Investigation on the interaction of catalase with sodium lauryl sulfonate and the underlying mechanisms.

PubMed

Wang, Jing; Jia, Rui; Wang, Jiaxi; Sun, Zhiqiang; Wu, Zitao; Liu, Rutao; Zong, Wansong

2018-02-01

As a classic type of anionic surfactants, sodium lauryl sulfonate (SLS) might change the structure and function of antioxidant enzyme catalase (CAT) through their direct interactions. However, the underlying molecular mechanism is still unknown. This study investigated the direct interaction of SLS with CAT molecule and the underlying mechanisms using multi-spectroscopic methods, isothermal titration calorimetry, and molecular docking studies. No obvious effects were observed on CAT structure and activity under low SLS concentration exposure. The particle size of CAT molecule decreased and CAT activity was slightly inhibited under high SLS concentration exposure. SLS prefers to bind to the interface of CAT mainly via van der Waals' forces and hydrogen bonds. Subsequently, SLS interacts with the amino acid residues around the heme groups of CAT via hydrophobic interactions and might inhibit CAT activity. © 2017 Wiley Periodicals, Inc.

A role for direct interactions in the modulation of rhodopsin by -3 polyunsaturated lipids

NASA Astrophysics Data System (ADS)

Grossfield, Alan; Feller, Scott E.; Pitman, Michael C.

2006-03-01

Rhodopsin, the G protein-coupled receptor primarily responsible for sensing light, is found in an environment rich in polyunsaturated lipid chains and cholesterol. Biophysical experiments have shown that lipid unsaturation and cholesterol both have significant effects on rhodopsin's stability and function; -3 polyunsaturated chains, such as docosahexaenoic acid (DHA), destabilize rhodopsin and enhance the kinetics of the photocycle, whereas cholesterol has the opposite effect. Here, we use molecular dynamics simulations to investigate the possibility that polyunsaturated chains modulate rhodopsin stability and kinetics via specific direct interactions. By analyzing the results of 26 independent 100-ns simulations of dark-adapted rhodopsin, we found that DHA routinely forms tight associations with the protein in a small number of specific locations qualitatively different from the nonspecific interactions made by saturated chains and cholesterol. Furthermore, the presence of tightly packed DHA molecules tends to weaken the interhelical packing. These results are consistent with recent NMR work, which proposes that rhodopsin binds DHA, and they suggest a molecular rationale for DHA's effects on rhodopsin stability and kinetics. cholesterol | molecular dynamics | fatty acid | protein-lipid interactions

Defining the molecular basis of BubR1 kinetochore interactions and APC/C-CDC20 inhibition.

PubMed

D'Arcy, Sheena; Davies, Owen R; Blundell, Tom L; Bolanos-Garcia, Victor M

2010-05-07

BubR1 is essential for the mitotic checkpoint that prevents aneuploidy in cellular progeny by triggering anaphase delay in response to kinetochores incorrectly/not attached to the mitotic spindle. Here, we define the molecular architecture of the functionally significant N-terminal region of human BubR1 and present the 1.8 A crystal structure of its tetratricopeptide repeat (TPR) domain. The structure reveals divergence from the classical TPR fold and is highly similar to the TPR domain of budding yeast Bub1. Shared distinctive features include a disordered loop insertion, a 3(10)-helix, a tight turn involving glycine positive Phi angles, and noncanonical packing of and between the TPR motifs. We also define the molecular determinants of the interaction between BubR1 and kinetochore protein Blinkin. We identify a shallow groove on the concave surface of the BubR1 TPR domain that forms multiple discrete and potentially cooperative interactions with Blinkin. Finally, we present evidence for a direct interaction between BubR1 and Bub1 mediated by regions C-terminal to their TPR domains. This interaction provides a mechanism for Bub1-dependent kinetochore recruitment of BubR1. We thus present novel molecular insights into the structure of BubR1 and its interactions at the kinetochore-microtubule interface. Our studies pave the way for future structure-directed engineering aimed at dissecting the roles of kinetochore-bound and other pools of BubR1 in vivo.

