GAGs are key regulators to the quality of interactions with the functional proteins involved in biological events. This report discusses the solution conformation of each GAG type analyzed by one or more of the above-mentioned methods. PMID:24560989

Pomin, Vitor H

2014-04-01

224

Some Progress in Conformal Geometry  

E-print Network

This is a survey paper of our current research on the theory of partial differential equations in conformal geometry. Our intention is to describe some of our current works in a rather brief and expository fashion. We are not giving a comprehensive survey on the subject and references cited here are not intended to be complete. We introduce a bubble tree structure to study the degeneration of a class of Yamabe metrics on Bach flat manifolds satisfying some global conformal bounds on compact manifolds of dimension 4. As applications, we establish a gap theorem, a finiteness theorem for diffeomorphism type for this class, and diameter bound of the $\\sigma_2$-metrics in a class of conformal 4-manifolds. For conformally compact Einstein metrics we introduce an eigenfunction compactification. As a consequence we obtain some topological constraints in terms of renormalized volumes.

Chang, Sun-Yung A; Yang, Paul

2007-01-01

225

HAMP Domain Conformers That Propagate Opposite Signals in Bacterial Chemoreceptors  

PubMed Central

HAMP domains are signal relay modules in >26,000 receptors of bacteria, eukaryotes, and archaea that mediate processes involved in chemotaxis, pathogenesis, and biofilm formation. We identify two HAMP conformations distinguished by a four- to two-helix packing transition at the C-termini that send opposing signals in bacterial chemoreceptors. Crystal structures of signal-locked mutants establish the observed structure-to-function relationships. Pulsed dipolar electron spin resonance spectroscopy of spin-labeled soluble receptors active in cells verify that the crystallographically defined HAMP conformers are maintained in the receptors and influence the structure and activity of downstream domains accordingly. Mutation of HR2, a key residue for setting the HAMP conformation and generating an inhibitory signal, shifts HAMP structure and receptor output to an activating state. Another HR2 variant displays an inverted response with respect to ligand and demonstrates the fine energetic balance between “on” and “off” conformers. A DExG motif found in membrane proximal HAMP domains is shown to be critical for responses to extracellular ligand. Our findings directly correlate in vivo signaling with HAMP structure, stability, and dynamics to establish a comprehensive model for HAMP-mediated signal relay that consolidates existing views on how conformational signals propagate in receptors. Moreover, we have developed a rational means to manipulate HAMP structure and function that may prove useful in the engineering of bacterial taxis responses. PMID:23424282

Airola, Michael V.; Sukomon, Nattakan; Samanta, Dipanjan; Borbat, Peter P.; Freed, Jack H.; Watts, Kylie J.; Crane, Brian R.

2013-01-01

226

Induction of protein conformational change inside the charged electrospray droplet.  

PubMed

The behavior of the analyte molecules inside the neutral core of the charged electrospray (ES) droplet is not unambiguously known to date. The possibility of protein conformational change inside the charged ES droplet has been investigated. The ES droplets encapsulating the protein molecules were exposed to the acetic acid vapor in the ionization chamber to absorb the acetic acid vapor. Because of the faster evaporation of water than that of acetic acid, the droplets became enriched with acetic acid and thus altered the solvent environment (e.g. pH and polarity) of the final charged droplets from where the naked charged analytes (proteins) are formed. Thus, the perturbation of the ES droplet solvent environment resulted in the protein conformational change (unfolding) during the short lifespan of the ES droplet and that is reflected by the multimodal charge state distribution in the corresponding mass spectra. Further, the extent of this conformational change inside the ES droplet was found to be related to the structural flexibility of the protein. Although the protein conformational change inside the ES droplet has been driven by using acetic acid vapor in the present study, the results would help in the near future to understand the spontaneity of the conformational change of the analyte on the millisecond timescale of phase transition in the natural way of ES process. PMID:23378092

Banerjee, Shibdas

2013-02-01

227

Solvation and conformational dynamics of dicarboxylic suberic acid  

NASA Astrophysics Data System (ADS)

Solvation structure and conformational preferences of the dicarboxylic suberic acid, HOOC(CH2)6COOH, both neutral and protolyzed in water and neutral in methanol have been studied using molecular-dynamics (MO) computer simulations. According to results from MD simulations in water solution, the backbone hydrocarbon chain shows a very clear tendency to curl up into a helical structure, forming either a tgggt or a tg'g'g't conformation. The carboxylic head groups are strongly hydrated in the water solution, while the hydrophobic hydrocarbon skeleton is surrounded by water molecules in a packed structure. In the helical conformation, the surface area of the nonpolar part of the fatty acid is minimized against water phase. Transitions between the right and the left-handed helices are observed in neutral and mono-anionic forms of suberic acid in water solution. Suberic acid dissolved in methanol does not show any conformational preferences. Along the hydrocarbon chain, g, g', and t conformers are equally populated. The head group torsional angles, however, strongly prefer trans conformation due to dipolar interactions between the carboxyl groups and the solvent hydroxyl groups. In addition to MD simulations, corresponding water and methanol solutions are prepared and 13C NMR (nuclear magnetic resonance) chemical shifts are measured in both solutions. Using a time-averaged geometry for suberic acid from MD simulations in water, chemical shielding constants are calculated quantum chemically. Agreement between the theoretical and the experimental chemical shifts is good, and gives indirect support to the simulated conformations of suberic acid in the investigated solutions. The simulation results are also consistent with recent Raman investigations of suberic acid in both water and methanol solutions.

Nilsson, J. Arvid; Laaksonen, A.; Eriksson, Leif A.

1998-08-01

228

Extensive conformational heterogeneity within protein cores.  

PubMed

Basic principles of statistical mechanics require that proteins sample an ensemble of conformations at any nonzero temperature. However, it is still common to treat the crystallographic structure of a protein as the structure of its native state, largely because high-resolution structural characterization of protein flexibility remains a profound challenge. To assess the typical degree of conformational heterogeneity within folded proteins, we construct Markov state models describing the thermodynamics and kinetics of proteins ranging from 72 to 263 residues in length. Each of these models is built from hundreds of microseconds of atomically detailed molecular dynamics simulations. Examination of the side-chain degrees of freedom reveals that almost every residue visits at least two rotameric states over this time frame, with rotamer transition rates spanning a wide range of time scales (from nanoseconds to tens of microseconds). We also report substantial backbone dynamics on time scales longer than are typically addressed by experimental measures of protein flexibility, such as NMR order parameters. Finally, we demonstrate that these extensive rearrangements are consistent with NMR and crystallographic data, which supports the validity of our models. Altogether, these results depict the interior of proteins not as well-ordered solids, as is often imagined, but instead as dense fluids, which undergo substantial structural fluctuations despite their high packing fraction. PMID:24564338

Bowman, Gregory R; Geissler, Phillip L

2014-06-19

229

Sequential conformational rearrangements in flavivirus membrane fusion  

PubMed Central

The West Nile Virus (WNV) envelope protein, E, promotes membrane fusion during viral cell entry by undergoing a low-pH triggered conformational reorganization. We have examined the mechanism of WNV fusion and sought evidence for potential intermediates during the conformational transition by following hemifusion of WNV virus-like particles (VLPs) in a single particle format. We have introduced specific mutations into E, to relate their influence on fusion kinetics to structural features of the protein. At the level of individual E subunits, trimer formation and membrane engagement of the threefold clustered fusion loops are rate-limiting. Hemifusion requires at least two adjacent trimers. Simulation of the kinetics indicates that availability of competent monomers within the contact zone between virus and target membrane makes trimerization a bottleneck in hemifusion. We discuss the implications of the model we have derived for mechanisms of membrane fusion in other contexts. DOI: http://dx.doi.org/10.7554/eLife.04389.001 PMID:25479384

Chao, Luke H; Klein, Daryl E; Schmidt, Aaron G; Peña, Jennifer M; Harrison, Stephen C

2014-01-01

230

Polyethylene glycol binding alters human telomere G-quadruplex structure by conformational selection  

PubMed Central

Polyethylene glycols (PEGs) are widely used to perturb the conformations of nucleic acids, including G-quadruplexes. The mechanism by which PEG alters G-quadruplex conformation is poorly understood. We describe here studies designed to determine how PEG and other co-solutes affect the conformation of the human telomeric quadruplex. Osmotic stress studies using acetonitrile and ethylene glycol show that conversion of the ‘hybrid’ conformation to an all-parallel ‘propeller’ conformation is accompanied by the release of about 17 water molecules per quadruplex and is energetically unfavorable in pure aqueous solutions. Sedimentation velocity experiments show that the propeller form is hydrodynamically larger than hybrid forms, ruling out a crowding mechanism for the conversion by PEG. PEGs do not alter water activity sufficiently to perturb quadruplex hydration by osmotic stress. PEG titration experiments are most consistent with a conformational selection mechanism in which PEG binds more strongly to the propeller conformation, and binding is coupled to the conformational transition between forms. Molecular dynamics simulations show that PEG binding to the propeller form is sterically feasible and energetically favorable. We conclude that PEG does not act by crowding and is a poor mimic of the intranuclear environment, keeping open the question of the physiologically relevant quadruplex conformation. PMID:23804761

Buscaglia, Robert; Miller, M. Clarke; Dean, William L.; Gray, Robert D.; Lane, Andrew N.; Trent, John O.; Chaires, Jonathan B.

2013-01-01

231

Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate**  

PubMed Central

Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole-type inhibitors are energetically poised to report faithfully on mannosidase transition-state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including ?-mannanases from families GH26 and GH113. Isofagomine-type inhibitors are poor mimics of transition-state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar-shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active-site residues involved in substrate recognition. PMID:24339341

Williams, Rohan J; Iglesias-Fernández, Javier; Stepper, Judith; Jackson, Adam; Thompson, Andrew J; Lowe, Elisabeth C; White, Jonathan M; Gilbert, Harry J; Rovira, Carme; Davies, Gideon J; Williams, Spencer J

2014-01-01

232

Replica exchange with guided annealing for accelerated sampling of disordered protein conformations.  

PubMed

We critically examine a recently proposed convective replica exchange (cRE) method for enhanced sampling of protein conformation based on theoretical and numerical analysis. The results demonstrate that cRE and related replica exchange with guided annealing (RE-GA) schemes lead to unbalanced exchange attempt probabilities and break detailed balance whenever the system undergoes slow conformational transitions (relative to the temperature diffusion timescale). Nonetheless, numerical simulations suggest that approximate canonical ensembles can be generated for systems with small conformational transition barriers. This suggests that RE-GA maybe suitable for simulating intrinsically disordered proteins, an important class of newly recognized functional proteins. The efficacy of RE-GA is demonstrated by calculating the conformational ensembles of intrinsically disordered kinase inducible domain protein. The results show that RE-GA helps the protein to escape nonspecific compact states more efficiently and provides several fold speedups in generating converged and largely correct ensembles compared to the standard temperature RE. PMID:24995857

Zhang, Weihong; Chen, Jianhan

2014-09-01

233

Physical studies of conformational plasticity in a recombinant prion protein.  

PubMed

PrP(Sc) is known to be the major, if not the only, component of the infectious prion. Limited proteolysis of PrP(Sc) produces an N-terminally truncated polypeptide of about 142 residues, designated PrP 27-30. Recently, a recombinant protein (rPrP) of 142 residues corresponding to the Syrian hamster PrP 27-30 was expressed in Escherichia coli and purified (Mehlhorn et al., 1996). rPrP has been refolded into both alpha-helical and beta-sheet structures as well as various intermediates in aqueous buffers. The beta-sheet state and two pH-dependent alpha-helical states were characterized by CD and NMR. The alpha-helical conformation occurred only after the formation of an intramolecular disulfide bond, whereas the beta-sheet form was accessible either with or without the disulfide. Of the different alpha-helical forms studied, only those refolded in the pH range 5-8 were substantially soluble at physiological pH, exhibiting similar conformations and monomeric analytical sedimentation profiles throughout the above pH range. Furthermore, refolded alpha-rPrP showed NMR chemical shift dispersion typical of proteins with native conformations, although 2D NMR indicated large segments of conformational flexibility. It displayed a cooperative thermal denaturation transition; at elevated temperatures, it converted rapidly and irreversibly to the thermodynamically more stable beta-sheet form. Unfolding of alpha-rPrP by GdnHCl revealed a two-phase transition with a relatively stable folding intermediate at 2 M GdnHCl. The deltaG values were estimated to be 1.9 +/- 0.4 kcal/mol for the first phase and 6.5 +/- 1.2 kcal/mol for the second, consistent with a folding core surrounded by significant segments of flexible conformation. By NMR, alpha-rPrP(acid) isolated at pH 2 without refolding exhibited heterogeneous line widths, consistent with an acid-denatured molten globular state. We conclude that to the extent that rPrP constitutes a relevant folding domain of PrP(C), the various conformations exhibited by rPrP suggest that the PrP sequence may be intrinsically plastic in its conformations; indeed, portions of PrP(C) may possess a relatively open conformation which makes it susceptible to conversion into PrP(Sc) under appropriate conditions. PMID:9132005

Zhang, H; Stockel, J; Mehlhorn, I; Groth, D; Baldwin, M A; Prusiner, S B; James, T L; Cohen, F E

1997-03-25

234

CONFORMANCE IMPROVEMENT USING GELS  

SciTech Connect

This report describes work performed during the second year of the project, ''Conformance Improvement Using Gels.'' The project has two objectives. The first objective is to identify gel compositions and conditions that substantially reduce flow through fractures that allow direct channeling between wells, while leaving secondary fractures open so that high fluid injection and production rates can be maintained. The second objective is to optimize treatments in fractured production wells, where the gel must reduce permeability to water much more than that to oil. Pore-level images from X-ray computed microtomography were re-examined for Berea sandstone and porous polyethylene. This analysis suggests that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than a gel-ripping mechanism. This finding helps to explain why aqueous gels can reduce permeability to water more than to oil. We analyzed a Cr(III)-acetate-HPAM gel treatment in a production well in the Arbuckle formation. The availability of accurate pressure data before, during, and after the treatment was critical for the analysis. After the gel treatment, water productivity was fairly constant at about 20% of the pre-treatment value. However, oil productivity was stimulated by a factor of 18 immediately after the treatment. During the six months after the treatment, oil productivity gradually decreased to approach the pre-treatment value. To explain this behavior, we proposed that the fracture area open to oil flow was increased substantially by the gel treatment, followed by a gradual closing of the fractures during subsequent production. For a conventional Cr(III)-acetate-HPAM gel, the delay between gelant preparation and injection into a fracture impacts the placement, leakoff, and permeability reduction behavior. Formulations placed as partially formed gels showed relatively low pressure gradients during placement, and yet substantially reduced the flow capacity of fractures (with widths from 1 to 4 mm) during brine and oil flow after placement. Regardless of gel age before placement, very little gel washed out from the fractures during brine or oil flow. However, increased brine or oil flow rate and cyclic injection of oil and water significantly decreased the level of permeability reduction. A particular need exists for gels that can plug large apertures (e.g., wide fractures and vugs). Improved mechanical strength and stability were demonstrated (in 1- to 4-mm-wide fractures) for a gel that contained a combination of high- and low-molecular weight polymers. This gel reduced the flow capacity of 2- and 4-mm-wide fractures by 260,000. In a 1-mm-wide fracture, it withstood 26 psi/ft without allowing any brine flow through the fracture. Cr(III)-acetate-HPAM gels exhibited disproportionate permeability reduction in fractures. The effect was most pronounced when the gel was placed as gelant or partially formed gels. The effect occurred to a modest extent with concentrated gels and with gels that were ''fully formed'' when placed. The effect was not evident in tubes. We explored swelling polymers for plugging fractures. Polymer suspensions were quickly prepared and injected. In concept, the partially dissolved polymer would lodge and swell to plug the fracture. For three types of swelling polymers, behavior was promising. However, additional development is needed before their performance will be superior to that of conventional gels.

Randall S. Seright

2003-09-01

235

Conformational transformations of sulfur-containing rings: 2-methyltetrahydrothiophene gas-phase structures.  

PubMed

Stable conformations of five-member rings with the prototype cyclopentane are well-known to exist as twist or envelope structures and are of general interest in chemistry. Here, we report on the conformational analysis of the sulfur-containing ring 2-methyltetrahydrothiophene studied by a combination of molecular beam Fourier transform microwave (MB-FTMW) spectroscopy and quantum chemistry. Two twist conformers were observed, whereby highly accurate molecular parameters could be determined. In addition, the (34) S-isotopologue of the most stable conformer was assigned in natural abundances. Geometry optimizations were performed at different levels of theory and the calculated rotational constants were compared with experimental values. Two transition states optimized at the MP2/6-311++G(d,p) level using the Berny algorithm could illustrate the intramolecular conversion between both conformers. PMID:25376652

Van, Vinh; Dindic, Christina; Nguyen, Ha Vinh Lam; Stahl, Wolfgang

2015-02-01

236

Conformations of n-butyl imidazole: Matrix isolation infrared and DFT studies.  

PubMed

Conformations of n-butyl imidazole (B-IMID) were studied using matrix isolation infrared spectroscopy by trapping in argon, xenon and nitrogen matrixes using an effusive nozzle source. The experimental studies were supported by DFT computations performed at the B3LYP/6-311++G(d,p) level. Computations identified nine unique minima for B-IMID, corresponding to conformers with tg(±)tt, tg(±)g(?)t, tg(±)g(±)t, tg(±)tg(±), tg(±)tg(?), tg(±)g(?)g(?), tg(±)g(±)g(±), tg(±)g(?)g(±) and tg(±)g(±)g(?) structures, given in order of increasing energy. Computations of the transition state structures connecting the higher energy conformers to the global minimum, tg(±)tt structure were carried out. The barriers for the conformer inter-conversion were found to be ?2kcal/mol. Natural Bond Orbital (NBO) analysis was performed to understand the reasons for conformational preferences in B-IMID. PMID:25554955

Ramanathan, N; Sundararajan, K; Sankaran, K

2015-03-15

237

Global Structure of Conformal Theories in the SU(3) Gauge Theory  

E-print Network

We investigate SU(3) gauge theories in four dimensions with Nf fundamental fermions, on a lattice using the Wilson fermion. Clarifying the vacuum structure in terms of Polyakov loops in spatial directions and properties of temporal propagators using a new method "local analysis", we conjecture that the "conformal region" exists together with the confining region and the deconfining region in the phase structure parametrized by beta and K, both in the cases of the large Nf QCD within the conformal window (referred as Conformal QCD) with an IR cutoff and small Nf QCD at T/Tc>1 with Tc being the chiral transition temperature (referred as High Temperature QCD). Our numerical simulation on a lattice of the size 16^3 x 64 shows the following evidence of the conjecture. In the conformal region we find the vacuum is the nontrivial Z(3) twisted vacuum modified by non-perturbative effects and temporal propagators of meson behave at large t as a power-law corrected Yukawa-type decaying form. The transition from the conformal region to the deconfining region or the confining region is a sharp transition between different vacua and therefore it suggests a first order transition both in Conformal QCD and in High Temperature QCD. Within our fixed lattice simulation, we find that there is a precise correspondence between Conformal QCD and High Temperature QCD in the temporal propagators under the change of the parameters Nf and T/Tc respectively. In particular, we find the correspondence between Conformal QCD with Nf = 7 and High Temperature QCD with Nf=2 at T ~ 2 Tc being in close relation to a meson unparticle model. From this we estimate the anomalous mass dimension gamma* = 1.2 (1) for Nf=7. We also show that the asymptotic state in the limit T/Tc --> infty is a free quark state in the Z(3) twisted vacuum.

K. -I. Ishikawa; Y. Iwasaki; Yu Nakayama; T. Yoshie

2014-05-16

238

Conformational Changes in Acetylcholine Binding Protein Investigated by Temperature Accelerated Molecular Dynamics  

PubMed Central

Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP), a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD) and Temperature Accelerated Molecular Dynamics (TAMD) simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit. PMID:24551117

Mohammad Hosseini Naveh, Zeynab; Malliavin, Therese E.; Maragliano, Luca; Cottone, Grazia; Ciccotti, Giovanni

2014-01-01

239

Anion transport across the red blood cell membrane and the conformation of the protein in Band 3.  

PubMed

Measuring the rate of dinitrophenylation of a specific lysine residue (called a) that is allosterically linked to the transfer site, it could be demonstrated that the anion transport protein may exist in two different conformational states, designated cis and trans. In the cis conformation a is easily accessible for reaction with dinitrofluorobenzene; in the trans conformation, a is less accessible. In the presence of the substrate anion Cl, the equilibrium between the cis and trans conformation is towards the cis conformation. Reversibly acting inhibitors of anion transport arrest the transport system, either predominantly in the cis or in the trans conformation. Phlorizin and certain positively charged derivatives of furosemide produce arrest in cis conformation, internal 2-(4'-aminophenyl)-6-methylbenzenethiazol-3',7-disulfonate (APMB) and Ca++ in trans conformation. Within this frame of reference, the different susceptibilities of the transfer site to internal and external 4,4' diacetamido-2,2'-stilbene disulfonate (DAS) are interpreted on the assumption that the conformation of the transfer site changes during the transition of the transport protein from the cis to the trans conformation, so that in the trans conformation a reaction with DAS is no longer possible. PMID:6772068

Passow, H; Fasold, H; Gärtner, E M; Legrum, B; Ruffing, W; Zaki, L

1980-01-01

240

Universality class in conformal inflation  

SciTech Connect

We develop a new class of chaotic inflation models with spontaneously broken conformal invariance. Observational consequences of a broad class of such models are stable with respect to strong deformations of the scalar potential. This universality is a critical phenomenon near the point of enhanced symmetry, SO(1,1), in case of conformal inflation. It appears because of the exponential stretching of the moduli space and the resulting exponential flattening of scalar potentials upon switching from the Jordan frame to the Einstein frame in this class of models. This result resembles stretching and flattening of inhomogeneities during inflationary expansion. It has a simple interpretation in terms of velocity versus rapidity near the Kähler cone in the moduli space, similar to the light cone of special theory of relativity. This effect makes inflation possible even in the models with very steep potentials. We describe conformal and superconformal versions of this cosmological attractor mechanism.

Kallosh, Renata; Linde, Andrei, E-mail: kallosh@stanford.edu, E-mail: alinde@stanford.edu [Department of Physics and SITP, Stanford University, Stanford, California 94305 (United States)

2013-07-01

241

Algebraic orbifold conformal field theories.  

PubMed

The unitary rational orbifold conformal field theories in the algebraic quantum field theory and subfactor theory framework are formulated. Under general conditions, it is shown that the orbifold of a given unitary rational conformal field theory generates a unitary modular category. Many new unitary modular categories are obtained. It is also shown that the irreducible representations of orbifolds of rank one lattice vertex operator algebras give rise to unitary modular categories and determine the corresponding modular matrices, which has been conjectured for some time. PMID:11106383

Xu, F

2000-12-19

242

Algebraic orbifold conformal field theories  

PubMed Central

The unitary rational orbifold conformal field theories in the algebraic quantum field theory and subfactor theory framework are formulated. Under general conditions, it is shown that the orbifold of a given unitary rational conformal field theory generates a unitary modular category. Many new unitary modular categories are obtained. It is also shown that the irreducible representations of orbifolds of rank one lattice vertex operator algebras give rise to unitary modular categories and determine the corresponding modular matrices, which has been conjectured for some time. PMID:11106383

Xu, Feng

2000-01-01

243

The conformational analysis of 2-halocyclooctanones.  