Developing a molecular picture of soil organic matter–mineral interactions by quantifying organo–mineral binding

DOE PAGES

Newcomb, C. J.; Qafoku, N. P.; Grate, J. W.; ...

2017-08-30

Long residence times of soil organic matter have been attributed to reactive mineral surface sites that sorb organic species and cause inaccessibility due to isolation and chemical stabilization at the organic-mineral interface. Instrumentation for probing this interface is limited. As a result, much of the micron- and molecular-scale knowledge about organic-mineral interactions remains largely qualitative. We report the use of force spectroscopy to directly measure the binding between organic ligands with known chemical functionalities to soil minerals in aqueous environments. By systematically studying the role of organic functional group chemistry with model minerals, we demonstrate that the chemistry of bothmore » the organic ligand and mineral contribute to values of binding free energy and that changes in pH and ionic strength produce significant differences in binding energies. These direct measurements of molecular binding provide mechanistic insights into organo-mineral interactions, which could potentially inform land-carbon models that explicitly include mineral-bound C pools.« less

Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models.

PubMed

Saglam, Ali S; Chong, Lillian T

2016-01-14

An essential baseline for determining the extent to which electrostatic interactions enhance the kinetics of protein-protein association is the "basal" kon, which is the rate constant for association in the absence of electrostatic interactions. However, since such association events are beyond the milliseconds time scale, it has not been practical to compute the basal kon by directly simulating the association with flexible models. Here, we computed the basal kon for barnase and barstar, two of the most rapidly associating proteins, using highly efficient, flexible molecular simulations. These simulations involved (a) pseudoatomic protein models that reproduce the molecular shapes, electrostatic, and diffusion properties of all-atom models, and (b) application of the weighted ensemble path sampling strategy, which enhanced the efficiency of generating association events by >130-fold. We also examined the extent to which the computed basal kon is affected by inclusion of intermolecular hydrodynamic interactions in the simulations.

Developing a molecular picture of soil organic matter–mineral interactions by quantifying organo–mineral binding

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

Newcomb, C. J.; Qafoku, N. P.; Grate, J. W.

Long residence times of soil organic matter have been attributed to reactive mineral surface sites that sorb organic species and cause inaccessibility due to isolation and chemical stabilization at the organic-mineral interface. Instrumentation for probing this interface is limited. As a result, much of the micron- and molecular-scale knowledge about organic-mineral interactions remains largely qualitative. We report the use of force spectroscopy to directly measure the binding between organic ligands with known chemical functionalities to soil minerals in aqueous environments. By systematically studying the role of organic functional group chemistry with model minerals, we demonstrate that the chemistry of bothmore » the organic ligand and mineral contribute to values of binding free energy and that changes in pH and ionic strength produce significant differences in binding energies. These direct measurements of molecular binding provide mechanistic insights into organo-mineral interactions, which could potentially inform land-carbon models that explicitly include mineral-bound C pools.« less

Isotope separation apparatus and method

DOEpatents

Cotter, Theodore P.

1982-12-28

The invention relates to a method and apparatus for laser isotope separation by photodeflection. A molecular beam comprising at least two isotopes to be separated intersects, preferable substantially perpendicular to one broad side of the molecular beam, with a laser beam traveling in a first direction. The laser beam is reflected back through the molecular beam, preferably in a second direction essentially opposite to the first direction. The laser beam comprises .pi.-pulses of a selected wavelength which excite unexcited molecules, or cause stimulated emission of excited molecules of one of the isotopes. Excitation caused by first direction .pi.-pulses moves molecules of the isotope excited thereby in the first direction. Stimulated emission of excited molecules of the isotope is brought about by returning .pi.-pulses traveling in the second direction. Stimulated emission moves emitting molecules in a direction opposite to the photon emitted. Because emitted photons travel in the second direction, emitting molecules move in the first direction. Substantial molecular movement is accomplished by a large number of .pi.-pulse-molecule interactions. A beam corer collects the molecules in the resulting enriched divergent portions of the beam.

MIMO: an efficient tool for molecular interaction maps overlap

PubMed Central

2013-01-01

Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways. PMID:23672344

MPP1 directly interacts with flotillins in erythrocyte membrane - Possible mechanism of raft domain formation.

PubMed

Biernatowska, Agnieszka; Augoff, Katarzyna; Podkalicka, Joanna; Tabaczar, Sabina; Gajdzik-Nowak, Weronika; Czogalla, Aleksander; Sikorski, Aleksander F

2017-11-01

Flotillins are prominent, oligomeric protein components of erythrocyte (RBC) membrane raft domains and are considered to play an important structural role in lateral organization of the plasma membrane. In our previous work on erythroid membranes and giant plasma membrane vesicles (GPMVs) derived from them we have shown that formation of functional domains (resting state rafts) depends on the presence of membrane palmitoylated protein 1 (MPP1/p55), pointing to its new physiological role. Exploration of the molecular mechanism of MPP1 function in organizing membrane domains described here, through searching for its molecular partners in RBC membrane by using different methods, led to the identification of the raft-marker proteins, flotillin 1 and flotillin 2, as hitherto unreported direct MPP1 binding-partners in the RBC membrane. These proteins are found in high molecular-weight complexes in native RBC membrane and, significantly, their presence was shown to be separate from the well-known protein 4.1-dependent interactions of MPP1 with membrane proteins. Furthermore, FLIM analysis revealed that loss of the endogenous MPP1-flotillins interactions resulted in significant changes in RBC membrane-fluidity, emphasizing the physiological importance of such interactions in vivo. Therefore, our data establish a new perspective on the role of MPP1 in erythroid cells and suggests that direct MPP1-flotillins interactions could be the major driving-force behind the formation of raft domains in RBC. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Molecular Force Spectroscopy on Cells

NASA Astrophysics Data System (ADS)

Liu, Baoyu; Chen, Wei; Zhu, Cheng

2015-04-01

Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

A Molecular Dynamic Modeling of Hemoglobin-Hemoglobin Interactions

NASA Astrophysics Data System (ADS)

Wu, Tao; Yang, Ye; Sheldon Wang, X.; Cohen, Barry; Ge, Hongya

2010-05-01

In this paper, we present a study of hemoglobin-hemoglobin interaction with model reduction methods. We begin with a simple spring-mass system with given parameters (mass and stiffness). With this known system, we compare the mode superposition method with Singular Value Decomposition (SVD) based Principal Component Analysis (PCA). Through PCA we are able to recover the principal direction of this system, namely the model direction. This model direction will be matched with the eigenvector derived from mode superposition analysis. The same technique will be implemented in a much more complicated hemoglobin-hemoglobin molecule interaction model, in which thousands of atoms in hemoglobin molecules are coupled with tens of thousands of T3 water molecule models. In this model, complex inter-atomic and inter-molecular potentials are replaced by nonlinear springs. We employ the same method to get the most significant modes and their frequencies of this complex dynamical system. More complex physical phenomena can then be further studied by these coarse grained models.

Identification of novel direct protein-protein interactions by irradiating living cells with femtosecond UV laser pulses.

PubMed

Itri, Francesco; Monti, Daria Maria; Chino, Marco; Vinciguerra, Roberto; Altucci, Carlo; Lombardi, Angela; Piccoli, Renata; Birolo, Leila; Arciello, Angela

2017-10-07

The identification of protein-protein interaction networks in living cells is becoming increasingly fundamental to elucidate main biological processes and to understand disease molecular bases on a system-wide level. We recently described a method (LUCK, Laser UV Cross-linKing) to cross-link interacting protein surfaces in living cells by UV laser irradiation. By using this innovative methodology, that does not require any protein modification or cell engineering, here we demonstrate that, upon UV laser irradiation of HeLa cells, a direct interaction between GAPDH and alpha-enolase was "frozen" by a cross-linking event. We validated the occurrence of this direct interaction by co-immunoprecipitation and Immuno-FRET analyses. This represents a proof of principle of the LUCK capability to reveal direct protein interactions in their physiological environment. Copyright © 2017 Elsevier Inc. All rights reserved.

Direct observation of salt effects on molecular interactions through explicit-solvent molecular dynamics simulations: differential effects on electrostatic and hydrophobic interactions and comparisons to Poisson-Boltzmann theory.