PubMed

The establishment of the most stable structures of eight membered rings is a challenging task to the field of conformational analysis. In this work, a series of 2-halocyclooctanones were synthesized (including fluorine, chlorine, bromine and iodine derivatives) and submitted to conformational studies using a combination of theoretical calculation and infrared spectroscopy. For each compound, four conformations were identified as the most important ones. These conformations are derived from the chair-boat conformation of cyclooctanone. The pseudo-equatorial (with respect to the halogen) conformer is preferred in vacuum and in low polarity solvents for chlorine, bromine and iodine derivatives. For 2-fluorocyclooctanone, the preferred conformation in vacuum is pseudo-axial. In acetonitrile, the pseudo-axial conformer becomes the most stable for the chlorine derivative. According to NBO calculations, the conformational preference is not dictated by electron delocalization, but by classical electrostatic repulsions. PMID:25218227

Rozada, Thiago C; Gauze, Gisele F; Rosa, Fernanda A; Favaro, Denize C; Rittner, Roberto; Pontes, Rodrigo M; Basso, Ernani A

2015-02-25

244

The conformational analysis of 2-halocyclooctanones  

NASA Astrophysics Data System (ADS)

The establishment of the most stable structures of eight membered rings is a challenging task to the field of conformational analysis. In this work, a series of 2-halocyclooctanones were synthesized (including fluorine, chlorine, bromine and iodine derivatives) and submitted to conformational studies using a combination of theoretical calculation and infrared spectroscopy. For each compound, four conformations were identified as the most important ones. These conformations are derived from the chair-boat conformation of cyclooctanone. The pseudo-equatorial (with respect to the halogen) conformer is preferred in vacuum and in low polarity solvents for chlorine, bromine and iodine derivatives. For 2-fluorocyclooctanone, the preferred conformation in vacuum is pseudo-axial. In acetonitrile, the pseudo-axial conformer becomes the most stable for the chlorine derivative. According to NBO calculations, the conformational preference is not dictated by electron delocalization, but by classical electrostatic repulsions.

Rozada, Thiago C.; Gauze, Gisele F.; Rosa, Fernanda A.; Favaro, Denize C.; Rittner, Roberto; Pontes, Rodrigo M.; Basso, Ernani A.

2015-02-01

245

Transiting Exoplanets  

NASA Astrophysics Data System (ADS)

1. Our solar system from afar; 2. Exoplanet discoveries by the transit method; 3. What the transit lightcurve tells us; 4. The transiting exoplanet population; 5. Transmission spectroscopy and Rossiter-McLaughlin effect; 6. Secondary eclipses and phase variations; 7. Transit timing variations and orbital dynamics; 8. Brave new worlds: the future; Index.

Haswell, Carole A.

2010-07-01

246

Second Order Symmetries of the Conformal Laplacian  

NASA Astrophysics Data System (ADS)

Let (M,g) be an arbitrary pseudo-Riemannian manifold of dimension at least 3. We determine the form of all the conformal symmetries of the conformal (or Yamabe) Laplacian on (M,g), which are given by differential operators of second order. They are constructed from conformal Killing 2-tensors satisfying a natural and conformally invariant condition. As a consequence, we get also the classification of the second order symmetries of the conformal Laplacian. Our results generalize the ones of Eastwood and Carter, which hold on conformally flat and Einstein manifolds respectively. We illustrate our results on two families of examples in dimension three.

Michel, Jean-Philippe; Radoux, Fabian; Šilhan, Josef

2014-02-01

247

Transit Tracks  

NSDL National Science Digital Library

In this space science activity, learners explore transits and the conditions when a transit may be seen. Learners use models to investigate how a planet's size and distance from its star affects the behavior of transits. Learners also use mathematics to interpret graphs of brightness vs. time to deduce information about planet-star systems. This lesson includes educator instructions, photocopy masters for Transit Light Curves, Option Math for Transit Tracks, Keplerâs 3rd Law graphs, cube root tables, an account of Jeremiah Horrocks' 1639 observation of the transit of Venus, and an answer key for the Transit Tracks Light Curves.

Science, Lawrence H.

2008-01-01

248

On Conformally Kaehler, Einstein Manifolds  

E-print Network

We prove that any compact complex surface with positive first Chern class admits an Einstein metric which is conformally related to a Kaehler metric. The key new ingredient is the existence of such a metric on the blow-up of the complex projective plane at two distinct points.

Xiuxiong Chen; Claude LeBrun; Brian Weber

2007-05-07

249

Conformal dynamics for vortex motions  

Microsoft Academic Search

A new method to describe the dynamics of constant vorticity domains on the plane is proposed. The parameters of conformal mappings of the standard domain onto those latter are the new variables and a dynamical equation for their evolution is given. A perturbation theory around a basic elliptic shape of the vortex is formulated within this framework. As an illustration,

Bernard Legras; Vladimir Zeitlin

1992-01-01

250

Random Curves by Conformal Welding  

E-print Network

We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle given in terms of the exponential of Gaussian Free Field. We conjecture that our curves are locally related to SLE$(\\kappa)$ for $\\kappa<4$.

Astala, K; Kupiainen, A; Saksman, E

2009-01-01

251

Random Curves by Conformal Welding  

E-print Network

We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle given in terms of the exponential of Gaussian Free Field. We conjecture that our curves are locally related to SLE$(\\kappa)$ for $\\kappa<4$.

K. Astala; P. Jones; A. Kupiainen; E. Saksman

2009-12-17

252

Temperature: Human Regulating, Ants Conforming  

ERIC Educational Resources Information Center

Biological processes speed up as temperature rises. Procedures for demonstrating this with ants traveling on trails, and data gathered by students on the Argentine ant ("Linepithema humile") are presented. The concepts of temperature regulation and conformity are detailed with a focus on the processes rather than on terms that label the organisms.

Clopton, Joe R.

2007-01-01

253

Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates  

Microsoft Academic Search

Using distributed molecular dynamics simulations we located four distinct folding transitions for a 39-residue ???? protein fold. To characterize the nature of each room temperature transition, we calculated the probability of transmission for 500 points along each free energy barrier. We introduced a method for determining transition states by employing the transmission probability, Ptrans, and determined which conformations were transition

Christopher D. Snow; Young Min Rhee; Vijay S. Pande

2006-01-01

254

Impact of mutations on the allosteric conformational equilibrium  

PubMed Central

Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand binding, allostery involves a conformational equilibrium between one protein substate that binds the effector and a second substate that less strongly binds the effector. We run molecular dynamics simulations using simple, smooth energy landscapes to sample specific ligand-induced conformational transitions, as defined by the effector-bound and unbound protein structures. These simulations can be performed using our web server: http://salilab.org/allosmod/. We then develop a set of features to analyze the simulations and capture the relevant thermodynamic properties of the allosteric conformational equilibrium. These features are based on molecular mechanics energy functions, stereochemical effects, and structural/dynamic coupling between sites. Using a machine-learning algorithm on a dataset of 10 proteins and 179 mutations, we predict both the magnitude and sign of the allosteric conformational equilibrium shift by the mutation; the impact of a large identifiable fraction of the mutations can be predicted with an average unsigned error of 1 kBT. With similar accuracy, we predict the mutation effects for an 11th protein that was omitted from the initial training and testing of the machine-learning algorithm. We also assess which calculated thermodynamic properties contribute most to the accuracy of the prediction. PMID:23228330

Weinkam, Patrick; Chen, Yao Chi; Pons, Jaume; Sali, Andrej

2012-01-01

255

Conformational effects on optical rotation. 3-substituted 1-butenes.  

PubMed

A calculation of the optical rotation of (R)-(-)-3-chloro-1-butene found a remarkably large dependence on the C=C-C-C torsional angle. At tau = 0 degrees, [alpha](D) = +244 degrees, whereas at tau = 180 degrees, [alpha](D) = -526 degrees. The effect of conformation on the optical rotation was confirmed by a study of the temperature dependence of the rotation. An analysis of the data gave the difference in free energy between the low- and high-energy conformers as 1315 cal/mol and gave the optical rotation of the low-energy conformer and the average of the rotations of the higher energy forms. Although a large effect was found, the observed rotations are a factor of 2.6 smaller than the calculated values, independent of both conformation and wavelength from 589 to 365 nm. The effect of replacing Cl with F, CN, and CCH was examined theoretically. The effects of substituents are remarkably small despite large changes in the calculated electronic transition energies. PMID:12580616

Wiberg, Kenneth B; Vaccaro, Patrick H; Cheeseman, James R

2003-02-19

256

The impact of 4-thiaproline on polyproline conformation.  

PubMed

Proline is unique among the genetically coded amino acids; because of the presence of a saturated pyrrolidine ring, it favors a cis peptide bond more strongly than other amino acids. The prolyl peptide bond conformational preference can be modulated by alterations to the atoms or substitution groups on the ring. In the study of a simple Ac-Xaa-OMe system, (2R)-4-thiaproline (Thp) was shown to favor an endo ring pucker and a cis prolyl peptide bond. Herein, to investigate the effects of Thp on a more complex system, that is, the polyproline structure, we prepared a series of polyproline peptides with one or multiple proline residues substituted with Thp and used circular dichroism (CD) spectroscopy to characterize their structures. In contrast to the results obtained using the Ac-Xaa-OMe system, here we found that Thp not only destabilizes all-trans polyproline II conformation, but also disfavors all-cis polyproline I structure. On the basis of the hybrid density functional theory analysis, we demonstrate that this phenomenon could be due to the small transition barrier between an exo and an endo pucker for the thiazolidine ring of Thp in a PPI helix and a weak backbone n ? ?* interaction for Thp in PPII conformation. The combination of experimental and computational data allows us to gain new insights into the impact of 4-thiaproline on polyproline conformation. PMID:25158153

Lin, Yu-Ju; Chang, Chiao-Hsin; Horng, Jia-Cherng

2014-09-18

257

Functional Roles of Slow Enzyme Conformational Changes in Network Dynamics  

PubMed Central

Extensive studies from different fields reveal that many macromolecules, especially enzymes, show slow transitions among different conformations. This phenomenon is named such things as dynamic disorder, heterogeneity, hysteretic or mnemonic enzymes across these different fields, and has been directly demonstrated by single molecule enzymology and NMR studies recently. We analyzed enzyme slow conformational changes in the context of regulatory networks. A single enzymatic reaction with slow conformational changes can filter upstream network noises, and can either resonantly respond to the system stimulus at certain frequencies or respond adaptively for sustained input signals of the network fluctuations. It thus can serve as a basic functional motif with properties that are normally for larger intermolecular networks in the field of systems biology. We further analyzed examples including enzymes functioning against pH fluctuations, metabolic state change of Artemia embryos, and kinetic insulation of fluctuations in metabolic networks. The study also suggests that hysteretic enzymes may be building blocks of synthetic networks with various properties such as narrow-banded filtering. The work fills the missing gap between studies on enzyme biophysics and network level dynamics, and reveals that the coupling between the two is functionally important; it also suggests that the conformational dynamics of some enzymes may be evolutionally selected. PMID:23009855

Wu, Zhanghan; Xing, Jianhua

2012-01-01

258

Logarithmic exotic conformal Galilean algebras  

NASA Astrophysics Data System (ADS)

Logarithmic representations of the conformal Galilean algebra (CGA) and the Exotic Conformal Galilean algebra (ECGA) are constructed. This can be achieved by non-decomposable representations of the scaling dimensions or the rapidity indices, specific to conformal Galilean algebras. Logarithmic representations of the non-exotic CGA lead to the expected constraints on scaling dimensions and rapidities and also on the logarithmic contributions in the co-variant two-point functions. On the other hand, the ECGA admits several distinct situations which are distinguished by different sets of constraints and distinct scaling forms of the two-point functions. Two distinct realisations for the spatial rotations are identified as well. This is the first concrete example of a reducible, but non-decomposable representation, without logarithmic terms. Such cases had been anticipated before. One may try to generalise (1.3) further by extending the projective conformal (or Möbius) transformations in the time t to arbitrary conformal transformations. Taking the projective terms describing the transformation of the wave functions into account, the only cases with local generators which close as a Lie algebra are, besides evidently conformal transformations in space-time, the cases l=1/2 >,1 of the Schrödinger algebra and the CGA [12]. When considering the non-relativistic limit of space-time conformal transformations and assuming the existence of a dynamical exponent z, restriction to time-like and light-like geodesics reproduces exactly the Schrödinger algebra and the CGA, for z=2 and z=1, respectively [16]. Physical applications either refer to strongly anisotropic systems at equilibrium, where the ‘time' t is just a name for a peculiar spatial direction with strongly modified interactions such that z=? is better referred to as an ‘anisotropy exponent' (paradigmatic examples are uniaxial Lifshitz points in lattice spin models with competing interactions); or else to real dynamics, at or far away from equilibrium. In the first case, co-variant n-point functions (such as we shall calculate later on) will represent physical correlators; the second case, causality constraints

Henkel, Malte; Hosseiny, Ali; Rouhani, Shahin

2014-02-01

259

Conformational activation of ADAMTS13  

PubMed Central

A disintegrin and metalloprotease with thrombospondin motifs 13 (ADAMTS13) is a metalloprotease that regulates von Willebrand factor (VWF) function. ADAMTS13-mediated proteolysis is determined by conformational changes in VWF, but also may depend on its own conformational activation. Kinetic analysis of WT ADAMTS13 revealed ?2.5-fold reduced activity compared with ADAMTS13 lacking its C-terminal tail (MDTCS) or its CUB1-2 domains (WT?CUB1-2), suggesting that the CUB domains naturally limit ADAMTS13 function. Consistent with this suggestion, WT ADAMTS13 activity was enhanced ?2.5-fold by preincubation with either an anti-CUB mAb (20E9) or VWF D4CK (the natural binding partner for the CUB domains). Furthermore, the isolated CUB1-2 domains not only bound MDTCS, but also inhibited activity by up to 2.5-fold. Interestingly, a gain-of-function (GoF) ADAMTS13 spacer domain variant (R568K/F592Y/R660K/Y661F/Y665F) was ?2.5-fold more active than WT ADAMTS13, but could not be further activated by 20E9 mAb or VWF D4CK and was unable to bind or to be inhibited by the CUB1-2 domains, suggesting that the inhibitory effects of the CUB domains involve an interaction with the spacer domain that is disrupted in GoF ADAMTS13. Electron microscopy demonstrated a “closed” conformation of WT ADAMTS13 and suggested a more “open” conformation for GoF ADAMTS13. The cryptic spacer domain epitope revealed by conformational unfolding also represents the core antigenic target for autoantibodies in thrombotic thrombocytopenic purpura. We propose that ADAMTS13 circulates in a closed conformation, which is maintained by a CUB–spacer domain binding interaction. ADAMTS13 becomes conformationally activated on demand through interaction of its C-terminal CUB domains with VWF, making it susceptible to immune recognition. PMID:25512499

South, Kieron; Luken, Brenda M.; Crawley, James T. B.; Phillips, Rebecca; Thomas, Mari; Collins, Richard F.; Deforche, Louis; Vanhoorelbeke, Karen; Lane, David A.

2014-01-01

260

Flow of structural information between four DNA conformational levels.  

PubMed

Closed-circular supercoiled DNA molecules have been shown to form a cholesteric assembly within bacteria as well as in vitro under physiological DNA and salt concentrations. Circular dichroism and X-ray scattering studies indicate that the macroscopic structural properties of the chiral mesophase are directly and uniquely dictated by the supercoiling parameters of the constituent molecules. Specifically, we find that the pitch of the DNA cholesteric phase derived from supercoiled DNA is determined by the superhelical density, which, in turn, is modulated by secondary conformational changes. A direct interrelationship among four DNA structural levels, namely, DNA sequence, secondary structural transitions, the tertiary superhelical conformation, and the quaternary, supramolecular organization is accordingly pointed out. Since secondary conformational changes are both sequence and environment dependent, alterations of cellular conditions may effectively modulate the properties of the packed DNA organization, through their effects on secondary structural transitions and hence on the superhelical parameters. On the basis of these results we suggest that liquid crystallinity represents an effectively regulated packaging mode of plectonemic, nucleosome-free DNA molecules in living systems. PMID:8608136

Levin-Zaidman, S; Reich, Z; Wachtel, E J; Minsky, A

1996-03-01

261

Evolutionary alkaline transition in human cytochrome c.  

PubMed

Conformational transitions in cytochrome c (cyt c) are being realized to be responsible for its multi-functions. Among a number of conformational transitions in cyt c, the alkaline transition has attracted much attention. The cDNA of human cyt c is cloned by RT-PCR and a high-effective expression system for human cyt c has been developed in this study. The equilibrium and kinetics of the alkaline transition of human cyt c have been systematically investigated for the first time, and compared with those of yeast and horse cyt c from an evolutionary perspective. The pK(a) value for the alkaline transition of human cyt c is apparently higher than that of yeast and horse. Kinetic studies suggest that it is increasingly difficult for the alkaline transition of cyt c from yeast, horse and human. Molecular modeling of human cyt c shows that the omega loop where the lysine residue is located apparently further away from heme in human cyt c than in yeast iso-1 and horse heart cyt c. These results regarding alkaline conformational transition provide valuable information for understanding the molecular basis for the biological multi-functions of cyt c. PMID:19593652

Ying, Tianlei; Zhong, Fangfang; Xie, Jin; Feng, Yanjiao; Wang, Zhong-Hua; Huang, Zhong-Xian; Tan, Xiangshi

2009-06-01

262

Finding Transition Pathways on Manifolds  

E-print Network

We consider noise-induced transition paths in randomly perturbed dynami- cal systems on a smooth manifold. The classical Freidlin-Wentzell large devia- tion theory in Euclidean spaces is generalized and new forms of action functionals are derived in the spaces of functions and the space of curves to accommodate the intrinsic constraints associated with the manifold. Numerical meth- ods are proposed to compute the minimum action paths for the systems with constraints. The examples of conformational transition paths for a single and double rod molecules arising in polymer science are numerically investigated.

Tiejun Li; Xiaoguang Li; Xiang Zhou

2014-08-13

263

Myosin and tropomyosin stabilize the conformation of formin-nucleated actin filaments.  

PubMed

The conformational elasticity of the actin cytoskeleton is essential for its versatile biological functions. Increasing evidence supports that the interplay between the structural and functional properties of actin filaments is finely regulated by actin-binding proteins; however, the underlying mechanisms and biological consequences are not completely understood. Previous studies showed that the binding of formins to the barbed end induces conformational transitions in actin filaments by making them more flexible through long range allosteric interactions. These conformational changes are accompanied by altered functional properties of the filaments. To get insight into the conformational regulation of formin-nucleated actin structures, in the present work we investigated in detail how binding partners of formin-generated actin structures, myosin and tropomyosin, affect the conformation of the formin-nucleated actin filaments using fluorescence spectroscopic approaches. Time-dependent fluorescence anisotropy and temperature-dependent Förster-type resonance energy transfer measurements revealed that heavy meromyosin, similarly to tropomyosin, restores the formin-induced effects and stabilizes the conformation of actin filaments. The stabilizing effect of heavy meromyosin is cooperative. The kinetic analysis revealed that despite the qualitatively similar effects of heavy meromyosin and tropomyosin on the conformational dynamics of actin filaments the mechanisms of the conformational transition are different for the two proteins. Heavy meromyosin stabilizes the formin-nucleated actin filaments in an apparently single step reaction upon binding, whereas the stabilization by tropomyosin occurs after complex formation. These observations support the idea that actin-binding proteins are key elements of the molecular mechanisms that regulate the conformational and functional diversity of actin filaments in living cells. PMID:22753415

Ujfalusi, Zoltán; Kovács, Mihály; Nagy, Nikolett T; Barkó, Szilvia; Hild, Gábor; Lukács, András; Nyitrai, Miklós; Bugyi, Beáta

2012-09-14

264

Killing Initial Data on spacelike conformal boundaries  

E-print Network

We analyze Killing Initial Data on Cauchy surfaces in conformally rescaled vacuum space-times satisfying Friedrich's conformal field equations. As an application, we derive the KID equations on a spacelike $\\mathcal{J}^-$.

Tim-Torben Paetz

2014-03-11

265

Conformal Invariance and Probability S. Rohde, UW  

E-print Network

: 1. The self-avoiding walk 2. Basic theory of conformal maps: Riemann mapping theorem, distortion, diffusions, Dynkin's formula; applications: Conformal invariance of BM, recurrence vs transience, area, first

Rohde, Steffen

266

Systematic conformational search with constraint satisfaction  

E-print Network

Determining the conformations of biological molecules is a high scientific priority for biochemists and for the pharmaceutical industry. This thesis describes a systematic method for conformational search, an application ...

Tucker-Kellogg, Lisa, 1969-

2002-01-01

267

Conformational Variety of Polyanionic Peptides At Low Salt Concentrations  

NASA Astrophysics Data System (ADS)

Cordially dedicated to Dr. Leslie Orgel on the occasion of his 70th birthday. Sequential oligo- and polypeptides based on glutamic acid and leucine residues have been synthesized. In pure water, they exhibit a random coil conformation. Addition of very small amounts of divalent metallic cations induces the formation of ordered structure in the peptides which remain in solution. Higher salt concentrations precipitate the peptides. Polypeptides with alternating glutamic acid and leucine residues undergo a coil to ?-sheet transition in the presence of Ca^2+, Ba^2+, Mn^2+, Co^2+, Zn^2+ and Hg^2+. Addition of Cu^2+ or Fe^3+ induces the formation of an ?-helix. Solid amorphous CdS generates water soluble ?-sheets, as well. Sequential poly(Leu-Glu-Glu-Leu) adopts an ?-helix in the presence of divalent cations. The sequence-dependent conformational diversity was extended to poly(Asp-Leu) and poly(Leu-Asp-Asp-Leu).

Bertrand, Marylène; Brack, André

1997-12-01

268

Recent Applications of Conformal Geometric Anthony Lasenby  

E-print Network

Recent Applications of Conformal Geometric Algebra Anthony Lasenby Cavendish Laboratory, University://www.mrao.cam.ac.uk/�anthony Abstract. We discuss a new covariant approach to geometry, called conformal geometric algebra vectors. In the final sections, we discuss a new approach to the area of conformal geometric algebra

Cambridge, University of

269

Recent Applications of Conformal Geometric Anthony Lasenby  

E-print Network

Recent Applications of Conformal Geometric Algebra Anthony Lasenby Cavendish Laboratory, University://www.mrao.cam.ac.uk/~anthony Abstract. We discuss a new covariant approach to geometry, called conformal geometric algebra refer the reader to [3] (this volume), for a summary of the conformal geometric algebra approach

Cambridge, University of

270

Primordial gravitational waves from conformal gravity  

E-print Network

We investigate the evolution of cosmological perturbations generated during de Sitter inflation in the conformal gravity. Primordial gravitational waves are composed of vector and tensor modes. We obtain the constant vector and tensor power spectra which seems to be correct because the conformal gravity is invariant under conformal transformation like the Maxwell kinetic term.

Yun Soo Myung; Taeyoon Moon

2014-07-02

271

Conformal Window and Correlation Functions in Lattice Conformal QCD  

NASA Astrophysics Data System (ADS)

We discuss various aspects of Conformal Field Theories on the Lattice. We mainly investigate the SU(3) gauge theory with Nf degenerate fermions in the fundamental representation, employing the one-plaquette gauge action and the Wilson fermion action. First we make a brief review of our previous works on the phase structure of lattice gauge theories in terms of the gauge coupling constant and the quark mass. We thereby clarify the reason why we conjecture that the conformal window is 7 ? Nf ? 16. Secondly, we introduce a new concept, "conformal theories with IR cutof" and point out that any numerical simulation on a lattice is bounded by an IR cutoff ?IR. Then we make predictions that when Nf is within the conformal window, the propagator of a meson G(t) behaves at large t, as G(t) = c exp (-mHt)/t?, that is, a modified Yukawa-type decay form, instead of the usual exponential decay form exp (-mHt), in the small quark mass region. This holds on an any lattice for any coupling constant g, as far as g is between 0 and g*, where g* is the IR fixed point. We verify that numerical results really satisfy the predictions for the Nf = 7 case and the Nf = 16 case. Thirdly, we discuss small number of flavors (Nf = 2 ˜ 6) QCD at finite temperatures. We point out theoretically and verify numerically that the correlation functions at T/Tc > 1 exhibit the characteristics of the conformal function with IR cutoff, an exponential decay with power correction. Investigating our numerical data by a new method which we call the "local-analysis" of propagators, we observe that the Nf = 7 case and the Nf = 2 at T ˜ 2Tc case are similar to each other, while the Nf = 16 case and the Nf = 2 at T = 102 ˜ 105Tc cases are similar to each other. Further, we observe our data are consistent with the picture that the Nf = 7 case and the Nf = 2 at T ˜ 2Tc case are close to the meson unparticle model. On the other hand, the Nf = 16 case and the Nf = 2 at T = 102 ˜ 105Tc cases are close to a free state in the Z(3) twisted vacuum. All results are consistent with naive physical intuition and give clues for long standing issues at high temperatures such as why the free energy at high temperatures does not reach the Stefan-Boltzmann ideal gas limit even at T = 100Tc.