PubMed

Thomas, Andrew S; Elcock, Adrian H

2006-06-21

Proteins and other biomolecules function in cellular environments that contain significant concentrations of dissolved salts and even simple salts such as NaCl can significantly affect both the kinetics and thermodynamics of macromolecular interactions. As one approach to directly observing the effects of salt on molecular associations, explicit-solvent molecular dynamics (MD) simulations have been used here to model the association of pairs of the amino acid analogues acetate and methylammonium in aqueous NaCl solutions of concentrations 0, 0.1, 0.3, 0.5, 1, and 2 M. By performing simulations of 500 ns duration for each salt concentration properly converged estimates of the free energy of interaction of the two molecules have been obtained for all intermolecular separation distances and geometries. The resulting free energy surfaces are shown to give significant new insights into the way salt modulates interactions between molecules containing both charged and hydrophobic groups and are shown to provide valuable new benchmarks for testing the description of salt effects provided by the simpler but faster Poisson-Boltzmann method. In addition, the complex many-dimensional free energy surfaces are shown to be decomposable into a number of one-dimensional effective energy functions. This decomposition (a) allows an unambiguous view of the qualitative differences between the salt dependence of electrostatic and hydrophobic interactions, (b) gives a clear rationalization for why salt exerts different effects on protein-protein association and dissociation rates, and (c) produces simplified energy functions that can be readily used in much faster Brownian dynamics simulations.

Multiplex bioimaging of piRNA molecular pathway-regulated theragnostic effects in a single breast cancer cell using a piRNA molecular beacon.

PubMed

Lee, Youn Jung; Moon, Sung Ung; Park, Min Geun; Jung, Woon Yong; Park, Yong Keun; Song, Sung Kyu; Ryu, Je Gyu; Lee, Yong Seung; Heo, Hye Jung; Gu, Ha Na; Cho, Su Jeong; Ali, Bahy A; Al-Khedhairy, Abdulaziz A; Lee, Ilkyun; Kim, Soonhag

2016-09-01

Recently, PIWI-interacting small non-coding RNAs (piRNAs) have emerged as novel cancer biomarkers candidate because of their high expression level in various cancer types and role in the control of tumor suppressor genes. In this study, a novel breast cancer theragnostics probe based on a single system targeting the piRNA-36026 (piR-36026) molecular pathway was developed using a piR-36026 molecular beacon (MB). The piR-36026 MB successfully visualized endogenous piR-36026 biogenesis, which is highly expressed in MCF7 cells (a human breast cancer cell line), and simultaneously inhibited piR-36026-mediated cancer progression in vitro and in vivo. We discovered two tumor suppressor proteins, SERPINA1 and LRAT, that were directly regulated as endogenous piR-36026 target genes in MCF7 cells. Furthermore, multiplex bioimaging of a single MCF7 cell following treatment with piR-36026 MB clearly visualized the direct molecular interaction of piRNA-36026 with SERPINA1 or LRAT and subsequent molecular therapeutic responses including caspase-3 and PI in the nucleus. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessing the Impact of Electrostatic Drag on Processive Molecular Motor Transport.

PubMed

Smith, J Darby; McKinley, Scott A

2018-06-04

The bidirectional movement of intracellular cargo is usually described as a tug-of-war among opposite-directed families of molecular motors. While tug-of-war models have enjoyed some success, recent evidence suggests underlying motor interactions are more complex than previously understood. For example, these tug-of-war models fail to predict the counterintuitive phenomenon that inhibiting one family of motors can decrease the functionality of opposite-directed transport. In this paper, we use a stochastic differential equations modeling framework to explore one proposed physical mechanism, called microtubule tethering, that could play a role in this "co-dependence" among antagonistic motors. This hypothesis includes the possibility of a trade-off: weakly bound trailing molecular motors can serve as tethers for cargoes and processing motors, thereby enhancing motor-cargo run lengths along microtubules; however, this introduces a cost of processing at a lower mean velocity. By computing the small- and large-time mean-squared displacement of our theoretical model and comparing our results to experimental observations of dynein and its "helper protein" dynactin, we find some supporting evidence for microtubule tethering interactions. We extrapolate these findings to predict how dynein-dynactin might interact with the opposite-directed kinesin motors and introduce a criterion for when the trade-off is beneficial in simple systems.

Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Liu, Fu-Feng; Ji, Luo; Zhang, Lin; Dong, Xiao-Yan; Sun, Yan

2010-06-01

Molecular dynamics simulations of chymotrypsin inhibitor 2 in different polyols (glycerol, xylitol, sorbitol, trehalose, and sucrose) at 363 K were performed to probe the molecular basis of the stabilizing effect, and the data in water, ethanol, and glycol were compared. It is found that protein protection by polyols is positively correlated with both the molecular volume and the fractional polar surface area, and the former contributes more significantly to the protein's stability. Polyol molecules have only a few direct hydrogen bonds with the protein, and the number of hydrogen bonds between a polyol and the protein is similar for different polyols. Thus, it is concluded that the direct interactions contribute little to the stabilizing effect. It is clarified that the preferential exclusion of the polyols is the origin of their protective effects, and it increases with increasing polyol size. Namely, there is preferential hydration on the protein surface (2 Å), and polyol molecules cluster around the protein at a distance of about 4 Å. The preferential exclusion of polyols leads to indirect interactions that prevent the protein from thermal unfolding. The water structure becomes more ordered with increasing the polyol size. So, the entropy of water in the first hydration shell decreases, and a larger extent of decrease is observed with increasing polyol size, leading to larger transfer free energy. The findings suggest that polyols protect the protein from thermal unfolding via indirect interactions. The work has thus elucidated the molecular mechanism of structural stability of the protein in polyol solutions.

Effect of electron-vibration interactions on the thermoelectric efficiency of molecular junctions.

PubMed

Hsu, Bailey C; Chiang, Chi-Wei; Chen, Yu-Chang

2012-07-11

From first-principles approaches, we investigate the thermoelectric efficiency of a molecular junction where a benzene molecule is connected directly to the platinum electrodes. We calculate the thermoelectric figure of merit ZT in the presence of electron-vibration interactions with and without local heating under two scenarios: linear response and finite bias regimes. In the linear response regime, ZT saturates around the electrode temperature T(e) = 25 K in the elastic case, while in the inelastic case we observe a non-saturated and a much larger ZT beyond T(e) = 25 K attributed to the tail of the Fermi-Dirac distribution. In the finite bias regime, the inelastic effects reveal the signatures of the molecular vibrations in the low-temperature regime. The normal modes exhibiting structures in the inelastic profile are characterized by large components of atomic vibrations along the current density direction on top of each individual atom. In all cases, the inclusion of local heating leads to a higher wire temperature T(w) and thus magnifies further the influence of the electron-vibration interactions due to the increased number of local phonons.

An Observation of Diamond-Shaped Particle Structure in a Soya Phosphatidylcohline and Bacteriorhodopsin Composite Langmuir Blodgett Film Fabricated by Multilayer Molecular Thin Film Method

NASA Astrophysics Data System (ADS)

Tsujiuchi, Y.; Makino, Y.

A composite film of soya phosphatidylcohline (soya PC) and bacteriorhodopsin (BR) was fabricated by the multilayer molecular thin film method using fatty acid and lipid on a quartz substrate. Direct Force Microscopy (DFM), UV absorption spectra and IR absorption spectra of the film were characterized on the detail of surface structure of the film. The DFM data revealed that many rhombus (diamond-shaped) particles were observed in the film. The spectroscopic data exhibited the yield of M-intermediate of BR in the film. On our modelling of molecular configuration indicate that the coexistence of the strong inter-molecular interaction and the strong inter-molecular interaction between BR trimmers attributed to form the particles.

Multi-level molecular modelling for plasma medicine

NASA Astrophysics Data System (ADS)

Bogaerts, Annemie; Khosravian, Narjes; Van der Paal, Jonas; Verlackt, Christof C. W.; Yusupov, Maksudbek; Kamaraj, Balu; Neyts, Erik C.

2016-02-01

Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma-biomolecule interactions.

Direct Imaging of Lipid-Ion Network Formation under Physiological Conditions by Frequency Modulation Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Fukuma, Takeshi; Higgins, Michael J.; Jarvis, Suzanne P.