Iwasaki, Y.

272

Coordinate Confusion in Conformal Cosmology  

E-print Network

A straight-forward interpretation of standard Friedmann-Lemaitre-Robertson-Walker (FLRW) cosmologies is that objects move apart due to the expansion of space, and that sufficiently distant galaxies must be receding at velocities exceeding the speed of light. Recently, however, it has been suggested that a simple transformation into conformal coordinates can remove superluminal recession velocities, and hence the concept of the expansion of space should be abandoned. This work demonstrates that such conformal transformations do not eliminate superluminal recession velocities for open or flat matter-only FRLW cosmologies, and all possess superluminal expansion. Hence, the attack on the concept of the expansion of space based on this is poorly founded. This work concludes by emphasizing that the expansion of space is perfectly valid in the general relativistic framework, however, asking the question of whether space really expands is a futile exercise.

Geraint F. Lewis; Matthew J. Francis; Luke A. Barnes; J. Berian James

2007-07-13

273

Conformational disorder in long polyenes  

NASA Astrophysics Data System (ADS)

We have studied the temperature dependence of the absorption spectra of soluble, conjugated polymers of known chain length (˜100-1000 double bonds), synthesized by Schattenmann et al. [Macromolecules 29, 8990 (1996)] using living polymerization techniques. The polymer spectra show significant redshifts upon cooling from 300 to 80 K. To estimate the distributions of conjugated segments in these conformationally disordered samples, the spectra were fitted to a superposition of absorption spectra of conjugated segments of known lengths. These "experimental" distributions of conjugated segments then were compared to those predicted by theoretical models of conformational disorder. Although the low-temperature samples contain significant populations of long segments, the shortest polyene segments dominate all distributions. We compare these experimental results with distributions derived from the model of Yaliraki and Silbey [J. Chem. Phys. 104, 1245 (1996)]. Adjustment of relevant energy parameters gives good qualitative agreement between the experimental and theoretical distributions in long polyenes.

Wood, Phillip; Samuel, Ifor D. W.; Schrock, Richard; Christensen, Ronald L.

2001-12-01

274

Permeable conformal walls and holography  

Microsoft Academic Search

We study conformal field theories in two dimensions separated by domain walls, which preserve at least one Virasoro algebra. We develop tools to study such domain walls, extending and clarifying the concept of `folding' discussed in the condensed-matter literature. We analyze the conditions for unbroken supersymmetry, and discuss the holographic duals in AdS3 when they exist. One of the interesting

Constantin Bachas; Jan de Boer; Robbert Dijkgraaf; Hirosi Ooguri

2002-01-01

275

Mg2+-induced conformational changes in the btuB riboswitch from E. coli  

PubMed Central

Mg2+ has been shown to modulate the function of riboswitches by facilitating the ligand-riboswitch interactions. The btuB riboswitch from Escherichia coli undergoes a conformational change upon binding to its ligand, coenzyme B12 (adenosyl-cobalamine, AdoCbl), and down-regulates the expression of the B12 transporter protein BtuB in order to control the cellular levels of AdoCbl. Here, we discuss the structural folding attained by the btuB riboswitch from E. coli in response to Mg2+ and how it affects the ligand binding competent conformation of the RNA. The btuB riboswitch notably adopts different conformational states depending upon the concentration of Mg2+. With the help of in-line probing, we show the existence of at least two specific conformations, one being achieved in the complete absence of Mg2+ (or low Mg2+ concentration) and the other appearing above ?0.5 mM Mg2+. Distinct regions of the riboswitch exhibit different dissociation constants toward Mg2+, indicating a stepwise folding of the btuB RNA. Increasing the Mg2+ concentration drives the transition from one conformation toward the other. The conformational state existing above 0.5 mM Mg2+ defines the binding competent conformation of the btuB riboswitch which can productively interact with the ligand, coenzyme B12, and switch the RNA conformation. Moreover, raising the Mg2+ concentration enhances the ratio of switched RNA in the presence of AdoCbl. The lack of a AdoCbl-induced conformational switch experienced by the btuB riboswitch in the absence of Mg2+ indicates a crucial role played by Mg2+ for defining an active conformation of the riboswitch. PMID:24243114

Choudhary, Pallavi K.; Sigel, Roland K.O.

2014-01-01

276

Simple Model Study of Phase Transition Properties of Isolated and Aggregated Protein  

NASA Astrophysics Data System (ADS)

We investigate the phase transition properties of isolated and aggregated protein by exhaustive numerical study in the confined conformation space with maximally compact lattice model. The study within the confined conformation space shows some general folding properties. Various sequences show different folding properties: two-state folding, three-state folding and prion-like folding behavior. We find that the aggregated protein holds a more evident transition than isolated one and the transition temperature is generally lower than that in isolated case.

Ji, Yong-Yun; Yi, Wei-Qi; Zhang, Lin-Xi

2011-03-01

277

Conformation and chirality in liquid crystals  

NASA Astrophysics Data System (ADS)

High helical twisting powerchiral additives are required for an expanding variety of liquid crystal displays and devices. Molecular conformation plays a critical role in determining the helical twisting power, HTP, of chiral additives. We studied additives based on an isosorbide benzoate ester core. Molecular modeling revealed two low energy states with very different conformations for this core The ultra-violet absorption and NMR spectra show two stable isosorbide conformers These spectra reveal how the relative populations of these two conformations change with temperature and how this is related to the helical twisting power. Conformation changes can explain many of the observed anomalous responses of HPT to temperature.

West, John L.; Zhao, Lei

2013-09-01

278

Serpin latency transition at atomic resolution.  

PubMed

Protease inhibition by serpins requires a large conformational transition from an active, metastable state to an inactive, stable state. Similar reactions can also occur in the absence of proteases, and these latency transitions take hours, making their time scales many orders of magnitude larger than are currently accessible using conventional molecular dynamics simulations. Using a variational path sampling algorithm, we simulated the entire serpin active-to-latent transition in all-atom detail with a physically realistic force field using a standard computing cluster. These simulations provide a unifying picture explaining existing experimental data for the latency transition of the serpin plasminogen activator inhibitor-1 (PAI-1). They predict a long-lived intermediate that resembles a previously proposed, partially loop-inserted, prelatent state; correctly predict the effects of PAI-1 mutations on the kinetics; and provide a potential means to identify ligands able to accelerate the latency transition. Interestingly, although all of the simulated PAI-1 variants readily access the prelatent intermediate, this conformation is not populated in the active-to-latent transition of another serpin, ?1-antitrypsin, which does not readily go latent. Thus, these simulations also help elucidate why some inhibitory serpin families are more conformationally labile than others. PMID:25313058

Cazzolli, Giorgia; Wang, Fang; a Beccara, Silvio; Gershenson, Anne; Faccioli, Pietro; Wintrode, Patrick L

2014-10-28

279

Peptide conformational heterogeneity revealed from nonlinear vibrational spectroscopy and molecular-dynamics simulations  

NASA Astrophysics Data System (ADS)

Nonlinear time-resolved vibrational spectroscopy is used to compare spectral broadening of the amide I band of the small peptide trialanine with that of N-methylacetamide, a commonly used model system for the peptide bond. In contrast to N-methylacetamide, the amide I band of trialanine is significantly inhomogeneously broadened. Employing classical molecular-dynamics simulations combined with density-functional-theory calculations, the origin of the spectral inhomogeneity is investigated. While both systems exhibit similar hydrogen-bonding dynamics, it is found that the conformational dynamics of trialanine causes a significant additional spectral broadening. In particular, transitions between the poly(Gly)II and the ?R conformations are identified as the main source of the additional spectral inhomogeneity of trialanine. The experimental and computational results suggest that trialanine adopts essentially two conformations: poly(Gly)II (80%) and ?R (20%). The potential of the joint experimental and computational approach to explore conformational dynamics of peptides is discussed.

Woutersen, Sander; Pfister, Rolf; Hamm, Peter; Mu, Yuguang; Kosov, Daniel S.; Stock, Gerhard

2002-10-01

280

Conformational behavior of DNA-templated CdS inorganic nanowire  

NASA Astrophysics Data System (ADS)

We describe the conformational behavior and morphological control of DNA-mineralized CdS nanowires in a bulk solution. The conformational behavior of individual double-stranded DNA in the presence of cadmium ions and stoichiometric mixtures of cadmium ions and sulfide ions was directly visualized by fluorescence microscopy. It was found that in the presence of mixtures of cadmium ions and sulfide ions, DNA molecules exhibit a conformational transition from an elongated coil to a compacted state. Mineralized DNA nanowires possess a significant conformational freedom at a microscale, and flexibility in the micro- and nanodimensions. The density of the inorganic material on the nanowire can be controlled by varying the concentrations and the molar ratio of Na2S to Cd(ClO4)2.

Pu, Shengyan; Zinchenko, Anatoly; Murata, Shizuaki

2011-09-01

281

?-Helical to ?-Helical Conformation Change in the C-Terminal of the Mammalian Prion Protein  

NASA Astrophysics Data System (ADS)

We employ all-atom structure-based models with mixed basis contact maps to explore whether there are any significant geometric or energetic constraints limiting conjectured conformational transitions between the alpha-helical (?H) and the left handed beta helical (LHBH) conformations for the C-terminal (residues 166-226) of the mammalian prion protein. The LHBH structure has been proposed to describe infectious oligomers and one class of in vitro grown fibrils, as well as possibly self- templating the conversion of normal cellular prion protein to the infectious form. Our results confirm that the kinetics of the conformation change are not strongely limited by large scale geometry modification and there exists an overall preference for the LHBH conformation.

Singh, Jesse; Whitford, Paul; Hayre, Natha; Cox, Daniel; Onuchic, José.

2011-03-01

282

Conformally Equivariant Quantization for Spinning Particles  

NASA Astrophysics Data System (ADS)

This work takes place over a conformally flat spin manifold ( M, g). We prove existence and uniqueness of the conformally equivariant quantization valued in spinor differential operators, and provide an explicit formula for it when restricted to first order operators. The Poisson algebra of symbols is realized as a space of functions on the supercotangent bundle , endowed with a symplectic form depending on the metric g. It admits two different actions of the conformal Lie algebra: one tensorial and one Hamiltonian. They are intertwined by the uniquely defined conformally equivariant superization, for which an explicit formula is given. This map allows us to classify all the conformal supercharges of the spinning particle in terms of conformal Killing tensors, which are symmetric, skew-symmetric or with mixed symmetry. Higher symmetries of the Dirac operator are obtained by quantization of the conformal supercharges.

Michel, Jean-Philippe

2015-01-01

283

More transition amplitudes on the Riemann sphere  

SciTech Connect

We consider a conformal field theory for bosons on the Riemann sphere. Correlation functions are defined as singular limits of functional integrals. The main result is that these amplitudes define transition amplitudes, that is multilinear Hilbert-Schmidt functionals on a fixed Hilbert space.

Dimock, J. [Department of Mathematics, SUNY at Buffalo, Buffalo, New York 14260 (United States)

2008-06-15

284

Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ.  

PubMed

The conformational dynamics in ABC transporters is largely elusive. The ABC importer GlnPQ from Lactococcus lactis has different covalently linked substrate-binding domains (SBDs), thus making it an excellent model system to elucidate the dynamics and role of the SBDs in transport. We demonstrate by single-molecule spectroscopy that the two SBDs intrinsically transit from open to closed ligand-free conformation, and the proteins capture their amino acid ligands via an induced-fit mechanism. High-affinity ligands elicit transitions without changing the closed-state lifetime, whereas low-affinity ligands dramatically shorten it. We show that SBDs in the closed state compete for docking onto the translocator, but remarkably the effect is strongest without ligand. We find that the rate-determining steps depend on the SBD and the amino acid transported. We conclude that the lifetime of the closed conformation controls both SBD docking to the translocator and substrate release. PMID:25486304

Gouridis, Giorgos; Schuurman-Wolters, Gea K; Ploetz, Evelyn; Husada, Florence; Vietrov, Ruslan; de Boer, Marijn; Cordes, Thorben; Poolman, Bert

2015-01-01

285

VizieR Online Data Catalog: Three conformers of 1,2-propanediol (Bossa+, 2014)  

NASA Astrophysics Data System (ADS)

Three conformers of 1,2-propanediol have been studied in this work, aG'g, gG'a, and g'G'g. 1) The molecules are asymmetric top rotors. Watson's S-reduction was used in the representation Ir. Data below 26GHz are from previous work: Lovas et al., 2009 for all conformers; in the case of the aG'g conformer (table3.dat), the first set of lines between 6 and 18GHz is from Lockley et al., 2002, J. Mol. Struct., 612, 199. All data above 38.5GHz are from this work. The average frequency of blended lines (identical transition frequencies for two or more transitions) is identical to the intensity-weighted average. We therefore omitted the intensity-weighting specified in the line file after the uncertainties in SPFIT. 2) Internal coordinates are given in separate txt files. (6 data files).

Bossa, J. B.; Ordu, M. H.; Muller, H. S. P.; Lewen, F.; Schlemmer, S.

2014-08-01

286

Conformational, spectroscopic, and molecular dynamics DFT study of precursors for new potential antibacterial fluoroquinolone drugs.  

PubMed

Biological activity, functionality, and synthesis of (fluoro)quinolones is closely related to their precursors (for instance 3-fluoroanilinoethylene derivatives) (i.e., their functional groups, conformational behavior, and/or electronic structure). Herein, the theoretical study of 3-fluoroanilinoethylene derivatives is presented. Impact of substituents (acetyl, methyl ester, and ethyl ester) on the conformational analysis and the spectral behavior is investigated. The B3LYP/6-311++G** computational protocol is utilized. It is found that the intramolecular hydrogen bond N-H···O is responsible for the energetic preference of anti (a) conformer (anti position of 3-fluoroanilino group with respect to the C?C double bond). The Boltzmann ratios of the conformers are related to the differences of the particular dipole moments and/or their dependence on the solvent polarity. The studied acetyl, ethyl ester, and methyl ester substituted fluoroquinolone precursors prefer in the solvent either EZa, ZZa, or both conformers equally, respectively. In order to understand the degree of freedom of rotation of the trans ethyl ester group, B3LYP/6-311G** molecular dynamic simulations were carried out. Vibrational frequencies, electron transitions, as well as NMR spectra are analyzed with respect to conformational analysis, including the effect of the substituent. X-ray structures of the precursors are presented and compared with the results of the conformational analysis. PMID:25188903

Dorotíková, Sandra; Plevová, Kristína; Bu?inský, Lukáš; Mal?ek, Michal; Herich, Peter; Kucková, Lenka; Bobeni?ová, Miroslava; Šoralová, Stanislava; Kožíšek, Jozef; Fronc, Marek; Milata, Viktor; Dvoranová, Dana

2014-10-01

287

The protein folding transition state: Insights from kinetics and thermodynamics  

NASA Astrophysics Data System (ADS)

We perform extensive lattice Monte Carlo simulations of protein folding to construct and compare the equilibrium and the kinetic transition state ensembles of a model protein that folds to the native state with two-state kinetics. The kinetic definition of the transition state is based on the folding probability analysis method, and therefore on the selection of conformations with 0.4conformations for which the evaluated values of several reaction coordinates correspond to the maximum of the free energy measured as a function of those reaction coordinates. Our results reveal a high degree of structural similarity between the ensembles determined by the two methods. However, the folding probability distribution of the conformations belonging to our definition of the equilibrium transition state (0.2transition state.

Travasso, Rui D. M.; Faísca, Patrícia F. N.; Rey, Antonio

2010-09-01

288

Conformance Testing: Measurement Decision Rules  

NASA Technical Reports Server (NTRS)

The goal of a Quality Management System (QMS) as specified in ISO 9001 and AS9100 is to provide assurance to the customer that end products meet specifications. Measuring devices, often called measuring and test equipment (MTE), are used to provide the evidence of product conformity to specified requirements. Unfortunately, processes that employ MTE can become a weak link to the overall QMS if proper attention is not given to the measurement process design, capability, and implementation. Documented "decision rules" establish the requirements to ensure measurement processes provide the measurement data that supports the needs of the QMS. Measurement data are used to make the decisions that impact all areas of technology. Whether measurements support research, design, production, or maintenance, ensuring the data supports the decision is crucial. Measurement data quality can be critical to the resulting consequences of measurement-based decisions. Historically, most industries required simplistic, one-size-fits-all decision rules for measurements. One-size-fits-all rules in some cases are not rigorous enough to provide adequate measurement results, while in other cases are overly conservative and too costly to implement. Ideally, decision rules should be rigorous enough to match the criticality of the parameter being measured, while being flexible enough to be cost effective. The goal of a decision rule is to ensure that measurement processes provide data with a sufficient level of quality to support the decisions being made - no more, no less. This paper discusses the basic concepts of providing measurement-based evidence that end products meet specifications. Although relevant to all measurement-based conformance tests, the target audience is the MTE end-user, which is anyone using MTE other than calibration service providers. Topics include measurement fundamentals, the associated decision risks, verifying conformance to specifications, and basic measurement decisions rules.

Mimbs, Scott M.

2010-01-01

289

Conformance Verification of Privacy Policies  

NASA Astrophysics Data System (ADS)

Web applications are both the consumers and providers of information. To increase customer confidence, many websites choose to publish their privacy protection policies. However, policy conformance is often neglected. We propose a logic based framework for formally specifying and reasoning about the implementation of privacy protection by a web application. A first order extension of computation tree logic is used to specify a policy. A verification paradigm, built upon a static control/data flow analysis, is presented to verify if a policy is satisfied.

Fu, Xiang

290

Conformal invariance in (2+1)-dimensional stochastic systems.  

PubMed

Stochastic partial differential equations can be used to model second-order thermodynamical phase transitions, as well as a number of critical out-of-equilibrium phenomena. In (2+1) dimensions, many of these systems are conjectured (and some are indeed proved) to be described by conformal field theories. We advance, in the framework of the Martin-Siggia-Rose field-theoretical formalism of stochastic dynamics, a general solution of the translation Ward identities, which yields a putative conformal energy-momentum tensor. Even though the computation of energy-momentum correlators is obstructed, in principle, by dimensional reduction issues, these are bypassed by the addition of replicated fields to the original (2+1)-dimensional model. The method is illustrated with an application to the Kardar-Parisi-Zhang (KPZ) model of surface growth. The consistency of the approach is checked by means of a straightforward perturbative analysis of the KPZ ultraviolet region, leading, as expected, to its c=1 conformal fixed point. PMID:20481675

Moriconi, L; Moriconi, M

2010-04-01

291

Conformational diversity in prion protein variants influences intermolecular ?-sheet formation  

PubMed Central

A conformational transition of normal cellular prion protein (PrPC) to its pathogenic form (PrPSc) is believed to be a central event in the transmission of the devastating neurological diseases known as spongiform encephalopathies. The common methionine/valine polymorphism at residue 129 in the PrP influences disease susceptibility and phenotype. We report here seven crystal structures of human PrP variants: three of wild-type (WT) PrP containing V129, and four of the familial variants D178N and F198S, containing either M129 or V129. Comparison of these structures with each other and with previously published WT PrP structures containing M129 revealed that only WT PrPs were found to crystallize as domain-swapped dimers or closed monomers; the four mutant PrPs crystallized as non-swapped dimers. Three of the four mutant PrPs aligned to form intermolecular ?-sheets. Several regions of structural variability were identified, and analysis of their conformations provides an explanation for the structural features, which can influence the formation and conformation of intermolecular ?-sheets involving the M/V129 polymorphic residue. PMID:19927125

Lee, Seungjoo; Antony, Lizamma; Hartmann, Rune; Knaus, Karen J; Surewicz, Krystyna; Surewicz, Witold K; Yee, Vivien C

2010-01-01

292

Conformational analysis of a model synthetic prodiginine.  

PubMed

A conformational analysis of a synthetic model prodiginine was carried out. In solution this compound showed a strong preference for the ? conformation, in which all the heterocycles are mutually cis. This conformation provided an ideal alignment of the three N-H groups for interacting with anions when the molecule is protonated. A different conformation was also detected in d(6)-DMSO for the mesylate salt, assigned to the ? conformation, in which the C ring is engaged in an intramolecular hydrogen bond with the OMe group. The formation of a homodimer was observed in concentrated CDCl(3) solutions of the neutral free base form of this prodiginine derivative. DFT calculations and the solid state structures of the hydrochloric and methanesulfonic acid salts were in good agreement with the results observed in solution. A complete study of the relative energies of different tautomers, isomers, and supramolecular complexes supported the preference for the ? conformation both in water and in the gas phase. PMID:22812509

García-Valverde, María; Alfonso, Ignacio; Quiñonero, David; Quesada, Roberto

2012-08-01

293

Metrics with Galilean conformal isometry  

SciTech Connect

The Galilean conformal algebra (GCA) arises in taking the nonrelativistic limit of the symmetries of a relativistic conformal field theory in any dimensions. It is known to be infinite dimensional in all spacetime dimensions. In particular, the 2d GCA emerges out of a scaling limit of linear combinations of two copies of the Virasoro algebra. In this paper, we find metrics in dimensions greater than 2 which realize the finite 2d GCA (the global part of the infinite algebra) as their isometry by systematically looking at a construction in terms of cosets of this finite algebra. We list all possible subalgebras consistent with some physical considerations motivated by earlier work in this direction and construct all possible higher-dimensional nondegenerate metrics. We briefly study the properties of the metrics obtained. In the standard one higher-dimensional ''holographic'' setting, we find that the only nondegenerate metric is Minkowskian. In four and five dimensions, we find families of nontrivial metrics with a rather exotic signature. A curious feature of these metrics is that all but one of them are Ricci-scalar flat.

Bagchi, Arjun [School of Mathematics, University of Edinburgh, Edinburgh, EH9 3JZ (United Kingdom); Kundu, Arnab [Theory Group, Department of Physics, University of Texas at Austin, Austin, Texas 78712 (United States)

2011-03-15

294

Conformal inflation coupled to matter  

NASA Astrophysics Data System (ADS)

We formulate new conformal models of inflation and dark energy which generalise the Higgs-Dilaton scenario. We embed these models in unimodular gravity whose effect is to break scale invariance in the late time Universe. In the early Universe, inflation occurs close to a maximum of both the scalar potential and the scalar coupling to the Ricci scalar in the Jordan frame. At late times, the dilaton, which decouples from the dynamics during inflation, receives a potential term from unimodular gravity and leads to the acceleration of the Universe. We address two central issues in this scenario. First we show that the Damour-Polyalov mechanism, when non-relativistic matter is present prior to the start of inflation, sets the initial conditions for inflation at the maximum of the scalar potential. We then show that conformal invariance implies that matter particles are not coupled to the dilaton in the late Universe at the classical level. When fermions acquire masses at low energy, scale invariance is broken and quantum corrections induce a coupling between the dilaton and matter which is still small enough to evade the gravitational constraints in the solar system.

Brax, Philippe; Davis, Anne-Christine

2014-05-01

295

Conformal Geodesics on Vacuum Space-times  

Microsoft Academic Search

:  ?We discuss properties of conformal geodesics on general, vacuum, and warped product space-times and derive a system of conformal\\u000a deviation equations. It is then shown how to construct on the Schwarzschild-Kruskal space-time globally defined systems of\\u000a conformal Gauss coordinates which extend smoothly and without degeneracy to future and past null infinity.