2007-03-01

Various metal cations in physiological solutions interact with lipid headgroups in biological membranes, having an impact on their structure and stability, yet little is known about the molecular-scale dynamics of the lipid-ion interactions. Here we directly investigate the extensive lipid-ion interaction networks and their transient formation between headgroups in a dipalmitoylphosphatidylcholine bilayer under physiological conditions. The spatial distribution of ion occupancy is imaged in real space by frequency modulation atomic force microscopy with sub-Ångstrom resolution.

Interaction of PLGA and trimethyl chitosan modified PLGA nanoparticles with mixed anionic/zwitterionic phospholipid bilayers studied using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Novak, Brian; Astete, Carlos; Sabliov, Cristina; Moldovan, Dorel

2012-02-01

Poly(lactic-co-glycolic acid) (PLGA) is a biodegradable polymer. Nanoparticles of PLGA are commonly used for drug delivery applications. The interaction of the nanoparticles with the cell membrane may influence the rate of their uptake by cells. Both PLGA and cell membranes are negatively charged, so adding positively charged polymers such as trimethyl chitosan (TMC) which adheres to the PLGA particles improves their cellular uptake. The interaction of 3 nm PLGA and TMC-modified-PLGA nanoparticles with lipid bilayers composed of mixtures of phosphatidylcholine and phosphatidylserine lipids was studied using molecular dynamics simulations. The free energy profiles as function of nanoparticles position along the normal direction to the bilayers were calculated, the distribution of phosphatidylserine lipids as a function of distance of the particle from the bilayer was calculated, and the time scale for particle motion in the directions parallel to the bilayer surface was estimated.

Quantum dynamics of light-driven chiral molecular motors.

PubMed

Yamaki, Masahiro; Nakayama, Shin-ichiro; Hoki, Kunihito; Kono, Hirohiko; Fujimura, Yuichi

2009-03-21

The results of theoretical studies on quantum dynamics of light-driven molecular motors with internal rotation are presented. Characteristic features of chiral motors driven by a non-helical, linearly polarized electric field of light are explained on the basis of symmetry argument. The rotational potential of the chiral motor is characterized by a ratchet form. The asymmetric potential determines the directional motion: the rotational direction is toward the gentle slope of the asymmetric potential. This direction is called the intuitive direction. To confirm the unidirectional rotational motion, results of quantum dynamical calculations of randomly-oriented molecular motors are presented. A theoretical design of the smallest light-driven molecular machine is presented. The smallest chiral molecular machine has an optically driven engine and a running propeller on its body. The mechanisms of transmission of driving forces from the engine to the propeller are elucidated by using a quantum dynamical treatment. The results provide a principle for control of optically-driven molecular bevel gears. Temperature effects are discussed using the density operator formalism. An effective method for ultrafast control of rotational motions in any desired direction is presented with the help of a quantum control theory. In this method, visible or UV light pulses are applied to drive the motor via an electronic excited state. A method for driving a large molecular motor consisting of an aromatic hydrocarbon is presented. The molecular motor is operated by interactions between the induced dipole of the molecular motor and the electric field of light pulses.

SPR Biosensors in Direct Molecular Fishing: Implications for Protein Interactomics.

PubMed

Florinskaya, Anna; Ershov, Pavel; Mezentsev, Yuri; Kaluzhskiy, Leonid; Yablokov, Evgeniy; Medvedev, Alexei; Ivanov, Alexis

2018-05-18

We have developed an original experimental approach based on the use of surface plasmon resonance (SPR) biosensors, applicable for investigation of potential partners involved in protein⁻protein interactions (PPI) as well as protein⁻peptide or protein⁻small molecule interactions. It is based on combining a SPR biosensor, size exclusion chromatography (SEC), mass spectrometric identification of proteins (LC-MS/MS) and direct molecular fishing employing principles of affinity chromatography for isolation of potential partner proteins from the total lysate of biological samples using immobilized target proteins (or small non-peptide compounds) as ligands. Applicability of this approach has been demonstrated within the frame of the Human Proteome Project (HPP) and PPI regulation by a small non-peptide biologically active compound, isatin.