Helmut Friedrich

2003-01-01

296

Magnetically-conformed, Variable Area Discharge Chamber for Hall Thruster, and Method  

NASA Technical Reports Server (NTRS)

The invention is a Hall thruster that incorporates a discharge chamber having a variable area channel including an ionization zone, a transition region, and an acceleration zone. The variable area channel is wider through the acceleration zone than through the ionization zone. An anode is located in a vicinity of the ionization zone and a cathode is located in a vicinity of the acceleration zone. The Hall thruster includes a magnetic circuit which is capable of forming a local magnetic field having a curvature within the transition region of the variable area channel whereby the transition region conforms to the curvature of the local magnetic field. The Hall thruster optimizes the ionization and acceleration efficiencies by the combined effects of the variable area channel and magnetic conformity.

Hofer, Richard R. (Inventor)

2013-01-01

297

Rotational Spectroscopy Unveils Eleven Conformers of Adrenaline  

NASA Astrophysics Data System (ADS)

Recent improvements in our LA-MB-FTMW instrumentation have allowed the characterization of eleven and eight conformers for the neurotransmitters adrenaline and noradrenaline respectively. The observation of this rich conformational behavior is in accordance with the recent observation of seven conformers for dopamine and in sharp contrast with the conformational reduction proposed for catecholamines. C. Cabezas, I. Peña, J. C. López, J. L. Alonso J. Phys. Chem. Lett. 2013, 4, 486. H. Mitsuda, M. Miyazaki, I. B. Nielsen, P. Carcabal,C. Dedonder, C. Jouvet, S. Ishiuchi, M. Fujii J. Phys. Chem. Lett. 2010, 1, 1130.

Cabezas, C.; Cortijo, V.; Mata, S.; Lopez, J. C.; Alonso, J. L.

2013-06-01

298

Pyrrolidine nucleotide analogs with a tunable conformation  

PubMed Central

Summary Conformational preferences of the pyrrolidine ring in nucleotide analogs 7–14 were investigated by means of NMR and molecular modeling. The effect of the relative configuration of hydroxy and nucleobase substituents as well as the effect of the alkylation or acylation of the pyrrolidine nitrogen atom on the conformation of the pyrrolidine ring were studied. The results of a conformational analysis show that the alkylation/acylation can be effectively used for tuning the pyrrolidine conformation over the whole pseudorotation cycle. PMID:25246956

Poštová Slav?tínská, Lenka; Rejman, Dominik

2014-01-01

299

Explorations in conformal symmetry for quantum relativity  

NASA Astrophysics Data System (ADS)

The conformal group is a supergroup of the Poincare group that leaves Maxwell's equations invariant. Conformal symmetry has many applications in physics. Can conformal symmetry be applied to bring together special relativity, which treats space and time on the same level, and quantum theory, which does not? Quantum relativity, as developed by Jaekel and Reynaud [1], introduces operators X^? for space-time localization from the generators of the conformal group in an Einsteinian operational way. We explore how this approach can help describe elementary space-time processes like pair creation and pair annihilation. [1] M.T. Jaekel and S. Reynaud, Found.Phys.28, 439-456 (1998).

Earl, Lucas; van Huele, Jean-Francois

2007-10-01

300

Functionally important conformations of the Met20 loop in dihydrofolate reductase are populated by rapid thermal fluctuations  

PubMed Central

Conformational changes in enzymes are well recognized to play an important role in the organization of the reactive groups for efficient catalysis. This study reveals atomic and energetic details of the conformational change process that precedes the catalytic reaction of the enzyme dihydrofolate reductase. The computed free energy profile provides insights into the ligand binding mechanism and a quantitative estimate of barrier heights separating different conformational states along the pathway. Studies show that the ternary complex comprised of NADPH cofactor and substrate dihydrofolate undergoes transitions between a closed state and an occluded state via an intermediate “open” conformation. During these transitions the largest conformational change occurs in the Met20 loop of DHFR and is accompanied by the motion of the cofactor into and out of the binding pocket. When the cofactor is out of the binding pocket, the enzyme frequently samples open and occluded conformations with a small (? 5 kBT) free energy barrier between the two states. However, when the cofactor is in the binding pocket, the closed conformation is thermodynamically most favored. The determination of a profile characterizing the position-dependent diffusion of the Met20 loop allowed us to apply reaction rate theory and deduce the kinetics of loop motions based on the computed free energy landscape. PMID:19323547

Arora, Karunesh; Brooks, Charles L.

2009-01-01

301

Functionally important conformations of the Met20 loop in dihydrofolate reductase are populated by rapid thermal fluctuations.  

PubMed

Conformational changes in enzymes are well recognized to play an important role in the organization of the reactive groups for efficient catalysis. This study reveals atomic and energetic details of the conformational change process that precedes the catalytic reaction of the enzyme dihydrofolate reductase. The computed free energy profile provides insights into the ligand binding mechanism and a quantitative estimate of barrier heights separating different conformational states along the pathway. Studies show that the ternary complex comprised of NADPH cofactor and substrate dihydrofolate undergoes transitions between a closed state and an occluded state via an intermediate "open" conformation. During these transitions the largest conformational change occurs in the Met20 loop of DHFR and is accompanied by the motion of the cofactor into and out of the binding pocket. When the cofactor is out of the binding pocket, the enzyme frequently samples open and occluded conformations with a small (approximately 5 k(B)T) free energy barrier between the two states. However, when the cofactor is in the binding pocket, the closed conformation is thermodynamically most favored. The determination of a profile characterizing the position-dependent diffusion of the Met20 loop allowed us to apply reaction rate theory and deduce the kinetics of loop motions based on the computed free energy landscape. PMID:19323547

Arora, Karunesh; Brooks Iii, Charles L

2009-04-22

302

Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies  

E-print Network

The conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis ...

Kim, Do-Nyun

303

Work Transitions  

ERIC Educational Resources Information Center

Individuals make choices in, and adjust to, a world of work that is often a moving target. Because work is so central to human functioning, and transitions in and out of work can have major mental health repercussions, the authors argue that applied psychologists in health services need to understand those transitions. This article focuses on the…

Fouad, Nadya A.; Bynner, John

2008-01-01

304

Transition Checklist.  

ERIC Educational Resources Information Center

This transition checklist is intended to be a guide for North Dakota students with disabilities, teachers, parents, and agency personnel to help drive the transition process in an orderly and organized manner. The checklist provides suggestions and activities for grades 8-12 and students ages 14-21. The information is organized in sequence to…

North Dakota State Dept. of Public Instruction, Bismarck. Div. of Special Education.

305

Transitional Care  

ERIC Educational Resources Information Center

Transitional care encompasses a broad range of services and environments designed to promote the safe and timely passage of patients between levels of health care and across care settings. High-quality transitional care is especially important for older adults with multiple chronic conditions and complex therapeutic regimens, as well as for their…

Naylor, Mary; Keating, Stacen A.

2008-01-01

306

Unimodular conformal and projective relativity  

NASA Astrophysics Data System (ADS)

Existing approaches to quantum gravity fail to fully reconcile the background independence of general relativity and the role of the quantum of action in quantum-mechanical theories. They disagree as to which classical space-time quantities (or observables) should be quantized, and use quantization techniques without taking into consideration the role of measurability analysis in assuring consistency between the definability of these observables and their individual measurability and joint co-measurability by some idealized process. This thesis outlines the framework of a new approach, called Unimodular Conformal and Projective Relativity (UCPR), discusses the classical measurability of all of its basic observables, and examines the problem of extending this analysis to a physically motivated theory of quantum gravity. We consider the unimodular group of transformations (i.e., those with the unit determinant), rather than the full diffeomorphism group, as the basic symmetry group of the theory. This reduction leads to a natural decomposition of the linear affine connection into a projective connection and an affine one-form, and of the Riemannian pseudo-metric into a conformal metric and a volume-element. The geometric representation of all four structures is motivated by their physical interpretation. The projective connection and affine one-form are motivated by the law of inertia; the first determines the paths traversed by massive particles moving only under the combined influence of inertia and gravitation, while the second assures that these particles move at constant speed. The conformal metric determines constant-phase wave-fronts of zero rest-mass fields, while the volume-element permits the averaging of physical fields independently of other space-time structures. Using the UCPR framework, we decompose the usual general-relativistic Lagrangian, and derive the homogenous and inhomogenous field equations and compatibility conditions for the four fundamental fields. The application of this formalism to systems including only zero rest-mass fields is presented. Finally, we outline some approaches to classical measurability analysis of all the relevant structures, and their possible extension to phenomena in which the quantum of action plays a significant role.

Bradonjic, Kaca

307

Entropy and Barrier-Controlled Fluctuations Determine Conformational Viscoelasticity of Single Biomolecules  

PubMed Central

Biological macromolecules have complex and nontrivial energy landscapes, endowing them with a unique conformational adaptability and diversity in function. Hence, understanding the processes of elasticity and dissipation at the nanoscale is important to molecular biology and emerging fields such as nanotechnology. Here we analyze single molecule fluctuations in an atomic force microscope, using a generic model of biopolymer viscoelasticity that includes local “internal” conformational dissipation. Comparing two biopolymers, dextran and cellulose (polysaccharides with and without local bistable transitions), demonstrates that signatures of simple conformational change are minima in both the elastic and internal friction constants around a characteristic force. A novel analysis of dynamics on a bistable energy landscape provides a simple explanation: an elasticity driven by the entropy, and friction by a barrier-controlled hopping time of populations between states, which is surprisingly distinct to the well-known relaxation time. This nonequilibrium microscopic analysis thus provides a means of quantifying new dynamical features of the energy landscape of the glucopyranose ring, revealing an unexpected underlying roughness and information on the shape of the barrier of the chair-boat transition in dextran. The results presented herein provide a basis toward probing the viscoelasticity of macromolecular conformational transitions on more complex energy landscapes, such as during protein folding. PMID:17158578

Khatri, Bhavin S.; Kawakami, Masaru; Byrne, Katherine; Smith, D. Alastair; McLeish, Tom C. B.

2007-01-01

308

Effect of exciton self-trapping and molecular conformation on photophysical properties of oligofluorenes  

NASA Astrophysics Data System (ADS)

Electronic absorption and fluorescence transitions in fluorene oligomers of differing lengths are studied experimentally and using density functional theory (DFT) and time-dependent DFT. Experimental values are determined in two ways: from the measured molar absorption coefficient and from the radiative rate deduced from a combination of fluorescence quantum yield and lifetime measurements. Good agreement between the calculated and measured transition dipoles is achieved. In both theory and experiment a gradual increase in transition dipoles with increasing oligomer length is found. In absorption the transition dipole follows an ˜n0.5 dependence on the number of fluorene units n for the range of 2?n?12, whereas a clear saturation of the transition dipole with oligomer length is found in fluorescence. This behavior is attributed to structural relaxation of the molecules in the excited state leading to localization of the excitation (exciton self-trapping) in the middle of the oligomer for both twisted and planar backbone conformations. Twisted oligofluorene chains were found to adopt straight or bent geometries depending on alternation of the dihedral angle between adjacent fluorene units. These different molecular conformations show the same values for the transition energies and the magnitude of the transition dipole.

Schumacher, Stefan; Ruseckas, Arvydas; Montgomery, Neil A.; Skabara, Peter J.; Kanibolotsky, Alexander L.; Paterson, Martin J.; Galbraith, Ian; Turnbull, Graham A.; Samuel, Ifor D. W.

2009-10-01

309

Bootstrapping phase transitions in QCD and frustrated spin systems  

NASA Astrophysics Data System (ADS)

In view of its physical importance in predicting the order of chiral phase transitions in QCD and frustrated spin systems, we perform the conformal bootstrap program of [O (n )×O (2 ) ]-symmetric conformal field theories in d =3 dimensions with a special focus on n =3 and 4. The existence of renormalization group fixed points with these symmetries has been controversial over the years, but our conformal bootstrap program provides nonperturbative evidence. In both the n =3 and 4 cases, we find singular behaviors in the bounds of scaling dimensions of operators in two different sectors, which we claim correspond to chiral and collinear fixed points, respectively. In contrast to the cases with larger values of n , we find no evidence for the antichiral fixed point. Our results indicate the possibility that the chiral phase transitions in QCD and frustrated spin systems are continuous with the critical exponents that we predict from the conformal bootstrap program.

Nakayama, Yu; Ohtsuki, Tomoki

2015-01-01

310

Structure and conformational stability of protonated dialanine.  

PubMed

A systematic investigation on the structure and stability of the four conformers of the protonated dialanine cation (transA1, transA2, transO1, cisA3) was performed employing the HF, MP2, and hybrid DFT methods with various basis sets which ranged from the 6-31G* to the basis set larger than the correlation consistent aug-cc-pVTZ basis set. It is found that the backbone dihedral angles and energies of the conformers are sensitive to the electron correlation level and basis set, especially manifesting slow convergence of conformer structure and energetics with basis set at the MP2 level. At the MP2 basis set limit corrected by CCSD(T) correlation effect, the lowest transA1 conformer is almost isoenergetic with the cisA3 conformer, followed by the transA2 conformer ( approximately 0.5 kcal/mol above transA1), and, last, the transO1 conformer ( approximately 1.2 kcal/mol above transA1). Vibrational and thermal (entropic) factors appear to have an important effect on the relative stability between conformers at room temperature, reducing the energy difference between transA1 and transA2 conformers and making cisA3 higher in energy than transA1 or transA2, which is in accord with the recent infrared multiphoton dissociation experimental data on this cation. According to the polarizable continuum model calculations, solvation of protonated dialanine in water would significantly enhance the stability of the transA2 conformer, making it most populated in aqueous solution at room temperature. Among the tested hybrid DFT methods in this study, B3LYP/6-31G* was found to be the most effective for predicting the conformational structures and relevant stability of protonated dialanine cation in the gas phase. PMID:20572657

Sohn, Woon Yong; Lee, Jae Shin

2010-07-22

311

NONCOMMUTATIVE GEOMETRY AND CONFORMAL GEOMETRY. I. LOCAL INDEX FORMULA AND CONFORMAL INVARIANTS  

E-print Network

NONCOMMUTATIVE GEOMETRY AND CONFORMAL GEOMETRY. I. LOCAL INDEX FORMULA AND CONFORMAL INVARIANTS geometry and con- formal geometry. In this paper, elaborating on ideas of Connes and Moscovici, we establish a local index formula in conformal-diffeomorphism invariant geometry. The existence

Ponge, Raphaël

312

Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method  

E-print Network

Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space of these is the Reservoir Replica Exchange Method (R-REM), in which the conformational search and temperature equilibration are separated by exchanging with a pre-existing reservoir of structures. This approach allows the integration

Lee, Jooyoung

313

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.  

PubMed

Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost. PMID:24134878

Mishra, Sushil Kumar; Kara, Mahmut; Zacharias, Martin; Koca, Jaroslav

2014-01-01

314

Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signalling  

PubMed Central

MutS protein recognizes mispaired bases in DNA and targets them for mismatch repair. Little is known about the transient conformations of MutS as it signals initiation of repair. We have used single-molecule fluorescence resonance energy transfer (FRET) measurements to report the conformational dynamics of MutS during this process. We find that the DNA-binding domains of MutS dynamically interconvert among multiple conformations when the protein is free and while it scans homoduplex DNA. Mismatch recognition restricts MutS conformation to a single state. Steady-state measurements in the presence of nucleotides suggest that both ATP and ADP must be bound to MutS during its conversion to a sliding clamp form that signals repair. The transition from mismatch recognition to the sliding clamp occurs via two sequential conformational changes. These intermediate conformations of the MutS:DNA complex persist for seconds, providing ample opportunity for interaction with downstream proteins required for repair. PMID:22505031

Qiu, Ruoyi; DeRocco, Vanessa C; Harris, Credle; Sharma, Anushi; Hingorani, Manju M; Erie, Dorothy A; Weninger, Keith R

2012-01-01

315

Molecular dynamics simulations reveal that apo-HisJ can sample a closed conformation.  

PubMed

The Escherichia coli histidine binding protein HisJ is a type II periplasmic binding protein (PBP) that preferentially binds histidine and interacts with its cytoplasmic membrane ABC transporter, HisQMP2 , to initiate histidine transport. HisJ is a bilobal protein where the larger Domain 1 is connected to the smaller Domain 2 via two linking strands. Type II PBPs are thought to undergo "Venus flytrap" movements where the protein is able to reversibly transition from an open to a closed conformation. To explore the accessibility of the closed conformation to the apo state of the protein, we performed a set of all-atom molecular dynamics simulations of HisJ starting from four different conformations: apo-open, apo-closed, apo-semiopen, and holo-closed. The simulations reveal that the closed conformation is less dynamic than the open one. HisJ experienced closing motions and explored semiopen conformations that reverted to closed forms resembling those found in the holo-closed state. Essential dynamics analysis of the simulations identified domain closing/opening and twisting as main motions. The formation of specific inter-hinge strand and interdomain polar interactions contributed to the adoption of the closed apo-conformations although they are up to 2.5-fold less prevalent compared with the holo-closed simulations. The overall sampling of the closed form by apo-HisJ provides a rationale for the binding of unliganded PBPs with their cytoplasmic membrane ABC transporters. PMID:23966221

Chu, B C H; Chan, D I; DeWolf, T; Periole, X; Vogel, H J

2014-03-01

316

Lipid Regulated Conformational Dynamics of the Longin SNARE Protein Ykt6 Revealed by Molecular Dynamics Simulations.  

PubMed

The conformation and subcellular localization of R-SNARE protein Ykt6 are regulated by the lipidation state of its C-terminal CCAIM motif. Biochemical and crystallography studies showed that lipid molecules binding at a hydrophobic pocket at the interface between the longin domain and the SNARE core can lock Ykt6 at a closed conformation and mimic the farnesylated state of Ykt6. In this study, we performed in silico farnesylation of Ykt6 and explored the conformational dynamics of Ykt6 using conventional and steered MD simulations. We found that the farnesylated Ykt6 model structure is stable during the 2 ?s simulation and the farnesyl group adopts conformations similar to those of the DPC molecule bound to Ykt6. Both DPC binding and farnesylation were found to reduce the conformational flexibility of Ykt6 and hinder the dissociation of SNARE core from the longin domain. The dissociation of the ?F-?G segment is the rate-limiting step during the putative closed-to-open conformational transition of Ykt6, and the key residues involved in this process are consistent with the experimental mutagenesis study. PMID:25268560

Weng, Jingwei; Yang, Yanhong; Wang, Wenning

2014-10-14

317

Gravitomagnetic effects in conformal gravity  

E-print Network

Gravitomagnetic effects are characterized by two phenomena: first, the geodetic effect which describes the precession of the spin of a gyroscope in a free orbit around a massive object, second, the Lense-Thirring effect which describes the precession of the orbital plane about a rotating source mass. We calculate both these effects in the fourth-order theory of conformal Weyl gravity for the test case of circular orbits. We show that for the geodetic effect a linear term arises which may be interesting for high radial orbits, whereas for the Lense-Thirring effect the additional term has a diminishing effect for most orbits. Circular orbits are also considered in general leading up to a generalization of Kepler's third law.

Said, Jackson Levi; Adami, Kristian Zarb

2014-01-01

318

Conformal Frame Dependence of Inflation  

E-print Network

Physical equivalence between different conformal frames in scalar-tensor theory of gravity is a known fact. However, assuming that matter minimally couples to the metric of a particular frame, which we call the matter Jordan frame, the matter point of view of the universe may vary from frame to frame. Thus, there is a clear distinction between gravitational sector (curvature and scalar field) and matter sector. In this paper, focusing on a simple power-law inflation model in the Einstein frame, two examples are considered; a super-inflationary and a bouncing universe Jordan frames. Then we consider a spectator curvaton minimally coupled to a Jordan frame, and compute its contribution to the curvature perturbation power spectrum. In these specific examples, we find a blue tilt at short scales for the super-inflationary case, and a blue tilt at large scales for the bouncing case.

Domènech, Guillem

2015-01-01

319

Using Solutes and Kinetics to Probe Large Conformational Changes in the Steps of Transcription Initiation  

PubMed Central

Summary Small solutes are useful probes of large conformational changes in RNA polymerase (RNAP)-promoter interactions and other biopolymer processes. In general, a large effect of a solute on an equilibrium constant (or rate constant) indicates a large change in water-accessible biopolymer surface area in the corresponding step (or transition state), resulting from conformational changes, interface formation, or both. Here, we describe nitrocellulose filter binding assays from series used to determine the urea dependence of open complex formation and dissociation with Escherichia coli RNAP and ?PR promoter DNA. Then, we describe the subsequent data analysis and interpretation of these solute effects. PMID:25665568

Ruff, Emily; Kontur, Wayne S.; Record, M. Thomas

2014-01-01

320

Global structure of conformal theories in the SU(3) gauge theory  

NASA Astrophysics Data System (ADS)

We investigate SU(3) gauge theories in four dimensions with Nf fundamental fermions on a lattice using the Wilson fermion. Clarifying the vacuum structure in terms of Polyakov loops in spatial directions and properties of temporal propagators using a new method that we call "local analysis," we conjecture that the "conformal region" exists together with the confining region and the deconfining region in the phase structure parametrized by ? and K, both in the cases of the large Nf QCD within the conformal window (referred as conformal QCD) with an IR cutoff and small Nf QCD at T/Tc>1 with Tc being the chiral transition temperature (referred to as high-temperature QCD). Our numerical simulation on a lattice of the size 163×64 shows the following evidence of the conjecture. In the conformal region, we find that the vacuum is the nontrivial Z(3) twisted vacuum modified by nonperturbative effects and that temporal propagators of mesons behave at large t as a power-law-corrected Yukawa-type decaying form. The transition from the conformal region to the deconfining region or the confining region is a sharp transition between different vacua, and therefore, it suggests a first-order transition both in conformal QCD and high-temperature QCD. To confirm the conjecture and distinguish it from the possibility of crossover phenomena, we need to take the continuum/thermodynamic limit, which we do not attempt in this work. Within our fixed-lattice simulation, we find that there is a precise correspondence between conformal QCD and high-temperature QCD in the temporal propagators under the change of the parameters Nf and T/Tc, respectively: one boundary is close to meson states, and the other is close to free quark states. In particular, conformal QCD with Nf=7 corresponds to high-temperature QCD with Nf=2 at T˜2Tc, both of which are in close relation to a meson unparticle model. From this, we estimate the anomalous mass dimension ?*=1.2(1) for Nf=7. We also show that the asymptotic state in the limit T/Tc?? is a free quark state in the Z(3) twisted vacuum. The approach to a free quark state is very slow; even at T/Tc˜105, the state is affected by nonperturbative effects. This is possibly connected with the slow approach of the free energy to the Stefan-Boltzmann ideal gas limit.

Ishikawa, K.-I.; Iwasaki, Y.; Nakayama, Yu; Yoshie, T.

2014-06-01

321

Assignment of side-chain conformation using adiabatic energy mapping, free energy perturbation, and molecular dynamic simulations.  

PubMed Central

NMR spectroscopic analysis of the C-terminal Kunitz domain fragment (alpha3(VI)) from the human alpha3-chain of type VI collagen has revealed that the side chain of Trp21 exists in two unequally populated conformations. The major conformation (M) is identical to the conformation observed in the X-ray crystallographic structure, while the minor conformation (m) cannot structurally be resolved in detail by NMR due to insufficient NOE data. In the present study, we have applied: (1) rigid and adiabatic mapping, (2) free energy simulations, and (3) molecular dynamic simulations to elucidate the structure of the m conformer and to provide a possible pathway of the Trp21 side chain between the two conformers. Adiabatic energy mapping of conformations of the Trp21 side chain obtained by energy minimization identified two energy minima: One corresponding to the conformation of Trp21 observed in the X-ray crystallographic structure and solution structure of alpha3(VI) (the M conformation) and the second corresponding to the m conformation predicted by NMR spectroscopy. A transition pathway between the M and m conformation is suggested. The free-energy difference between the two conformers obtained by the thermodynamic integration method is calculated to 1.77+/-0.7 kcal/mol in favor of the M form, which is in good agreement with NMR results. Structural and dynamic properties of the major and minor conformers of the alpha3(VI) molecule were investigated by molecular dynamic. Essential dynamics analysis of the two resulting 800 ps trajectories reveals that when going from the M to the m conformation only small, localized changes in the protein structure are induced. However, notable differences are observed in the mobility of the binding loop (residues Thr13-Ile18), which is more flexible in the m conformation than in the M conformation. This suggests that the reorientation of Trp2 might influence the inhibitory activity against trypsin, despite the relative large distance between the binding loop and Trp21. PMID:10210180

Frimurer, T. M.; Peters, G. H.; Sørensen, M. D.; Led, J. J.; Olsen, O. H.

1999-01-01

322

Solvent Microenvironments and Copper Binding Alters the Conformation and Toxicity of a Prion Fragment  

PubMed Central

The secondary structures of amyloidogenic proteins are largely influenced by various intra and extra cellular microenvironments and metal ions that govern cytotoxicity. The secondary structure of a prion fragment, PrP(111-126), was determined using circular dichroism (CD) spectroscopy in various microenvironments. The conformational preferences of the prion peptide fragment were examined by changing solvent conditions and pH, and by introducing external stress (sonication). These physical and chemical environments simulate various cellular components at the water-membrane interface, namely differing aqueous environments and metal chelating ions. The results show that PrP(111-126) adopts different conformations in assembled and non-assembled forms. Aging studies on the PrP(111-126) peptide fragment in aqueous buffer demonstrated a structural transition from random coil to a stable ?-sheet structure. A similar, but significantly accelerated structural transition was observed upon sonication in aqueous environment. With increasing TFE concentrations, the helical content of PrP(111-126) increased persistently during the structural transition process from random coil. In aqueous SDS solution, PrP(111-126) exhibited ?-sheet conformation with greater ?-helical content. No significant conformational changes were observed under various pH conditions. Addition of Cu2+ ions inhibited the structural transition and fibril formation of the peptide in a cell free in vitro system. The fact that Cu2+ supplementation attenuates the fibrillar assemblies and cytotoxicity of PrP(111-126) was witnessed through structural morphology studies using AFM as well as cytotoxicity using MTT measurements. We observed negligible effects during both physical and chemical stimulation on conformation of the prion fragment in the presence of Cu2+ ions. The toxicity of PrP(111-126) to cultured astrocytes was reduced following the addition of Cu2+ ions, owing to binding affinity of copper towards histidine moiety present in the peptide. PMID:24386462

Malkovskiy, Andrey V.; Carre, Antoine L.; Sivanesan, Senthilkumar; Hardesty, Jasper O.; Rajadas, Jayakumar

2013-01-01

323

Investigation of light-induced conformation changes in spiropyran-modified succinylated poly(L-lysine).  

PubMed

To determine the maximum range of coupling between side-chain photochromism and polypeptide conformation change, we modified the carboxylate side chains of succinylated poly(L-lysine) with a spiropyran to form polypeptide I. The extent of modification was determined to be 35.5%. The spacer group length between the polypeptide alpha-carbon and the dye was 12 atoms, providing minimum polypeptide-dye interaction. Conformation changes were monitored by circular dichroism as a function of light adaptation and solvent composition (hexafluoroisopropanol [HFIP] vs trifluoroethanol [TFE]). Under all solvent compositions, the dark-adapted dye was in the merocyanine form. Light adaptation by visible light converted the dye to the spiropyran form. When dissolved in TFE, I adopted a helical conformation insensitive to light adaptation. With increasing percentage HFIP, a solvent-induced helix-to-coil transition was observed around 80% (vol/vol) HFIP. At 100% HFIP, both light- and dark-adapted forms of I were in the coil state. Near the midpoint of the solvent-induced helix-to-coil transition, light adaptation caused conformation changes. Applying helix-to-coil transition theory, we measured a statistically significant difference in coil segment-HFIP binding constant for light- vs dark-adapted solutions (6.38 +/- 0.03 M-1 vs 6.56 +/- 0.03 M-1), but not for the nucleation parameter sigma (1.2 +/- 0.4 10(-3) vs 1.3 +/- 0.3 x 10(-3). The small binding constant difference translated to a light-induced binding energy difference of 17 cal/mol/monomer. Near the midpoint of the helix-to-coil transition, collective interactions between monomer units made possible the translation of a small energy difference (less than RT) into large macromolecular conformation changes.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7480135

Cooper, T M; Stone, M O; Natarajan, L V; Crane, R L

1995-08-01

324

Perceived Symbols of Authority and Their Influence on Conformity.  

ERIC Educational Resources Information Center

Although there are many variables that influence conformity, Bickman (1974) found that the apparel of the person making a request had a significant influence on conformity. To evaluate other factorswhicn may influence conformity (gender, age, status of the conforming subject, and altruism in conforming), 150 adult pedestrians (45% female, 71%…

Bushman, Brad J.

325

Surface Quasi-Conformal Mapping by Solving Beltrami Equations  

E-print Network

Riemann surfaces with conformal atlas {(U,} and {(V , } respectively, f : S1 S2 is a homeomorphism,Luo,Yau,Gu Quasi-Conformal Mapping #12;Theoretic Background Definition (Conformal Atlas) suppose S is a surface, then the atlas A is a conformal atlas. U U S (U) (U) Zeng,Luo,Yau,Gu Quasi-Conformal Mapping #12;Theoretic

326

Dirac fields in massive conformal gravity  

E-print Network

In this article we show that the gravitational field in massive conformal gravity couples consistently with Dirac spinor fields. We solve the problem of consistency by considering that the Dirac spinor fields couple with both the metric field and a scalar field, which are the gravitational field variables of massive conformal gravity.

Faria, F F

2014-01-01

327

Dirac fields in massive conformal gravity  

E-print Network

In this article we show that the gravitational field in massive conformal gravity couples consistently with Dirac spinor fields. We solve the problem of consistency by considering that the Dirac spinor fields couple with both the metric field and a scalar field, which are the gravitational field variables of massive conformal gravity.

F. F. Faria

2014-10-19

328

The quantum chiral Minkowski and conformal superspaces  

E-print Network

We give a quantum deformation of the chiral super Minkowski space in four dimensions as the big cell inside a quantum super Grassmannian. The quantization is performed in such way that the actions of the Poincar\\'e and conformal quantum supergroups on the quantum Minkowski and quantum conformal superspaces are presented.

Cervantes, D; Lledo, M A

2010-01-01

329

Conformal invariance, supersymmetry and string theory  

Microsoft Academic Search

Covariant quantization of string theories is developed in the context of conformal field theory and the BRST quantization procedure. The BRST method is used to covariantly quantize superstrings, and in particular to construct the vertex operators for string emission as well as the supersymmetry charge. The calculation of string loop diagrams is sketched. We discuss how conformal methods can be

Daniel Friedan; Emil Martinec; Stephen Shenker

1986-01-01

330

Conformal smectics and their many metrics  

NASA Astrophysics Data System (ADS)

We establish that equally spaced smectic configurations enjoy an infinite-dimensional conformal symmetry and show that there is a natural map between them and null hypersurfaces in maximally symmetric spacetimes. By choosing the appropriate conformal factor it is possible to restore additional symmetries of focal structures only found before for smectics on flat substrates.

Alexander, Gareth P.; Kamien, Randall D.; Mosna, Ricardo A.

2012-05-01

331

Regulatory Conformance Checking: Logic and Logical Form  

ERIC Educational Resources Information Center

We consider the problem of checking whether an organization conforms to a body of regulation. Conformance is studied in a runtime verification setting. The regulation is translated to a logic, from which we synthesize monitors. The monitors are evaluated as the state of an organization evolves over time, raising an alarm if a violation is…

Dinesh, Nikhil

2010-01-01

332

Conformal Smectics and their Many Metrics  

E-print Network

We establish that equally-spaced smectic configurations enjoy an infinite-dimensional conformal symmetry and show that there is a natural map between them and null hypersurfaces in maximally-symmetric spacetimes. By choosing the appropriate conformal factor it is possible to restore additional symmetries of focal structures only found before for smectics on flat substrates.

Gareth P. Alexander; Randall D. Kamien; Ricardo A. Mosna

2012-05-01

333

Conformal smectics and their many metrics.  

PubMed

We establish that equally spaced smectic configurations enjoy an infinite-dimensional conformal symmetry and show that there is a natural map between them and null hypersurfaces in maximally symmetric spacetimes. By choosing the appropriate conformal factor it is possible to restore additional symmetries of focal structures only found before for smectics on flat substrates. PMID:23004696

Alexander, Gareth P; Kamien, Randall D; Mosna, Ricardo A

2012-05-01

334

Limbless Conforming Gaits with Modular Robots  

Microsoft Academic Search

This paper presents experimentation using the PolyBot modular robot of two limbless gaits which conform to environment. A conforming loop gait is low profile and traverses over a variety of obstacles where the ratio of the height of the obstacle to robot is up to 1.3. A concertina snake gait is capable of negotiating narrow passages (for example a width

Mark Yim; Craig Eldershaw; Ying Zhang; David Duff

2004-01-01

335

Electroweak phase transition in ultraminimal technicolor  

SciTech Connect

We unveil the temperature-dependent electroweak phase transition in new extensions of the standard model in which the electroweak symmetry is spontaneously broken via strongly coupled, nearly conformal dynamics achieved by the means of multiple matter representations. In particular, we focus on the low energy effective theory introduced to describe ultra minimal walking technicolor at the phase transition. Using the one-loop effective potential with ring improvement, we identify regions of parameter space, which yield a strong first-order transition. A striking feature of the model is the existence of a second phase transition associated to the electroweak-singlet sector. The interplay between these two transitions leads to an extremely rich phase diagram.

Jaervinen, Matti; Sannino, Francesco [University of Southern Denmark, Campusvej 55, DK-5230 Odense M (Denmark); Ryttov, Thomas A. [Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen O (Denmark)

2009-05-01

336

Transition metals  

PubMed Central

Transition metals such as Iron (Fe) and Copper (Cu) are essential for plant cell development. At the same time, due their capability to generate hydroxyl radicals they can be potentially toxic to plant metabolism. Recent works on hydroxyl-radical activation of ion transporters suggest that hydroxyl radicals generated by transition metals could play an important role in plant growth and adaptation to imbalanced environments. In this mini-review, the relation between transition metals uptake and utilization and oxidative stress-activated ion transport in plant cells is analyzed, and a new model depicting both apoplastic and cytosolic mode of ROS signaling to plasma membrane transporters is suggested. PMID:23333964

Rodrigo-Moreno, Ana; Poschenrieder, Charlotte; Shabala, Sergey

2013-01-01

337

Performance of Conformable Ablators in Aerothermal Environments  

NASA Technical Reports Server (NTRS)

Conformable Phenolic Impregnated Carbon Ablator, a cousin of Phenolic Impregnated Carbon Ablator (PICA), was developed at NASA Ames Research Center as a lightweight thermal protection system under the Fundamental Aeronautics Program. PICA is made using a brittle carbon substrate, which has a very low strain to failure. Conformable PICA is made using a flexible carbon substrate, a felt in this case. The flexible felt significantly increases the strain to failure of the ablator. PICA is limited by its thermal mechanical properties. Future NASA missions will require heatshields that are more fracture resistant than PICA and, as a result, NASA Ames is working to improve PICAs performance by developing conformable PICA to meet these needs. Research efforts include tailoring the chemistry of conformable PICA with varying amounts of additives to enhance mechanical properties and testing them in aerothermal environments. This poster shows the performance of conformable PICA variants in arc jets tests. Some mechanical and thermal properties will also be presented.

Thornton, J.; Fan, W.; Skokova, K.; Stackpoole, M.; Beck, R.; Chavez-Garcia, J.

2012-01-01

338

Conformations of folded proteins in restricted spaces.  

PubMed

A new method is presented to examine the complete range of folded topologies accessible in the compact state of globular proteins. The procedure is to generate all conformations, with volume exclusion, upon a lattice in a space restricted to the individual protein's known compact conformational space. Using one lattice point per residue, we find 10(2)-10(4) possible compact conformations for the five small globular proteins studied. Subsequently, these conformations are evaluated in terms of residue-specific, pairwise contact energies that favor nonbonded, hydrophobic interactions. Native structures for the five proteins are always found within the best 2% of all conformers generated. This novel method is simple and general and can be used to determine a small group of most favorable overall arrangements for the folding of specific amino acid sequences within a restricted space. PMID:2334692

Covell, D G; Jernigan, R L

1990-04-01

339

Tryptophol cation conformations studied with ZEKE spectroscopy.  

PubMed

The relative energies of several conformations of the tryptophol cation are determined by zero kinetic energy (ZEKE) photoelectron spectroscopy and photoionization efficiency measurements. Recently published high-resolution electronic spectroscopy on the neutral species determined the absolute configuration of the different conformers in the S1 spectrum. These assignments are utilized in the photoelectron experiments by pumping through conformer specific S1 resonances yielding ZEKE spectra of the specific, assigned conformations. The adiabatic ionization of one specific conformation is definitively determined, and two others are estimated. The photoelectron spectra, coupled with calculations, reveal that structural changes upon ionization are dominated by interactions of the hydroxyl group with the changes of electronic structure in the aromatic system. PMID:17305323

Gu, Quanli; Basu, Swarna; Knee, J L

2007-03-15

340

Rapid roll Inflation with Conformal Coupling  

E-print Network

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-antiD3 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, ...

Kofman, Lev

2007-01-01

341

Transit Math  

NSDL National Science Digital Library

This is a collection of mathematical problems about transits in the solar system. Learners can work problems created to be authentic glimpses of modern science and engineering issues, often involving actual research data.

342

Observing the unfolding transition of [beta]-hairpin peptides with nonlinear infrared spectroscopy  

E-print Network

The biological function of a protein is in large measure determined by its three-dimensional structure. To date, however, the transition of the protein between the native and non-native conformations is not well-understood. ...

Smith, Adam Wilcox, 1977-

2008-01-01

343

Electronic transitions of cobalt monoboride  

NASA Astrophysics Data System (ADS)

Electronic transition spectrum of cobalt monoboride (CoB) in the visible region between 495 and 560 nm has been observed and analyzed using laser-induced fluorescence spectroscopy. CoB molecule was produced by the reaction of laser-ablated cobalt atom and diborane (B2H6) seeded in argon. Fifteen vibrational bands with resolved rotational structure have been recorded, which included transitions of both Co10B and Co11B isotopic species. Our analysis showed that the observed transition bands are ?? = 0 transitions with ?? = 2 and ?? = 3 lower states. Four transition systems have been assigned, namely, the [18.1]3?2-X3?2, the [18.3]3?3-X3?3, the [18.6]3- X3?3, and the [19.0]2-X3?2 systems. The bond length, ro, of the X 3?3 state of CoB is determined to be 1.705 Å. The observed rotational lines showed unresolved hyperfine structure arising from the nuclei, which conforms to the Hund's case (a?) coupling scheme. This work represents the first experimental investigation of the CoB spectrum.

Ng, Y. W.; Pang, H. F.; Cheung, A. S.-C.

2011-11-01

344

Electronic transitions of cobalt monoboride.  

PubMed

Electronic transition spectrum of cobalt monoboride (CoB) in the visible region between 495 and 560 nm has been observed and analyzed using laser-induced fluorescence spectroscopy. CoB molecule was produced by the reaction of laser-ablated cobalt atom and diborane (B(2)H(6)) seeded in argon. Fifteen vibrational bands with resolved rotational structure have been recorded, which included transitions of both Co(10)B and Co(11)B isotopic species. Our analysis showed that the observed transition bands are ?? = 0 transitions with ?" = 2 and ?" = 3 lower states. Four transition systems have been assigned, namely, the [18.1](3)?(2)-X(3)?(2), the [18.3](3)?(3)-X(3)?(3), the [18.6]3- X(3)?(3), and the [19.0]2-X(3)?(2) systems. The bond length, r(o), of the X(3)?(3) state of CoB is determined to be 1.705 Å. The observed rotational lines showed unresolved hyperfine structure arising from the nuclei, which conforms to the Hund's case (a(?)) coupling scheme. This work represents the first experimental investigation of the CoB spectrum. PMID:22128936

Ng, Y W; Pang, H F; Cheung, A S-C

2011-11-28

345

Author's personal copy Ligand Binding Reduces Conformational Flexibility  

E-print Network

Author's personal copy Ligand Binding Reduces Conformational Flexibility in the Active Site loop is disordered and the general acid loop adopts an open conformation, placing the catalytic site experience motions on multiple timescales, consistent with a combination of conformational

Wood, Thomas K.

346

21 CFR 26.70 - Conformity assessment bodies.  

Code of Federal Regulations, 2010 CFR

...Conformity assessment bodies. 26.70 Section...DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ...MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND...Conformity assessment bodies. Each party recognizes...conformity assessment bodies (CAB's)...

2010-04-01

347

21 CFR 26.70 - Conformity assessment bodies.  

Code of Federal Regulations, 2013 CFR

...Conformity assessment bodies. 26.70 Section...DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ...MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND...Conformity assessment bodies. Each party recognizes...conformity assessment bodies (CAB's)...

2013-04-01

348

21 CFR 26.70 - Conformity assessment bodies.  

Code of Federal Regulations, 2011 CFR

...Conformity assessment bodies. 26.70 Section...DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ...MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND...Conformity assessment bodies. Each party recognizes...conformity assessment bodies (CAB's)...

2011-04-01

349

21 CFR 26.70 - Conformity assessment bodies.  

...Conformity assessment bodies. 26.70 Section...DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ...MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND...Conformity assessment bodies. Each party recognizes...conformity assessment bodies (CAB's)...

2014-04-01

350

21 CFR 26.70 - Conformity assessment bodies.  

Code of Federal Regulations, 2012 CFR

...Conformity assessment bodies. 26.70 Section...DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ...MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS, AND...Conformity assessment bodies. Each party recognizes...conformity assessment bodies (CAB's)...

2012-04-01

351

Atomic layer deposition of transition metals  

NASA Astrophysics Data System (ADS)

Atomic layer deposition (ALD) is a process for depositing highly uniform and conformal thin films by alternating exposures of a surface to vapours of two chemical reactants. ALD processes have been successfully demonstrated for many metal compounds, but for only very few pure metals. Here we demonstrate processes for the ALD of transition metals including copper, cobalt, iron and nickel. Homoleptic N,N'-dialkylacetamidinato metal compounds and molecular hydrogen gas were used as the reactants. Their surface reactions were found to be complementary and self-limiting, thus providing highly uniform thicknesses and conformal coating of long, narrow holes. We propose that these ALD layers grow by a hydrogenation mechanism that should also operate during the ALD of many other metals. The use of water vapour in place of hydrogen gas gives highly uniform, conformal films of metal oxides, including lanthanum oxide. These processes should permit the improved production of many devices for which the ALD process has previously not been applicable.

Lim, Booyong S.; Rahtu, Antti; Gordon, Roy G.

2003-11-01

352

Voltage-dependent conformational changes in connexin channels?  

PubMed Central

Channels formed by connexins display two distinct types of voltage-dependent gating, termed Vj- or fast-gating and loop- or slow-gating. Recent studies, using metal bridge formation and chemical cross-linking have identified a region within the channel pore that contributes to the formation of the loop-gate permeability barrier. The conformational changes are remarkably large, reducing the channel pore diameter from 15 to 20 Å to less than 4 Å. Surprisingly, the largest conformational change occurs in the most stable region of the channel pore, the 310 or parahelix formed by amino acids in the 42–51 segment. The data provide a set of positional constraints that can be used to model the structure of the loop-gate closed state. Less is known about the conformation of the Vj-gate closed state. There appear to be two different mechanisms; one in which conformational changes in channel structure are linked to a voltage sensor contained in the N-terminus of Cx26 and Cx32 and a second in which the C-terminus of Cx43 and Cx40 may act either as a gating particle to block the channel pore or alternatively to stabilize the closed state. The later mechanismutilizes the same domains as implicated in effecting pH gating of Cx43 channels. It is unclear if the two Vj-gating mechanisms are related or if they represent different gating mechanisms that operate separately in different subsets of connexin channels. A model of the Vj-closed state of Cx26 hemichannel that is based on the X-ray structure of Cx26 and electron crystallographic structures of a Cx26 mutation suggests that the permeability barrier for Vj-gating is formed exclusively by the N-terminus, but recent information suggests that this conformation may not represent a voltage-closed state. Closed state models are considered from a thermodynamic perspective based on information from the 3.5 Å Cx26 crystal structure and molecular dynamics (MD) simulations. The applications of computational and experimental methods to define the path of allosteric molecular transitions that link the open and closed states are discussed. This article is part of a Special Issue entitled: The communicating junctions, composition, structure and functions. PMID:21978595

Bargiello, Thaddeus A.; Tang, Qingxiu; Oh, Seunghoon; Kwon, Taekyung

2011-01-01

353

[Conformational-functional relationships of tetragastrin analogs].  

PubMed

Sets of low-energy backbone conformations of the active tetragastrin analogue Boc-Trp-Leu-Asp-Phe-NH2 and two competitive antagonists Boc-Trp-Leu psi (CH2NH)-Asp-Phe-NH2 and Boc-Trp-Leu-Asp-O-CH2-CH2-C6H5 were obtained using theoretical conformational analysis methods. Groups of the conformations were selected for the three analogues, allowing a spatial matching of Trp, Asp and Phe residues responsible for the gastrin receptor binding. Three conformations possessing the lowest energies among the geometrically similar structures of these three peptides are suggested as a model for the "receptor-bound" conformations of these analogues. Backbone spatial folding resembling an alpha-helix turn is characteristic of these conformations. The correspondence of the proposed model to the available data on structure--activity relationships for tetragastrin analogues is discussed. Orientations of the putative receptor-bound conformations in a "water--lypophylic medium" two-phase system were investigated. PMID:1768290

Nikiforovich, G V; Liepinia, I T; Tse?tin, V M; Shenderovich, M D; Galaktionov, S G

1991-05-01

354

Utilizing conformational changes for patterning thin films of recombinant spider silk proteins.  

PubMed

Recombinant spider silk proteins mimicking the properties of dragline silk proteins represent a class of materials that hold great potential for future high-performance applications. Here we explore the self-assembly behavior of a recombinantly produced spider silk protein based on the dragline silk of the Araneus diadematus , eADF4 (C16), by selectively patterning its secondary structure using capillary transfer lithography and solvent-assisted microcontact molding. Two conformational transitions were observed, influenced by initial solvent composition: ?-helix/random coil conformation to a more densely packed ?-sheet conformation (by casting from 1,1,1,3,3,3-hexafluoro-propanol) and moderate initial ?-sheet content to higher ?-sheet content (casting from formic acid). Furthermore, by using the solvent-assisted microcontact molding technique, we were able to achieve a submicrometer spatial resolution and reveal fine details of morphological and mechanical changes in patterned regions and at interfaces. PMID:22947370

Young, Seth L; Gupta, Maneesh; Hanske, Christoph; Fery, Andreas; Scheibel, Thomas; Tsukruk, Vladimir V

2012-10-01

355

Autophosphorylation Activity of a Soluble Hexameric Histidine Kinase Correlates with the Shift in Protein Conformational Equilibrium  

PubMed Central

Summary In a commonly accepted model, in response to stimuli, bacterial histidine kinases undergo a conformational transition between an active and inactive form. Structural information on histidine kinases is limited. By using ion mobility-mass spectrometry (IM-MS), we demonstrate an exchange between two conformational populations of histidine kinase ExsG that are linked to different levels of kinase activity. ExsG is an atypical signaling protein that incorporates an uncommon histidine kinase catalytic core at the C terminus preceded by an N-terminal “receiver domain” that is normally associated with the response regulator proteins in two-component signal transduction systems. IM-MS analysis and enzymatic assays indicate that phosphorylation of the ExsG receiver domain stabilizes the “compact” form of the protein and inhibits kinase core activity; in contrast, nucleotide binding required for kinase activity is associated with the more open conformation of ExsG. PMID:24210218

Wojnowska, Marta; Yan, Jun; Sivalingam, Ganesh N.; Cryar, Adam; Gor, Jayesh; Thalassinos, Konstantinos; Djordjevic, Snezana

2013-01-01

356

How many conformations can a protein remember?  

PubMed

We show that a protein can be trained to recognize multiple conformations, analogous to an associative memory, and provide capacity calculations based on energy fluctuations and information theory. Unlike the linear capacity of a Hopfield network, the number of conformations which can be remembered by a protein sequence depends on the size of the amino acid alphabet as lnA, independent of protein length. This admits the possibility of certain proteins, such as prions, evolving to fold to independent stable conformations, as well as novel possibilities for protein and heteropolymer design. PMID:11690459

Fink, T M; Ball, R C

2001-11-01

357

Tabu search based strategies for conformational search.  

PubMed

This paper presents an application of the new nonlinear global optimization routine gradient only tabu search (GOTS) to conformational search problems. It is based on the tabu search strategy which tries to determine the global minimum of a function by the steepest descent-modest ascent strategy. The refinement of ranking procedure of the original GOTS method and the exploitation of simulated annealing elements are described, and the modifications of the GOTS algorithm necessary to adopt it to conformation searches are explained. The utility of the GOTS for conformational search problems is tested using various examples. PMID:19769347

Stepanenko, Svetlana; Engels, Bernd

2009-10-29

358

Tabu Search Based Strategies for Conformational Search  

NASA Astrophysics Data System (ADS)

This paper presents an application of the new nonlinear global optimization routine gradient only tabu search (GOTS) to conformational search problems. It is based on the tabu search strategy which tries to determine the global minimum of a function by the steepest descent-modest ascent strategy. The refinement of ranking procedure of the original GOTS method and the exploitation of simulated annealing elements are described, and the modifications of the GOTS algorithm necessary to adopt it to conformation searches are explained. The utility of the GOTS for conformational search problems is tested using various examples.

Stepanenko, Svetlana; Engels, Bernd

2009-09-01

359

Decoding the geometry of conformal field theories  

E-print Network

To certain geometries, string theory associates conformal field theories. We discuss techniques to perform the reverse procedure: To recover geometrical data from abstractly defined conformal field theories. This is done by introducing appropriate notions of limits of conformal field theories and their degenerations, and by applying techniques from noncommutative geometry. This note is a summary of our work hep-th/0308143 , aimed to be less technical than the original paper, along with some new calculations confirming our interpretation of the rescaled limiting zero mode of the Virasoro field.

Daniel Roggenkamp; Katrin Wendland

2008-03-05

360

On conformal conic mappings of spherical domains.  

PubMed

The problem of the generation of homogeneous grids for spherical domains is considered in the class of conformal conic mappings. The equivalence between secant and tangent projections is shown and splitting the set of conformal conic mappings into equivalence classes is presented. The problem of minimization of the mapping factor variation is solved in the class of conformal conic mappings. Obtained results can be used in applied sciences, such as geophysical fluid dynamics and cartography, where the flattening of the Earth surface is required. PMID:24558337

Bourchtein, Andrei; Bourchtein, Ludmila

2014-01-01

361

Matching univalent functions and conformal welding  

E-print Network

Given a conformal mapping $f$ of the unit disk $\\mathbb D$ onto a simply connected domain $D$ in the complex plane bounded by a closed Jordan curve, we consider the problem of constructing a matching conformal mapping, i.e., the mapping of the exterior of the unit disk $\\mathbb D^*$ onto the exterior domain $D^*$ regarding to $D$. The answer is expressed in terms of a linear differential equation with a driving term given as the kernel of an operator dependent on the original mapping $f$. Examples are provided. This study is related to the problem of conformal welding and to representation of the Virasoro algebra in the space of univalent functions.

Erlend Grong; Pavel Gumenyuk; Alexander Vasil'ev

2008-06-05

362

Matching univalent functions and conformal welding  

E-print Network

Given a conformal mapping $f$ of the unit disk $\\mathbb D$ onto a simply connected domain $D$ in the complex plane bounded by a closed Jordan curve, we consider the problem of constructing a matching conformal mapping, i.e., the mapping of the exterior of the unit disk $\\mathbb D^*$ onto the exterior domain $D^*$ regarding to $D$. The answer is expressed in terms of a linear differential equation with a driving term given as the kernel of an operator dependent on the original mapping $f$. Examples are provided. This study is related to the problem of conformal welding and to representation of the Virasoro algebra in the space of univalent functions.

Grong, Erlend; Vasil'ev, Alexander

2008-01-01

363

On Conformal Conic Mappings of Spherical Domains  

PubMed Central

The problem of the generation of homogeneous grids for spherical domains is considered in the class of conformal conic mappings. The equivalence between secant and tangent projections is shown and splitting the set of conformal conic mappings into equivalence classes is presented. The problem of minimization of the mapping factor variation is solved in the class of conformal conic mappings. Obtained results can be used in applied sciences, such as geophysical fluid dynamics and cartography, where the flattening of the Earth surface is required. PMID:24558337

Bourchtein, Ludmila

2014-01-01

364

Conformation sensitive charge transport in conjugated polymers  

SciTech Connect

Temperature dependent charge carrier mobility measurements using field effect transistors and density functional theory calculations are combined to show how the conformation dependent frontier orbital delocalization influences the hole- and electron mobilities in a donor-acceptor based polymer. A conformationally sensitive lowest unoccupied molecular orbital results in an electron mobility that decreases with increasing temperature above room temperature, while a conformationally stable highest occupied molecular orbital is consistent with a conventional hole mobility behavior and also proposed to be one of the reasons for why the material works well as a hole transporter in amorphous bulk heterojunction solar cells.

Mattias Andersson, L., E-mail: matan@ifm.liu.se [Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping SE-581 83 (Sweden); Hedström, Svante; Persson, Petter [Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund (Sweden)] [Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund (Sweden)

2013-11-18

365

Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules  

NASA Astrophysics Data System (ADS)

Fluorescence correlation spectroscopy (FCS) of fluorescence resonant energy transfer (FRET) on immobilized individual fluorophores was used to study the Mg2+-facilitated conformational change of an RNA three-helix junction, a structural element that initiates the folding of the 30S ribosomal subunit. Transitions of the RNA junction between open and folded conformations resulted in fluctuations in fluorescence by FRET. Fluorescence fluctuations occurring between two FRET states on the millisecond time scale were found to be dependent on Mg2+ and Na+ concentrations. Correlation functions of the fluctuations were used to determine transition rates between the two conformations as a function of Mg2+ or Na+ concentration. Both the opening and folding rates were found to vary with changing salt conditions. Assuming specific binding of divalent ions to RNA, the Mg2+ dependence of the observed rates cannot be explained by conformational change induced by Mg2+ binding/unbinding, but is consistent with a model in which the intrinsic conformational change of the RNA junction is altered by uptake of Mg2+ ion(s). This version of FCS/FRET on immobilized single molecules is demonstrated to be a powerful technique in the study of conformational dynamics of biomolecules over time scales ranging from microseconds to seconds.

Kim, Harold D.; Nienhaus, G. Ulrich; Ha, Taekjip; Orr, Jeffrey W.; Williamson, James R.; Chu, Steven

2002-04-01

366

Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules.  

PubMed

Fluorescence correlation spectroscopy (FCS) of fluorescence resonant energy transfer (FRET) on immobilized individual fluorophores was used to study the Mg2+-facilitated conformational change of an RNA three-helix junction, a structural element that initiates the folding of the 30S ribosomal subunit. Transitions of the RNA junction between open and folded conformations resulted in fluctuations in fluorescence by FRET. Fluorescence fluctuations occurring between two FRET states on the millisecond time scale were found to be dependent on Mg2+ and Na+ concentrations. Correlation functions of the fluctuations were used to determine transition rates between the two conformations as a function of Mg2+ or Na+ concentration. Both the opening and folding rates were found to vary with changing salt conditions. Assuming specific binding of divalent ions to RNA, the Mg2+ dependence of the observed rates cannot be explained by conformational change induced by Mg2+ binding/unbinding, but is consistent with a model in which the intrinsic conformational change of the RNA junction is altered by uptake of Mg2+ ion(s). This version of FCS/FRET on immobilized single molecules is demonstrated to be a powerful technique in the study of conformational dynamics of biomolecules over time scales ranging from microseconds to seconds. PMID:11929999

Kim, Harold D; Nienhaus, G Ulrich; Ha, Taekjip; Orr, Jeffrey W; Williamson, James R; Chu, Steven

2002-04-01

367

Single molecule conformational memory extraction: p5ab RNA hairpin.  

PubMed

Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others. PMID:24898871

Pressé, Steve; Peterson, Jack; Lee, Julian; Elms, Phillip; MacCallum, Justin L; Marqusee, Susan; Bustamante, Carlos; Dill, Ken

2014-06-19

368

Modeling the solid-liquid phase transition in saturated triglycerides  

NASA Astrophysics Data System (ADS)

We investigated theoretically two competing published scenarios for the melting transition of the triglyceride trilaurin (TL): those of (1) Corkery et al. [Langmuir 23, 7241 (2007)], in which the average state of each TL molecule in the liquid phase is a discotic "Y" conformer whose three chains are dynamically twisted, with an average angle of ˜120° between them, and those of (2) Cebula et al. [J. Am. Oil Chem. Soc. 69, 130 (1992)], in which the liquid-state conformation of the TL molecule in the liquid phase is a nematic h?-conformer whose three chains are in a modified "chair" conformation. We developed two competing models for the two scenarios, in which TL molecules are in a nematic compact-chair (or "h") conformation, with extended, possibly all-trans, chains at low-temperatures, and in either a Y conformation or an h? conformation in the liquid state at temperatures higher than the phase-transition temperature, T?=319 K. We defined an h-Y model as a realization of the proposal of Corkery et al. [Langmuir 23, 7241 (2007)], and explored its predictions by mapping it onto an Ising model in a temperature-dependent field, performing a mean-field approximation, and calculating the transition enthalpy ?H. We found that the most plausible realization of the h-Y model, as applied to the solid-liquid phase transition in TL, and likely to all saturated triglycerides, gave a value of ?H in reasonable agreement with the experiment. We then defined an alternative h-h? model as a realization of the proposal of Cebula et al. [J. Am. Oil Chem. Soc. 69, 130 (1992)], in which the liquid phase exhibits an average symmetry breaking similar to an h conformation, but with twisted chains, to see whether it could describe the TL phase transition. The h-h? model gave a value of ?H that was too small by a factor of ˜3-4. We also predicted the temperature dependence of the 1132 cm-1 Raman band for both models, and performed measurements of the ratios of three TL Raman bands in the temperature range of -20 °C?T ?90 °C. The experimental results were in accord with the predictions of the h-Y model and support the proposal of Corkery et al. [Langmuir 23, 7241 (2007)] that the liquid state is made up of molecules that are each, on average, in a Y conformation. Finally, we carried out computer simulations of minimal-model TLs in the liquid phase, and concluded that although the individual TL molecules are, on average, Y conformers, long-range discotic order is unlikely to exist.

Pink, David A.; Hanna, Charles B.; Sandt, Christophe; MacDonald, Adam J.; MacEachern, Ronald; Corkery, Robert; Rousseau, Dérick

2010-02-01

369

Transition Resources  

NSDL National Science Digital Library

This is a site for teachers that work with students with disabilities at the secondary level. This site is broken down into categories to help you with the transition aspect of the IEP. The categories are as follows: Employment/Training, For Students - Career Exploration and Profiles, Independent Living, Learning Styles & Trainings, Level 1 Assessments, Self-Determination, and Transition Resources. All of the resources included in this site are free! TRANSITION RESOURCES: 1.) Adult Career and Continuing Education Services (ACCES-VR) This website takes you directly to the ACCES-VR website, where you can find information about vocational rehabilitation and the referral process. 2,) Guide to Quality Individualized Education Program (IEP) Development and Implementation Created by the New York State Special Education Department to help answer questions regarding the New IEP. Great resource! Gives examples!! 3.) Indicator 13 Checklist Use this ...

Transition

2011-11-23

370

Non-conforming hybrid meshes for efficient 2-D wave propagation using the Discontinuous Galerkin Method  

NASA Astrophysics Data System (ADS)

We present a Discontinuous Galerkin finite element method using a high-order time integration technique for seismic wave propagation modelling on non-conforming hybrid meshes in two space dimensions. The scheme can be formulated to achieve the same approximation order in space and time and avoids numerical artefacts due to non-conforming mesh transitions or the change of the element type. A point-wise Gaussian integration along partially overlapping edges of adjacent elements is used to preserve the schemes accuracy while providing a higher flexibility in the problem-adapted mesh generation process. We describe the domain decomposition strategy of the parallel implementation and validate the performance of the new scheme by numerical convergence test and experiments with comparisons to independent reference solutions. The advantage of non-conforming hybrid meshes is the possibility to choose the mesh spacing proportional to the seismic velocity structure, which allows for simple refinement or coarsening methods even for regular quadrilateral meshes. For particular problems of strong material contrasts and geometrically thin structures, the scheme reduces the computational cost in the sense of memory and run-time requirements. The presented results promise to achieve a similar behaviour for an extension to three space dimensions where the coupling of tetrahedral and hexahedral elements necessitates non-conforming mesh transitions to avoid linking elements in form of pyramids.

Hermann, Verena; Käser, Martin; Castro, Cristóbal E.

2011-02-01

371

Conformational variation of the translocon enhancing chaperone SecDF.  

PubMed

The Sec translocon facilitates transportation of newly synthesized polypeptides from the cytoplasm to the lumen/periplasm across the phospholipid membrane. Although the polypeptide-conducting machinery is formed by the SecYEG-SecA complex in bacteria, its transportation efficiency is markedly enhanced by SecDF. A previous study suggested that SecDF assumes at least two conformations differing by a 120° rotation in the spatial orientation of the P1 head subdomain to the rigid base, and that the conformational dynamics plays a critical role in polypeptide translocation. Here we addressed this hypothesis by analyzing the 3D structure of SecDF using electron tomography and single particle reconstruction. Reconstruction of wt SecDF showed two major conformations; one resembles the crystal structure of full-length SecDF (F-form structure), while the other is similar to the hypothetical structural variant based on the crystal structure of the isolated P1 domain (I-form structure). The transmembrane domain of the I-form structure has a scissor like cleft open to the periplasmic side. We also report the structure of a double cysteine mutant designed to constrain SecDF to the I-form. This reconstruction has a protrusion at the periplasmic end that nicely fits the orientation of P1 in the I-from. These results provide firm evidence for the occurrence of the I-form in solution and support the proposed F- to I-transition of wt SecDF during polypeptide translocation. PMID:24368747

Mio, Kazuhiro; Tsukazaki, Tomoya; Mori, Hiroyuki; Kawata, Masaaki; Moriya, Toshio; Sasaki, Yoshikazu; Ishitani, Ryuichiro; Ito, Koreaki; Nureki, Osamu; Sato, Chikara

2014-09-01

372

Conformational changes of calmodulin upon Ca2+ binding studied with a microfluidic mixer  

PubMed Central

A microfluidic mixer is applied to study the kinetics of calmodulin conformational changes upon Ca2+ binding. The device facilitates rapid, uniform mixing by decoupling hydrodynamic focusing from diffusive mixing and accesses time scales of tens of microseconds. The mixer is used in conjunction with multiphoton microscopy to examine the fast Ca2+-induced transitions of acrylodan-labeled calmodulin. We find that the kinetic rates of the conformational changes in two homologous globular domains differ by more than an order of magnitude. The characteristic time constants are ?490 ?s for the transitions in the C-terminal domain and ?20 ms for those in the N-terminal domain of the protein. We discuss possible mechanisms for the two distinct events and the biological role of the stable intermediate, half-saturated calmodulin. PMID:18178620

Park, Hye Yoon; Kim, Sally A.; Korlach, Jonas; Rhoades, Elizabeth; Kwok, Lisa W.; Zipfel, Warren R.; Waxham, M. Neal; Webb, Watt W.; Pollack, Lois

2008-01-01

373

Conformal higher-order viscoelastic fluid mechanics  

E-print Network

We present a generally covariant formulation of conformal higher-order viscoelastic fluid mechanics with strain allowed to take arbitrarily large values. We give a general prescription to determine the dynamics of a relativistic viscoelastic fluid in a way consistent with the hypothesis of local thermodynamic equilibrium and the second law of thermodynamics. We then elaborately study the transient time scales at which the strain almost relaxes and becomes proportional to the gradients of velocity. We particularly show that a conformal second-order fluid with all possible parameters in the constitutive equations can be obtained without breaking the hypothesis of local thermodynamic equilibrium, if the conformal fluid is defined as the long time limit of a conformal second-order viscoelastic system. We also discuss how local thermodynamic equilibrium could be understood in the context of the fluid/gravity correspondence.

Masafumi Fukuma; Yuho Sakatani

2012-04-27

374

Hidden conformal symmetry of extremal black holes  

SciTech Connect

We study the hidden conformal symmetry of extremal black holes. We introduce a new set of conformal coordinates to write the SL(2,R) generators. We find that the Laplacian of the scalar field in many extremal black holes, including Kerr(-Newman), Reissner-Nordstrom, warped AdS{sub 3}, and null warped black holes, could be written in terms of the SL(2,R) quadratic Casimir. This suggests that there exist dual conformal field theory (CFT) descriptions of these black holes. From the conformal coordinates, the temperatures of the dual CFTs could be read directly. For the extremal black hole, the Hawking temperature is vanishing. Correspondingly, only the left (right) temperature of the dual CFT is nonvanishing, and the excitations of the other sector are suppressed. In the probe limit, we compute the scattering amplitudes of the scalar off the extremal black holes and find perfect agreement with the CFT prediction.

Chen Bin; Long Jiang; Zhang Jiaju [Department of Physics, and State Key Laboratory of Nuclear Physics Technology, and Center for High Energy Physics, Peking University, Beijing 100871 (China); Department of Physics, and State Key Laboratory of Nuclear Physics Technology, Peking University, Beijing 100871 (China)

2010-11-15

375

3D face recognition via conformal representation  

NASA Astrophysics Data System (ADS)

In this paper, we propose a 3D face recognition approach based on the conformal representation of facial surfaces. Firstly, facial surfaces are mapped onto the 2D unit disk by Riemann mapping. Their conformal representation (i.e. the pair of mean curvature (MC) and conformal factor (CF) ) are then computed and encoded to Mean Curvature Images (MCIs) and Conformal Factor Images (CFIs). Considering that different regions of face deform unequally due to expression variation, MCIs and CFIs are divided into five parts. LDA is applied to each part to obtain the feature vector. At last, five parts are fused on the distance level for recognition. Extensive experiments carried out on the BU-3DFE database demonstrate the effectiveness of the proposed approach.

Han, Junhui; Fang, Chi; Ding, Xiaoqing; Sun, Jian; Gu, Xianfeng D.

2014-03-01

376

Conformational electroresistance and hysteresis in nanoclusters.  

PubMed

The existence of multiple thermodynamically stable isomer states is one of the most fundamental properties of small clusters. This work shows that the conformational dependence of the Coulomb charging energy of a nanocluster leads to a giant electroresistance, where charging induced conformational distortion changes the blockade voltage. The intricate interplay between charging and conformation change is demonstrated in a nanocluster Zn3O4 by combining a first-principles calculation with a temperature-dependent transport model. The predicted hysteretic Coulomb blockade staircase in the current-voltage curve adds another dimension to the rich phenomena of tunneling electroresistance. The new mechanism provides a better controlled and repeatable platform to study conformational electroresistance. PMID:24987929

Li, Xiang-Guo; Zhang, X-G; Cheng, Hai-Ping

2014-08-13

377

Generalized Additivity in Unitary Conformal Field Theories  

E-print Network

It was demonstrated in recent work that $d=4$ unitary CFT's satisfy a special property: if a scalar operator with conformal dimension $\\Delta$ exists in the operator spectrum, then the conformal bootstrap demands that large spin primary operators have to exist in the operator spectrum of the CFT with a conformal twist close to $2\\Delta+2N$ for any integer $N$. In this paper the conformal bootstrap methods that were used to find the anomalous dimension of the $N=0$ operators have been generalized to find the anomalous dimension of all large spin operators of this class. In AdS these operators can be interpreted as the excited states of the product states of objects that were found in other works.

Gideon Vos

2014-11-28

378

Aluminized fiberglass insulation conforms to curved surfaces  

NASA Technical Reports Server (NTRS)

Layers of fiber glass with outer reflective films of vacuum-deposited aluminum or other reflective metal, provide thermal insulation which conforms to curved surfaces. This insulation has good potential for cryogenic systems.

1966-01-01

379

Supersymmetric Dualities beyond the Conformal Window  

SciTech Connect

Using the superconformal (SC) indices techniques, we construct Seiberg type dualities for N=1 supersymmetric field theories outside the conformal windows. These theories are physically distinguished by the presence of chiral superfields with small or negative R charges.

Spiridonov, V. P. [Bogoliubov Laboratory of Theoretical Physics, JINR, Dubna, Moscow Region 141980 (Russian Federation); Vartanov, G. S. [Max-Planck-Institut fuer Gravitationsphysik, Albert-Einstein-Institut 14476 Golm (Germany)

2010-08-06

380

Determination of cyclopeptide conformations in solution using NMR data and conformational energy calculations.  

PubMed

The three-dimensional structure of the cyclic analogs of bradykinin and substance P C-terminal hexapeptide was studied using conformational energy calculations. Initial conformations for energy minimization were selected with the aid of the measured intensities of local nuclear Overhauser effects (NOEs) and other 1H-NMR data. Expected values of the 1H-NMR parameters for low-energy conformations of the cyclopeptides were calculated and compared with those observed experimentally using semiquantitative gradation of NOE intensities. Several low-energy structures of the cyclic bradykinin analog, possessing similar backbone conformations stabilized by two beta-turns, are in agreement with experimental data. None of the low-energy conformations of the substance P cyclic hexapeptide were in satisfactory agreement with the experimental set of NOEs. The agreement was achieved only by averaging of the calculated 1H-NMR parameters over several combinations of the low-energy conformations. PMID:2466496

Shenderovich, M D; Nikiforovich, G V; Saulitis, J B; Chipens, G I

1988-08-01

381

Venus Transit  

NSDL National Science Digital Library

This is an activity about the Venus Transit and how it helped astronomers determine the scale of the solar system. Learners will use measurement, ratios, and graphing to construct a model of the solar system and determine the relationship of each planet to the Sun. They will explore the scales needed to represent the size of the planets and the distances to the Sun. This activity corresponds to the NASA CONNECT video, titled Venus Transit, and has supplemental questions to support the video viewing.

382

Metric transition  

NASA Technical Reports Server (NTRS)

This report describes NASA's metric transition in terms of seven major program elements. Six are technical areas involving research, technology development, and operations; they are managed by specific Program Offices at NASA Headquarters. The final program element, Institutional Management, covers both NASA-wide functional management under control of NASA Headquarters and metric capability development at the individual NASA Field Installations. This area addresses issues common to all NASA program elements, including: Federal, state, and local coordination; standards; private industry initiatives; public-awareness initiatives; and employee training. The concluding section identifies current barriers and impediments to metric transition; NASA has no specific recommendations for consideration by the Congress.

1992-01-01

383

Diffusion limited aggregation and iterated conformal maps  

Microsoft Academic Search

The creation of fractal clusters by diffusion limited aggregation (DLA) is studied by using iterated stochastic conformal maps following the method proposed recently by Hastings and Levitov. The object of interest is the function Phi(n) which conformally maps the exterior of the unit circle to the exterior of an n-particle DLA. The map Phi(n) is obtained from n stochastic iterations

Benny Davidovitch; H. G. Hentschel; Zeev Olami; Itamar Procaccia; Leonard M. Sander; Ellak Somfai

1999-01-01

384

On Useful Conformal Tranformations In General Relativity  

E-print Network

Local conformal transformations are known as a useful tool in various applications of the gravitational theory, especially in cosmology. We describe some new aspects of these transformations, in particular using them for derivation of Einstein equations for the cosmological and Schwarzschild metrics. Furthermore, the conformal transformation is applied for the dimensional reduction of the Gauss-Bonnet topological invariant in $d=4$ to the spaces of lower dimensions.

D. F. Carneiro; E. A. Freiras; B. Gonçalves; A. G. de Lima; I. L. Shapiro

2004-12-22

385

Some novel design techniques for conformal antennas  

Microsoft Academic Search

Design techniques for conformal antennas are presented including designs for dielectric-loaded cavity radiators quadrature parallel-plate antennas, integrated-random antennas, and edge-slot radiators. Working models designed for a variety of applications have been fabricated for operation in the frequency range from UHF to K-band. It is noted that aside from the weight and space saving features realized and the usage on conformal

H. S. Jones Jr.

1978-01-01

386

A Framework for Ethical Conformity in Marketing  

Microsoft Academic Search

The extant marketing literature provides little guidance for theory development or practice with regard to questions of ethical\\u000a conformity and the resulting market response. To begin to bridge this research gap, we advance a theoretical framework of\\u000a ethical conformity in marketing, appealing to marketing ethics, management strategy, and sociological foundations. We set\\u000a the stage for our theoretical arguments by considering

Kelly D. Martin; Jean L. Johnson

2008-01-01

387

Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation.  

PubMed

The universally conserved GTPase elongation factor G (EF-G) catalyzes the translocation of tRNA and mRNA on the ribosome after peptide bond formation. Despite numerous studies suggesting that EF-G undergoes extensive conformational rearrangements during translocation, high-resolution structures exist for essentially only one conformation of EF-G in complex with the ribosome. Here, we report four atomic-resolution crystal structures of EF-G bound to the ribosome programmed in the pre- and posttranslocational states and to the ribosome trapped by the antibiotic dityromycin. We observe a previously unseen conformation of EF-G in the pretranslocation complex, which is independently captured by dityromycin on the ribosome. Our structures provide insights into the conformational space that EF-G samples on the ribosome and reveal that tRNA translocation on the ribosome is facilitated by a structural transition of EF-G from a compact to an elongated conformation, which can be prevented by the antibiotic dityromycin. PMID:25594181

Lin, Jinzhong; Gagnon, Matthieu G; Bulkley, David; Steitz, Thomas A

2015-01-15

388

Effects of naturally occurring arginine 14 deletion on phospholamban conformational dynamics and membrane interactions.  

PubMed

Phospholamban (PLN) is a single-pass membrane protein that regulates the sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA). Phosphorylation of PLN at Ser16 reverses its inhibitory function under ?-adrenergic stimulation, augmenting Ca(2+) uptake in the sarcoplasmic reticulum and muscle contractility. PLN exists in two conformations; a T state, where the cytoplasmic domain is helical and adsorbed on the membrane surface, and an R state, where the cytoplasmic domain is unfolded and membrane detached. Previous studies have shown that the PLN conformational equilibrium is crucial to SERCA regulation. Here, we used a combination of solution and solid-state NMR to compare the structural topology and conformational dynamics of monomeric PLN (PLN(AFA)) with that of the PLN(R14del), a naturally occurring deletion mutant that is linked to the progression of dilated cardiomyopathy. We found that the behavior of the inhibitory transmembrane domain of PLN(R14del) is similar to that of the native sequence. Conversely, the conformational dynamics of R14del both in micelles and lipid membranes are enhanced. We conclude that the deletion of Arg14 in the cytoplasmic region weakens the interactions with the membrane and shifts the conformational equilibrium of PLN toward the disordered R state. This conformational transition is correlated with the loss-of-function character of this mutant and is corroborated by SERCA's activity assays. These findings support our hypothesis that SERCA function is fine-tuned by PLN conformational dynamics and begin to explain the aberrant regulation of SERCA by the R14del mutant. This article is part of a Special Issue entitled: NMR Spectroscopy for Atomistic Views of Biomembranes and Cell Surfaces. Guest Editors: Lynette Cegelski and David P. Weliky. PMID:25251363

Vostrikov, Vitaly V; Soller, Kailey J; Ha, Kim N; Gopinath, T; Veglia, Gianluigi

2015-01-01

389

Microwave, structural, conformational, vibrational studies and ab initio calculations of isocyanocyclopentane.  

PubMed

The infrared and Raman spectra (3200-50cm(-1)) of the gas, liquid or solution, and solid have been recorded of isocyanocyclopentane, c-C5H9NC. FT-microwave studies have also been carried out and 23 transitions were recorded for the envelope-axial (Ax) conformer. Variable temperature (-65 to -100°C) studies of the infrared spectra (3200-400cm(-1)) dissolved in liquid xenon have been carried out. From these data, both the Ax and envelope-equatorial (Eq) conformers have been identified and their relative stabilities obtained. The enthalpy difference has been determined to be 102±10cm(-1) (1.21±0.11kJmol(-1)) with the Ax conformer the more stable form. The percentage of the Eq conformer is estimated to be 38±1% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing several different basis sets up to aug-cc-pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been made for the observed bands for both conformers with initial predictions by MP2(full)/6-31G(d) ab initio calculations to obtain harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The structural parameter values for the Ax form are; for the heavy atom distances (Å): CN=1.176 (3); C?N=1.432 (3); C?C?,C?'=1.534 (3); C?C?,C?'=1.542 (3); C?C?'=1.554 (3) and angles (°):?C?NC=177.8 (5); ?C?C?N=110.4 (5); [Formula: see text] (5); ?C?C?C?=103.6 (5); [Formula: see text] (5). The results are discussed and compared to the corresponding properties of some related molecules. PMID:24480667

Durig, James R; Klaassen, Joshua J; Sawant, Dattatray K; Deodhar, Bhushan S; Panikar, Savitha S; Gurusinghe, Ranil M; Darkhalil, Ikhlas D; Tubergen, Michael J

2015-02-01

390

Triple-helix specific ligands stabilize H-DNA conformation.  

PubMed

Under superhelical stress, oligopurine-oligopyrimidine mirror-repeat sequences are able to adopt H-DNA conformations where a triple-helical and a single-stranded structure co-exist. We have previously shown that a benzo[e]pyridoindole derivative (BePI), an antitumor drug interacting more tightly with triplex than with duplex DNA, strongly stabilizes intermolecular triple helices formed upon binding of homopyrimidine oligonucleotides to the major groove of double-stranded DNA at oligopurine-oligopyrimidine sequences. Here we show that an intramolecular triple helix is also strongly stabilized by this ligand. In vitro elongation performed by different DNA polymerases (bacteriophage T7, Escherichia coli or Taq polymerase) could be irreversibly inhibited by the H-DNA structure in the presence of BePI. A mirror-repeat polypurine-polypyrimidine sequence inserted between the E. coli beta-lactamase gene (conferring ampicillin resistance) and its bla promoter strongly inhibited transcription of the beta-lactamase gene in vivo. In the absence of supercoiling, transition to the H-conformation did not occur, but BePI stabilized the H-DNA structure induced by supercoiling as shown by chemical probes (chloroacetaldehyde). The results presented here open a new field of investigation for antitumor agents targeted to a novel class of genetic structures able to regulate gene expression. PMID:7723037

Duval-Valentin, G; de Bizemont, T; Takasugi, M; Mergny, J L; Bisagni, E; Hélène, C

1995-04-14

391

Rapid roll inflation with conformal coupling  

SciTech Connect

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-D3 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. S{sup 3} of Klebanov-Strassler (KS) geometry) have solutions identical to conformally coupled modes and also cannot be responsible for cosmological fluctuations. We discuss other possibilities.

Kofman, Lev [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George st., Toronto, ON M5S 3H8 (Canada); Mukohyama, Shinji [Department of Physics and Research Center for the Early Universe, University of Tokyo, Tokyo 113-0033 (Japan)

2008-02-15

392

Rapid roll Inflation with Conformal Coupling  

E-print Network

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-anti D3 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. S^3 of KS geometry) have solutions identical to conformally coupled modes and also cannot be responsible for cosmological fluctuations. We discuss other possibilities.

Lev Kofman; Shinji Mukohyama

2007-09-13

393

Rapid roll inflation with conformal coupling  

NASA Astrophysics Data System (ADS)

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.

Kofman, Lev; Mukohyama, Shinji

2008-02-01

394

Conformation-specific crosslinking of mitochondrial complex I.  

PubMed

Complex I is the only component of the eukaryotic respiratory chain of which no high-resolution structure is yet available. A notable feature of mitochondrial complex I is the so-called active/de-active conformational transition of the idle enzyme from the active (A) to the de-active, (D) form. Using an amine- and sulfhydryl-reactive crosslinker of 6.8Å length (SPDP) we found that in the D-form of complex I the ND3 subunit crosslinked to the 39 kDa (NDUFA9) subunit. These proteins could not be crosslinked in the A-form. Most likely, both subunits are closely located in the critical junction region connecting the peripheral hydrophilic domain to the membrane arm of the enzyme where the entrance path for substrate ubiquinone is and where energy transduction takes place. PMID:23454639

Ciano, Margherita; Fuszard, Matthew; Heide, Heinrich; Botting, Catherine H; Galkin, Alexander

2013-04-01

395

75 FR 29537 - Draft Transportation Conformity Guidance for Quantitative Hot-spot Analyses in PM2.5  

Federal Register 2010, 2011, 2012, 2013

...Transportation Conformity Guidance for Quantitative Hot- spot Analyses in PM 2.5 and PM...quantitative PM 2.5 and PM 10 hot-spot analyses for project- level transportation...certain highway and transit projects. A hot-spot analysis includes an estimation...

2010-05-26

396

ATP-induced conformational changes in Hsp70: molecular dynamics and experimental validation of an in silico predicted conformation.  

PubMed

The 70 kDa heat shock proteins (Hsp70s) play important roles in preventing the misfolding of proteins and repairing damage under stress by coupling ATP binding and hydrolysis to protein substrate release and binding, respectively. ATP binding is believed to induce closing of the Hsp70 nucleotide binding domain (NBD) around the nucleotide. We report here a combined computational-experimental study of this open-closed transition. All-atom molecular dynamics simulations were performed for isolated open state NBDs with and without bound ATP. The nucleotide-free NBD samples a wide range of open configurations exhibiting flexible rearrangements of its four subdomains (IA-IIB). In contrast, the ATP-bound Hsp70 NBD closes to a range of configurations that is substantially more closed than the conformation observed in crystals of ATP-complexed NBDs. The close approach of subdomains IB and IIB observed in the simulations results in a strong coordination of the fluorescence probe Trp90 of IB with Arg261 of IIB, a feature not seen in the crystal structures. To determine if this computationally observed conformation occurs in solution, we constructed an R261A mutant. The mutation was found to increase the K(m) and k(cat) for ATP and to significantly reduce the extent of the fluorescence quench observed upon ATP binding. Our results thus account for the previously unexplained ATP-driven change in Trp90 fluorescence seen in the isolated NBD. PMID:19883127

Woo, Hyung-June; Jiang, Jianwen; Lafer, Eileen M; Sousa, Rui

2009-12-01

397

Characterization of Monomeric Intermediates during VSV Glycoprotein Structural Transition  

PubMed Central

Entry of enveloped viruses requires fusion of viral and cellular membranes, driven by conformational changes of viral glycoproteins. Crystal structures provide static pictures of pre- and post-fusion conformations of these proteins but the transition pathway remains elusive. Here, using several biophysical techniques, including analytical ultracentrifugation, circular dichroïsm, electron microscopy and small angle X-ray scattering, we have characterized the low-pH-induced fusogenic structural transition of a soluble form of vesicular stomatitis virus (VSV) glycoprotein G ectodomain (Gth, aa residues 1–422, the fragment that was previously crystallized). While the post-fusion trimer is the major species detected at low pH, the pre-fusion trimer is not detected in solution. Rather, at high pH, Gth is a flexible monomer that explores a large conformational space. The monomeric population exhibits a marked pH-dependence and adopts more elongated conformations when pH decreases. Furthermore, large relative movements of domains are detected in absence of significant secondary structure modification. Solution studies are complemented by electron micrographs of negatively stained viral particles in which monomeric ectodomains of G are observed at the viral surface at both pH 7.5 and pH 6.7. We propose that the monomers are intermediates during the conformational change and thus that VSV G trimers dissociate at the viral surface during the structural transition. PMID:22383886

Albertini, Aurélie A.; Mérigoux, Cécile; Libersou, Sonia; Madiona, Karine; Bressanelli, Stéphane; Roche, Stéphane; Lepault, Jean; Melki, Ronald; Vachette, Patrice; Gaudin, Yves

2012-01-01

398

Modeling the liquid-solid transition in saturated triglycerides  

NASA Astrophysics Data System (ADS)

Corkery et al. have proposed that the high-temperature state of the triglyceride trilaurin (TL) is a Y-conformer, in which the three hydrocarbon chains are dynamically twisted with an average angle of ˜120 between them. Using computer simulations, we first show that the high-temperature state is indeed the Y conformation. We then develop a theory of the liquid-solid transition of this system, in which TL molecules are in a chair (h) conformation, with extended, possibly all-trans, chains at low-temperatures, and are in a Y conformation in the liquid phase at temperatures higher than the transition temperature, T* 319K. We map this ``h-Y model'' onto an Ising model in a temperature-dependent field, perform a mean-field approximation, and calculate the transition enthalpy, which is in good agreement with experiment. We also predict the temperature-dependence of the 1132 cm-1 Raman band. Our results support the proposal that the liquid state is made up of molecules in the Y conformation.

Hanna, C. B.; Pink, D. A.; MacDonald, A. J.; Thillainadarajah, K.; Corkery, R.; Rousseau, D.

2007-03-01

399

Cation-specific conformational behavior of polyelectrolyte brushes: from aqueous to nonaqueous solvent.  

PubMed

We have investigated changes in the cation-specific conformational behavior of poly(sodium styrenesulfonate) (PSS) brushes as the solvent changes from water to methanol using a quartz crystal microbalance with dissipation (QCM-D). A solvation to desolvation transition of the grafted chains accompanied by swelling to the collapse transition of the brushes is observed for Na(+). In the case of Cs(+), the brushes undergo solvation to desolvation to resolvation accompanied by swelling to collapse to reswelling transitions. The resolvation and reswelling transitions for Cs(+) are induced by the charge inversion of the brushes via van der Waals interactions between Cs(+) and the brushes. All of the transitions for monovalent cations become less obvious as the methanol content increases. For divalent Ca(2+) and trivalent La(3+), a solvation to desolvation to resolvation transition of the grafted chains accompanied by a swelling to collapse to reswelling transition of the brushes can be observed. The resolvation and reswelling of the brushes for the multivalent cations are induced by the charge inversion of the brushes via charge-image charge interactions. The extent of the transitions for the PSS brushes in the presence of multivalent cations is only slightly influenced by the methanol content. PMID:25300430

Wang, Tao; Long, Yunchao; Liu, Lvdan; Wang, Xiaowen; Craig, Vincent S J; Zhang, Guangzhao; Liu, Guangming

2014-11-01

400

Hawking-Page phase transition on the brane  

SciTech Connect

We show that the Hawking-Page phase transition of a conformal field theory on AdS{sub d-1} weakly coupled to gravity has a dual bulk description in terms of a phase transition between a black string and a thermal gas on AdS{sub d}. At even lower temperatures the black string develops a Gregory Laflamme instability, which is dual to black hole evaporation in the boundary theory.

Chamblin, A. [Department of Physics, University of Louisville, Louisville, Kentucky 40292 (United States); Karch, A. [Department of Physics, University of Washington, Seattle, Washington 98195-1560 (United States)

2005-09-15

401

Cyclic Constraints on Conformational Flexibility in ?-PEPTIDES: Conformation-Specific IR and UV Spectroscopy  

NASA Astrophysics Data System (ADS)

Spectroscopic studies of flexible peptides in the gas phase can provide insight to their inherent structural preferences in the absence of solvent. Recently, there has been increased attention paid to synthetic foldamers containing non-natural residues that can be specifically engineered to robustly form particular secondary structures. These engineered peptides have potential in therapeutic drug design because they are resistant to enzymatic degradation. Specifically, the Gellman group has synthesized a ?-peptide with a six membered cyclic constraint in the ?^{4}-?^{3} position and an ethyl group at the ?^{2} position (?_{ACHC}). The three stereocenters have a well-defined chirality [S,S,S]. These two features constrain the relative orientation of adjacent amide groups, thereby favoring a particular "pitch" to the turn. Solution phase results indicate that constrained ?-peptides induce the formation of a 14-helix. Ac-?_{ACHC}-NHBz, its monohydrate and Ac-?_{ACHC}-?_{ACHC}-NHBz have been studied using ultraviolet (UV) and infrared (IR) double-resonance methods to obtain conformation-specific spectra under jet-cooled conditions in the gas phase. IR spectra in the hydride stretch (3300-3750 cm^{-1}), amide I/II and OH bend (1400-1800 cm^{-1}) were recorded and compared to predictions using density functional methods (DFT) and harmonic frequency calculations. We will compare the present results on constrained ?-peptides with corresponding results on unconstrained analogs. Data obtained for the monohydrated water cluster of Ac-?_{ACHC}-NHBz will also be presented, including assignment of the water bend fundamental, which appears in the midst of transitions due to the amide II vibrations. L. Guo, W. Zhang, A. G. Reidenbach, M. W. Giuliano, I. A. Guzei, L. C. Spencer and S. H. Gellman Angew. Chem. Int. Ed. 2011, 50, 5843-5846

Walsh, Patrick S.; Kusaka, Ryoji; Zwier, Timothy S.; Fisher, Brian F.; Gellman, Samuel H.

2013-06-01

402

Anomalous dimensions of leading twist conformal operators  

NASA Astrophysics Data System (ADS)

We extend and develop a method for perturbative calculations of anomalous dimensions and mixing matrices of leading twist conformal primary operators in conformal field theories. Such operators lie on the unitarity bound and hence are conserved (irreducible) in the free theory. The technique relies on the known pattern of breaking of the irreducibility conditions in the interacting theory. We relate the divergence of the conformal operators via the field equations to their descendants involving an extra field and accompanied by an extra power of the coupling constant. The ratio of the two-point functions of descendants and of their primaries determines the anomalous dimension, allowing us to gain an order of perturbation theory. We demonstrate the efficiency of the formalism on the lowest-order analysis of anomalous dimensions and mixing matrices which is required for two-loop calculations of the former. We compare these results to another method based on anomalous conformal Ward identities and constraints from the conformal algebra. It also permits us to gain a perturbative order in computations of mixing matrices. We show the complete equivalence of both approaches.

Belitsky, A. V.; Henn, J.; Jarczak, C.; Müller, D.; Sokatchev, E.

2008-02-01

403

A conformal field theory for eternal inflation?  

NASA Astrophysics Data System (ADS)

We study a statistical model defined by a conformally invariant distribution of overlapping spheres in arbitrary dimension d. The model arises as the asymptotic distribution of cosmic bubbles in d+1 dimensional de Sitter space, and also as the asymptotic distribution of bubble collisions with the domain wall of a fiducial ``observation bubble'' in d+2 dimensional de Sitter space. In this note we calculate the 2-, 3-, and 4-point correlation functions of exponentials of the ``bubble number operator'' analytically in d = 2. We find that these correlators are free of infrared divergences, covariant under the global conformal group, charge conserving, and transform with positive conformal dimensions that are related in a novel way to the charge. Although by themselves these operators probably do not define a full-fledged conformal field theory, one can use the partition function on a sphere to compute an approximate central charge in the 2D case. The theory in any dimension has a noninteracting limit when the nucleation rate of the bubbles in the bulk is very large. The theory in two dimensions is related to some models of continuum percolation, but it is conformal for all values of the tunneling rate.

Freivogel, Ben; Kleban, Matthew

2009-12-01

404

Global attractors of complete conformal foliations  

SciTech Connect

We prove that every complete conformal foliation (M,F) of codimension q{>=}3 is either Riemannian or a (Conf(S{sup q}), S{sup q})-foliation. We further prove that if (M,F) is not Riemannian, it has a global attractor which is either a nontrivial minimal set or a closed leaf or a union of two closed leaves. In this theorem we do not assume that the manifold M is compact. In particular, every proper conformal non-Riemannian foliation (M,F) has a global attractor which is either a closed leaf or a union of two closed leaves, and the space of all nonclosed leaves is a connected q-dimensional orbifold. We show that every countable group of conformal transformations of the sphere S{sup q} can be realized as the global holonomy group of a complete conformal foliation. Examples of complete conformal foliations with exceptional and exotic minimal sets as global attractors are constructed. Bibliography: 20 titles.

Zhukova, Nina I [N.I. Lobachevsky Nizhni Novgorod State University, Nizhnii Novgorod (Russian Federation)

2012-03-31

405

Arcjet Testing of Advanced Conformal Ablative TPS  

NASA Technical Reports Server (NTRS)

A conformable TPS over a rigid aeroshell has the potential to solve a number of challenges faced by traditional rigid TPS materials (such as tiled Phenolic Impregnated Carbon Ablator (PICA) system on MSL. The compliant (high strain to failure) nature of the conformable ablative materials will allow integration of the TPS with the underlying aeroshell structure much easier and enable monolithic-like configuration and larger segments (or parts) to be used. In May of 2013 the CA250 project executed an arcjet test series in the Ames IHF facility to evaluate a phenolic-based conformal system (named Conformal-PICA) over a range of test conditions from 40-400Wcm2. The test series consisted of four runs in the 13-inch diameter nozzle. Test models were based on SPRITE configuration (a 55-deg sphere cone), as it was able to provide a combination of required heat flux, pressure and shear within a single entry. The preliminary in-depth TC data acquired during that test series allowed a mid-fidelity thermal response model for conformal-PICA to be created while testing of seam models began to address TPS attachment and joining of multiple segments for future fabrication of large-scale aeroshells. Discussed in this paper are the results.

Gasch, Matthew; Beck, Robin; Agrawal, Parul

2014-01-01

406

Conformal anomaly of super Wilson loop  

NASA Astrophysics Data System (ADS)

Classically supersymmetric Wilson loop on a null polygonal contour possesses all symmetries required to match it onto non-MHV amplitudes in maximally supersymmetric Yang-Mills theory. However, to define it quantum mechanically, one is forced to regularize it since perturbative loop diagrams are not well defined due to presence of ultraviolet divergences stemming from integration in the vicinity of the cusps. A regularization that is adopted by practitioners by allowing one to use spinor helicity formalism, on the one hand, and systematically go to higher orders of perturbation theory is based on a version of dimensional regularization, known as Four-Dimensional Helicity scheme. Recently it was demonstrated that its use for the super Wilson loop at one loop breaks both conformal symmetry and Poincaré supersymmetry. Presently, we exhibit the origin for these effects and demonstrate how one can undo this breaking. The phenomenon is alike the one emerging in renormalization group mixing of conformal operators in conformal theories when one uses dimensional regularization. The rotation matrix to the diagonal basis is found by means of computing the anomaly in the Ward identity for the conformal boost. Presently, we apply this ideology to the super Wilson loop. We compute the one-loop conformal anomaly for the super Wilson loop and find that the anomaly depends on its Grassmann coordinates. By subtracting this anomalous contribution from the super Wilson loop we restore its interpretation as a dual description for reduced non-MHV amplitudes which are expressed in terms of superconformal invariants.

Belitsky, A. V.

2012-09-01

407

Statistical Mechanics and Shape Transitions in Microscopic Plates  

NASA Astrophysics Data System (ADS)

Unlike macroscopic multistable mechanical systems such as snap bracelets or elastic shells that must be physically manipulated into various conformations, microscopic systems can undergo spontaneous conformation switching between multistable states due to thermal fluctuations. Here we investigate the statistical mechanics of shape transitions in small elastic elliptical plates and shells driven by noise. By assuming that the effects of edges are small, which we justify exactly for plates and shells with a lenticular section, we decompose the shapes into a few geometric modes whose dynamics are easy to follow. We use Monte Carlo simulations to characterize the shape transitions between conformational minimal as a function of noise strength, and corroborate our results using a Fokker-Planck formalism to study the stationary distribution and the mean first passage time problem. Our results are applicable to objects such as graphene flakes or protein ? sheets, where fluctuations, geometry, and finite size effects are important.

Yong, Ee Hou; Mahadevan, L.

2014-01-01

408

The conformal method and the conformal thin-sandwich method are the same  

NASA Astrophysics Data System (ADS)

The conformal method developed in the 1970s and the more recent Lagrangian and Hamiltonian conformal thin-sandwich methods are techniques for finding solutions of the Einstein constraint equations. We show that they are manifestations of a single conformal method: there is a straightforward way to convert back and forth between the parameters for these methods so that the corresponding solutions of the Einstein constraint equations agree. The unifying idea is the need to clearly distinguish tangent and cotangent vectors to the space of conformal classes on a manifold, and we introduce a vocabulary for working with these objects without reference to a particular representative background metric. As a consequence of these conceptual advantages, we demonstrate how to strengthen previous near-CMC (constant mean curvature) existence and non-existence theorems for the original conformal method to include metrics with scalar curvatures that change sign.

Maxwell, David

2014-07-01

409

Solution conformation of 2-aminopurine (2-AP) dinucleotide determined by ultraviolet 2D fluorescence spectroscopy (UV-2D FS)  

PubMed Central

We have observed the conformation-dependent electronic coupling between the monomeric subunits of a dinucleotide of 2-aminopurine (2-AP), a fluorescent analog of the nucleic acid base adenine. This was accomplished by extending two-dimensional fluorescence spectroscopy (2D FS) – a fluorescence-detected variation of 2D electronic spectroscopy – to excite molecular transitions in the ultraviolet (UV) regime. A collinear sequence of four ultrafast laser pulses centered at 323 nm was used to resonantly excite the coupled transitions of 2-AP dinucleotide. The phases of the optical pulses were continuously swept at kilohertz frequencies, and the ensuing nonlinear fluorescence was phase-synchronously detected at 370 nm. Upon optimization of a point-dipole coupling model to our data, we found that in aqueous buffer the 2-AP dinucleotide adopts an average conformation in which the purine bases are non-helically stacked (center-to-center distance R12 = 3.5 Å ± 0.5 Å, twist angle ?12 = 5° ± 5°), which differs from the conformation of such adjacent bases in duplex DNA. These experiments establish UV-2D FS as a method for examining the local conformations of an adjacent pair of fluorescent nucleotides substituted into specific DNA or RNA constructs, which will serve as a powerful probe to interpret, in structural terms, biologically significant local conformational changes within the nucleic acid framework of protein-nucleic acid complexes. PMID:24223491

Widom, Julia R.; Johnson, Neil P.; von Hippel, Peter H.; Marcus, Andrew H.

2013-01-01

410

The Conforming Brain and Deontological Resolve  

PubMed Central

Our personal values are subject to forces of social influence. Deontological resolve captures how strongly one relies on absolute rules of right and wrong in the representation of one's personal values and may predict willingness to modify one's values in the presence of social influence. Using fMRI, we found that a neurobiological metric for deontological resolve based on relative activity in the ventrolateral prefrontal cortex (VLPFC) during the passive processing of sacred values predicted individual differences in conformity. Individuals with stronger deontological resolve, as measured by greater VLPFC activity, displayed lower levels of conformity. We also tested whether responsiveness to social reward, as measured by ventral striatal activity during social feedback, predicted variability in conformist behavior across individuals but found no significant relationship. From these results we conclude that unwillingness to conform to others' values is associated with a strong neurobiological representation of social rules. PMID:25170989

Pincus, Melanie; LaViers, Lisa; Prietula, Michael J.; Berns, Gregory

2014-01-01

411

QCD evolution equations from conformal symmetry  

E-print Network

QCD evolution equations in $\\text{MS}$-like schemes can be recovered from the same equations in a modified theory, QCD in non-integer $d=4-2\\epsilon$ dimensions, which enjoys exact scale and conformal invariance at the critical point. Restrictions imposed by the conformal symmetry of the modified theory allow one to obtain complete evolution kernels in integer (physical) dimensions at the given order of perturbation theory from the spectrum of anomalous dimensions added by the calculation of the special conformal anomaly at one order less. We use this technique to derive two-loop evolution equations for flavor-nonsinglet quark-antiquark light-ray operators that encode the scale dependence of generalized hadron parton distributions.

V. M. Braun; A. N. Manashov

2014-08-28

412

Conformal coatings : challenging environments lead to growth.  

SciTech Connect

Advances in technology have resulted in the need for electronic devices to continue functioning even when placed in harsh environments. Widespread use of cell phones, laptop computers, and other personal electronic devices, the increased number of electronic controls in home appliances, and the ever more extensive utilization of digital technology in the automotive industry have led to a growing demand for printed circuit boards (PCBs) that can perform under difficult conditions. Conformal coatings provide a protective barrier that enables the PCBs to function in these demanding environments. This growth in demand comes despite the cost and numerous difficulties associated with the application of these coatings. Many conformal coatings manufacturers are investing in the development of new technologies that minimize these difficulties. Others are involved in developing disruptive technologies that will serve as alternatives to traditional conformal coatings processes.

Challener, Cynthia A.

2005-08-01

413

Multi-field conformal cosmological attractors  

NASA Astrophysics Data System (ADS)

We describe a broad class of multi-field inflationary models with spontaneously broken conformal invariance. It generalizes the recently discovered class of cosmological attractors with a single inflaton field [1]. In the new multi-field theories, just as in the single-field models of [1], the moduli space has a boundary (Kähler cone) in terms of the original homogeneous conformal variables. Upon spontaneous breaking of the conformal invariance and switching to the Einstein frame, this boundary moves to infinity in terms of the canonically normalized inflaton field. This results in the exponential stretching and flattening of scalar potentials in the vicinity of the boundary of the moduli space, which makes even very steep potentials perfectly suitable for the slow-roll inflation. These theories, just like their single-field versions, typically lead to inflationary perturbations with ns = 1-2/N and r = 12/N2, where N is the number of e-foldings.

Kallosh, Renata; Linde, Andrei

2013-12-01

414

Understanding Modern Magnets through Conformal Mapping  

SciTech Connect

When I had to choose, within some narrow range, the topic of this paper, I received great help from a colleague in Berkeley and from Prof. Little when it was suggested that I should pick among the possible subjects of my talk the subject that Prof. Bloch would have enjoyed most. Since Prof. Bloch would prefer a scalpel over a sword every time, I hope and think that most people will approve my choice. When one intends to talk about a subject that is as old as conformal mapping and one does not want to lose the audience in a very short time, it is advisable to start by explaining both the motivation for the talk as well as the goals one has in mind when giving the talk. This particular talk has been motivated by the increasing frequency with which one hears, from people that ought to know better, statements like: 'Conformal mapping is really a thing of the past because of all the marvelous computer programs that we now have'. Even though, or more likely because, I have been intimately involved in the development of some large and widely used computer codes, I am deeply disturbed by such statements since they indicate a severe lack of understanding of the purpose of conformal mapping techniques, computers, and computer codes. In my view, conformal mapping can be an extremely powerful computational technique, and the easy availability of computers has made that aspect even more important now than it has been in the past. Additionally, and more importantly, conformal mapping can give very deep and unique insight into problems, giving often solutions to problems that can not be obtained with any other method, in particular not with computers. Wanting to demonstrate in particular the latter part, I set myself two goals for this talk: (1) I want to show with the help of a number of examples that conformal mapping is a unique and enormously powerful tool for thinking about, and solving, problems. Usually one has to write down only a few equations, and sometimes none at all. When I started getting involved in work for which conformal mapping seemed to be a powerful tool, I did not think that I would ever be able to use that technique successfully because it seemed to require a nearly encyclopedic memory, an impression that was strengthened when I saw H.Kober's Dictionary of Conformal Representations (ref. 1). This attitude changed when I started to realize that beyond the basics of the theory of a function of a complex variable, I needed to know only about a handful of conformal maps and procedures. Consequently, my second goal for this talk is to: (2) Show that in most cases conformal mapping functions can be obtained by formulating the underlying physics appropriately. This means particularly that encyclopedic knowledge of conformal maps is not necessary for successful use of conformal mapping techniques. To demonstrate these facts I have chosen examples from an area of physics/engineering in which I am active, namely accelerator physics. In order to do that successfully I start with a brief introduction into high energy charged particle storage ring technology, even though not all examples used in this paper to elucidate my points come directly from this particular field of accelerator technology. This is followed by a brief summary of the most important properties of functions of a complex variable. When reading this introduction into the relevant mathematics, the reader needs to keep in mind that this is not a mathematics essay, but a demonstration how beautiful and powerful, but not always appreciated, mathematics can be if used by a physicist or engineer to solve some real life problems.

Halbach, K.

1989-10-27

415

Conformal invariants associated to a measure  

PubMed Central

In this note, we study some conformal invariants of a Riemannian manifold (Mn, g) equipped with a smooth measure m. In particular, we show that there is a natural definition of the Ricci and scalar curvatures associated to such a space, both of which are conformally invariant. We also adapt the methods of Fefferman and Graham [Fefferman, C. & Graham, C. R. (1985) Astérisque, Numero Hors Serie, 95–116] and Graham, Jenne, Mason, and Sparling [Graham, C. R., Jenne, R., Mason, L. J., & Sparling, G. A. J. (1992) J. London Math. Soc. 46, 557–565] to construct families of conformally covariant operators defined on these spaces. Certain variational problems in this setting are considered, including a generalization of the Einstein–Hilbert action. PMID:16473942

Chang, Sun-Yung A.; Gursky, Matthew J.; Yang, Paul

2006-01-01

416

Black holes in massive conformal gravity  

E-print Network

We analyze the classical stability of Schwarzschild black hole in massive conformal gravity which was recently proposed for another massive gravity model. This model in the Jordan frame is conformally equivalent to the Einstein-Weyl gravity in the Einstein frame. The coupled linearized Einstein equation is decomposed into the traceless and trace equation when one chooses $6m^2\\varphi=\\delta R$. Solving the traceless equation exhibits unstable modes featuring the Gregory-Laflamme $s$-mode instability of five-dimensional black string, while we find no unstable modes when solving the trace equation. It is shown that the instability of the black hole in massive conformal gravity arises from the massiveness where the geometry of extra dimension trades for mass.

Yun Soo Myung

2014-02-04

417

Conformal Symmetry for General Black Holes  

E-print Network

We show that the warp factor of a generic asymptotically flat black hole in five dimensions can be adjusted such that a conformal symmetry emerges. The construction preserves all near horizon properties of the black holes, such as the thermodynamic potentials and the entropy. We interpret the geometry with modified asymptotic behavior as the "bare" black hole, with the ambient flat space removed. Our warp factor subtraction generalizes hidden conformal symmetry and applies whether or not rotation is significant. We also find a relation to standard AdS/CFT correspondence by embedding the black holes in six dimensions. The asymptotic conformal symmetry guarantees a dual CFT description of the general rotating black holes.

Mirjam Cveti?; Finn Larsen

2011-06-16

418

Spectral Analysis of a Protein Conformational Switch  

NASA Astrophysics Data System (ADS)

The existence of conformational switching in proteins, induced by single amino acid mutations, presents an important challenge to our understanding of the physics of protein folding. Sequence-local methods, commonly used to detect structural homology, are incapable of accounting for this phenomenon. We examine a set of proteins, derived from the GA and GB domains of Streptococcus protein G, which are known to show a dramatic conformational change as a result of single-residue replacement. It is shown that these sequences, which are almost identical locally, can have very different global patterns of physical properties. These differences are consistent with the observed complete change in conformation. These results suggest that sequence-local methods for identifying structural homology can be misleading. They point to the importance of global sequence analysis in understanding sequence-structure relationships.

Rackovsky, S.

2011-06-01

419

Proper conformal symmetries in SD Einstein spaces  

E-print Network

Proper conformal symmetries in self-dual (SD) Einstein spaces are considered. It is shown, that such symmetries are admitted only by the Einstein spaces of the type [N]x[N]. Spaces of the type [N]x[-] are considered in details. Existence of the proper conformal Killing vector implies existence of the isometric, covariantly constant and null Killing vector. It is shown, that there are two classes of [N]x[-]-metrics admitting proper conformal symmetry. They can be distinguished by analysis of the associated anti-self-dual (ASD) null strings. Both classes are analyzed in details. The problem is reduced to single linear PDE. Some general and special solutions of this PDE are presented.

Adam Chudecki; Michal Dobrski

2014-03-07

420

Logarithm conformal mapping brings the cloaking effect  

PubMed Central

Over the past years, invisibility cloaks have been extensively discussed since transformation optics emerges. Generally, the electromagnetic parameters of invisibility cloaks are complicated tensors, yet difficult to realize. As a special method of transformation optics, conformal mapping helps us design invisibility cloak with isotropic materials of a refractive index distribution. However, for all proposed isotropic cloaks, the refractive index range is at such a breadth that challenges current experimental fabrication. In this work, we propose two new kinds of logarithm conformal mappings for invisible device designs. For one of the mappings, the refractive index distribution of conformal cloak varies from 0 to 9.839, which is more feasible for future implementation. Numerical simulations by using finite element method are performed to confirm the theoretical analysis. PMID:25359138

Xu, Lin; Chen, Huanyang

2014-01-01

421

Supersymmetric extension of Galilean conformal algebras  

SciTech Connect

The Galilean conformal algebra has recently been realized in the study of the nonrelativistic limit of the AdS/CFT conjecture. This was obtained by a systematic parametric group contraction of the parent relativistic conformal field theory. In this paper, we extend the analysis to include supersymmetry. We work at the level of the coordinates in superspace to construct the N=1 super-Galilean conformal algebra. One of the interesting outcomes of the analysis is that one is able to naturally extend the finite algebra to an infinite one. This looks structurally similar to the N=1 superconformal algebra in two dimensions, but is different. We also comment on the extension of our construction to cases of higher N.

Bagchi, Arjun; Mandal, Ipsita [Harish-Chandra Research Institute, Chhatnag Road, Jhusi, Allahabad 211019 (India)

2009-10-15

422

Conformal Higgs model: predicted dark energy density  

E-print Network

Postulated universal Weyl conformal scaling symmetry provides an alternative to the $\\Lambda$CDM paradigm for cosmology. Recent applications to galactic rotation velocities, Hubble expansion, and a model of dark galactic halos explain qualitative phenomena and fit observed data without invoking dark matter. Significant revision of theory relevant to galactic collisions and clusters is implied, but not yet tested. Dark energy is found to be a consequence of conformal symmetry for the Higgs scalar field of electroweak physics. The present paper tests this implication. The conformal Higgs model acquires a gravitational effect described by a modified Friedmann cosmic evolution equation, shown to fit cosmological data going back to the cosmic microwave background epoch. The tachyonic mass parameter of the Higgs model becomes dark energy in the Friedmann equation. A dynamical model of this parameter, analogous to the Higgs mechanism for gauge boson mass, is derived and tested here. An approximate calculation yields a result consistent with the empirical magnitude inferred from Hubble expansion.

R. K. Nesbet

2014-11-03

423

Precise dipole moments and quadrupole coupling constants of the cis and trans conformers of 3-aminophenol: determination of the absolute conformation.  

PubMed

The rotational constants and the nitrogen nuclear quadrupole coupling constants of cis-3-aminophenol and trans-3-aminophenol are determined using Fourier-transform microwave spectroscopy. We examine several J = 2 <-- 1 and 1 <-- 0 hyperfine-resolved rotational transitions for both conformers. The transitions are fit to a rigid rotor Hamiltonian including nuclear quadrupole coupling to account for the 14N nuclear spin. For cis-3-aminophenol we obtain rotational constants of A = 3734.930 MHz, B = 1823.2095 MHz, and C = 1226.493 MHz, for trans-3-aminophenol of A = 3730.1676 MHz, B = 1828.25774 MHz, and C = 1228.1948 MHz. The dipole moments are precisely determined using Stark effect measurements for several hyperfine transitions to micro(a) = 1.7718 D, micro(b) = 1.517 D for cis-3-aminophenol and micro(a) = 0.5563 D, micro(h) = 0.5375 D for trans-3-aminophenol. Whereas the rotational constants and quadrupole coupling constants do not allow to determinate the absolute configuration of the two conformers, this assignment is straightforward based on the dipole moments. High-level ab initio calculations (B3LYP/6-31G* to MP2/aug-cc-pVTZ) are performed providing error estimates of rotational constants and dipole moments obtained for large molecules by these theoretical methods. PMID:19791450

Filsinger, Frank; Wohlfart, Kirstin; Schnell, Melanie; Grabow, Jens-Uwe; Küpper, Jochen

2008-02-01

424

Salt-Induced Z-A-Z Transition Sequence in the Mixed Ribo-Deoxyribo Copolymer poly(rG-dC)\\\\cdot poly(rG-dC)  

Microsoft Academic Search

The left-handed helical conformation of various polynucleotides has been seen in solution at higher salt concentration than has the right-handed helical conformation of the corresponding polymer. We report here, however, studies of conformational transitions in the mixed polymer poly(rG-dC)\\\\cdot poly(rG-dC) This polynucleotide appears to exist in a Z conformation under low-salt conditions, converts to an A helix at intermediate salt,

Hai-Young Wu; Michael J. Behe

1984-01-01

425

From Induced Fit to Conformational Selection: A Continuum of Binding Mechanism Controlled by the Timescale of Conformational Transitions  

E-print Network

D D D + -= + (5b) The six constants, A1, A2, B1, B2, A, and B, are determined by the continuity of the receptor-ligand pair takes different values, Da and Di, while the receptor is in the active and inactive the active receptor is in contact with the ligand. The complex formation is modeled by a partially reflecting

Weston, Ken

426

Game Theory and Social Psychology: Conformity Games  

NASA Astrophysics Data System (ADS)

Game models can contribute to understanding of how social biases and pressures to conform can lead to puzzling behaviour in social groups. A model of the psychological biases false uniqueness and false consensus is set out. The model predicts the phenomenon of pluralistic ignorance, which is well-studied in social psychology, showing how it arises as a result of the prevalence of false uniqueness and the desire to conform. An efficient method is developed for finding Nash equilibria of the model under certain restrictions.

Alessio, Danielle; Kilgour, D. Marc

2011-11-01

427

Collisions of Einstein-Conformal Scalar Waves  

E-print Network

A large class of solutions of the Einstein-conformal scalar equations in D=2+1 and D=3+1 is identified. They describe the collisions of asymptotic conformal scalar waves and are generated from Einstein-minimally coupled scalar spacetimes via a (generalized) Bekenstein transformation. Particular emphasis is given to the study of the global properties and the singularity structure of the obtained solutions. It is shown, that in the case of the absence of pure gravitational radiation in the initial data, the formation of the final singularity is not only generic, but is even inevitable.

C. Klim?{\\'?}k; P. Koln{\\'?}k

1992-12-18

428

A Lewis acid-mediated conformational switch.  

PubMed

Molecules that change conformation in response to a stimulus have numerous uses, such as artificial chemoreceptors, novel drug delivery strategies and liquid crystal technology. Here we describe the design, synthesis and conformational behaviour of an isonicotinamide-substituted diphenylacetylene upon recognition of Lewis acids, including metalloporphyrins. Binding of these at a remote site - the pyridyl nitrogen - increases hydrogen-bond donor ability of the proximal amide NH, causing an increased preference for the alkyne rotamer in which this hydrogen bond is maintained. PMID:25184700

Knipe, Peter C; Lingard, Hannah; Jones, Ian M; Thompson, Sam; Hamilton, Andrew D

2014-10-28

429

Conformal pure radiation with parallel rays  

NASA Astrophysics Data System (ADS)

We define pure radiation metrics with parallel rays to be n-dimensional pseudo-Riemannian metrics that admit a parallel null line bundle K and whose Ricci tensor vanishes on vectors that are orthogonal to K. We give necessary conditions in terms of the Weyl, Cotton and Bach tensors for a pseudo-Riemannian metric to be conformal to a pure radiation metric with parallel rays. Then, we derive conditions in terms of the tractor calculus that are equivalent to the existence of a pure radiation metric with parallel rays in a conformal class. We also give analogous results for n-dimensional pseudo-Riemannian pp-waves.

Leistner, Thomas; Nurowski, Pawe?

2012-03-01

430

Bounds on SCFTs from Conformal Perturbation Theory  

E-print Network

The operator product expansion (OPE) in 4d (super)conformal field theory is of broad interest, for both formal and phenomenological applications. In this paper, we use conformal perturbation theory to study the OPE of nearly-free fields coupled to SCFTs. Under fairly general assumptions, we show that the OPE of a chiral operator of dimension $\\Delta = 1+\\epsilon$ with its complex conjugate always contains an operator of dimension less than $2 \\Delta$. Our bounds apply to Banks-Zaks fixed points and their generalizations, as we illustrate using several examples.

Daniel Green; David Shih

2012-04-09

431

Jet Quenching in Non-Conformal Holography  

E-print Network

We use our non-conformal holographic bottom-up model for QCD described in 1012.0116 to further study the effect of the QCD trace anomaly on the energy loss of both light and heavy quarks in a strongly coupled plasma. We compute the nuclear modification factor $R_{AA}$ for bottom and charm quarks in an expanding plasma with Glauber initial conditions. We find that the maximum stopping distance of light quarks in a non-conformal plasma scales with the energy with a temperature (and energy) dependent effective power.

Andrej Ficnar; Jorge Noronha; Miklos Gyulassy

2011-06-30

432

Conformal gravity holography in four dimensions.  

PubMed

We formulate four-dimensional conformal gravity with (anti-)de Sitter boundary conditions that are weaker than Starobinsky boundary conditions, allowing for an asymptotically subleading Rindler term concurrent with a recent model for gravity at large distances. We prove the consistency of the variational principle and derive the holographic response functions. One of them is the conformal gravity version of the Brown-York stress tensor, the other is a "partially massless response". The on shell action and response functions are finite and do not require holographic renormalization. Finally, we discuss phenomenologically interesting examples, including the most general spherically symmetric solutions and rotating black hole solutions with partially massless hair. PMID:24702345

Grumiller, Daniel; Irakleidou, Maria; Lovrekovic, Iva; McNees, Robert

2014-03-21

433

Simulating Massive Conformation Changes within Polypeptide Systems  

NASA Astrophysics Data System (ADS)

In this dissertation I employ all-atom structure based models with stable energy basins to several existing and novel polypeptide systems (postulated conformation changes of the mammalian prion protein and structurally dual proteins). The common themes are finding unfolding and refolding pathways between highly dissimilar protein structures as a means of understanding exactly how and why a protein may misfold. The modeling is based on the energy funnel landscape theory of protein conformation space. The principle of minimal frustration is considered as the model includes parameters which vary the roughness of the landscape and give rise to off-pathway misfoldings. The dual basin model is applied to the C-terminal (residues 166-226) of the mammalian prion protein. One basin represents the known alpha-helical (aH) structure while the other represents the same residues in a lefthanded beta-helical (LHBH) conformation. The LHBH structure has been proposed to help describe one class of in vitro grown fibrils, as well as possibly self-templating the conversion of normal cellular prion protein to the infectious form. Yet, it is unclear how the protein may make this global rearrangement. Our results demonstrate that the conformation changes are not strongly limited by large-scale geometry modification and that there may exist an overall preference for the LHBH conformation. Furthermore, our model presents novel intermediate trapping conformations with twisted LHBH