Molecular-Scale Structural Controls on Nanoscale Growth Processes: Step-Specific Regulation of Biomineral Morphology

NASA Astrophysics Data System (ADS)

Dove, P. M.; Davis, K. J.; De Yoreo, J. J.; Orme, C. A.

2001-12-01

Deciphering the complex strategies by which organisms produce nanocrystalline materials with exquisite morphologies is central to understanding biomineralizing systems. One control on the morphology of biogenic nanoparticles is the specific interactions of their surfaces with the organic functional groups provided by the organism and the various inorganic species present in the ambient environment. It is now possible to directly probe the microscopic structural controls on crystal morphology by making quantitative measurements of the dynamic processes occurring at the mineral-water interface. These observations can provide crucial information concerning the actual mechanisms of growth that is otherwise unobtainable through macroscopic techniques. Here we use in situ molecular-scale observations of step dynamics and growth hillock morphology to directly resolve roles of principal impurities in regulating calcite surface morphologies. We show that the interactions of certain inorganic as well as organic impurities with the calcite surface are dependent upon the molecular-scale structures of step-edges. These interactions can assume a primary role in directing crystal morphology. In calcite growth experiments containing magnesium, we show that growth hillock structures become modified owing to the preferential inhibition of step motion along directions approximately parallel to the [010]. Compositional analyses have shown that Mg incorporates at different levels into the two types of nonequivalent steps, which meet at the hillock corner parallel to [010]. A simple calculation of the strain caused by this difference indicates that we should expect a significant retardation at this corner, in agreement with the observed development of [010] steps. If the low-energy step-risers produced by these [010] steps is perpendicular to the c-axis as seems likely from crystallographic considerations, this effect provides a plausible mechanism for the elongated calcite crystal habits found in natural environments that contain magnesium. In a separate study, step-specific interactions are also found between chiral aspartate molecules and the calcite surface. The L and D- aspartate enantiomers exhibit structure preferences for the different types of step-risers on the calcite surface. These site-specific interactions result in the transfer of asymmetry from the organic molecule to the crystal surface through the formation of chiral growth hillocks and surface morphologies. These studies yield direct experimental insight into the molecular-scale structural controls on nanocrystal morphology in biomineralizing systems.

Diverse Molecular Targets for Chalcones with Varied Bioactivities

PubMed Central

Zhou, Bo; Xing, Chengguo

2015-01-01

Natural or synthetic chalcones with different substituents have revealed a variety of biological activities that may benefit human health. The underlying mechanisms of action, particularly with respect to the direct cellular targets and the modes of interaction with the targets, have not been rigorously characterized, which imposes challenges to structure-guided rational development of therapeutic agents or chemical probes with acceptable target-selectivity profile. This review summarizes literature evidence on chalcones’ direct molecular targets in the context of their biological activities. PMID:26798565

Manipulating 3D-Printed and Paper Models Enhances Student Understanding of Viral Replication

ERIC Educational Resources Information Center

Couper, Lisa; Johannes, Kristen; Powers, Jackie; Silberglitt, Matt; Davenport, Jodi

2016-01-01

Understanding key concepts in molecular biology requires reasoning about molecular processes that are not directly observable and, as such, presents a challenge to students and teachers. We ask whether novel interactive physical models and activities can help students understand key processes in viral replication. Our 3D tangible models are…

Molecular Design of High Performance Molecular Devices Based on Direct Ab-initio Molecular Dynamics Method: Diffusion of Lithium Ion on Fluorinated Amorphous Carbon

NASA Astrophysics Data System (ADS)

Kawabata, Hiroshi; Iyama, Tetsuji; Tachikawa, Hiroto

2008-01-01

Hybrid density functional theory (DFT) calculations have been carried out for the lithium adsorbed on a fluorinated graphene surface (F-graphene, C96F24) to elucidate the effect of fluorination of amorphous carbon on the diffusion mechanism of lithium ion. Also, direct molecular orbital-molecular dynamics (MO-MD) calculation [H. Tachikawa and A. Shimizu: J. Phys. Chem. B 109 (2005) 13255] was applied to diffusion processes of the Li+ ion on F-graphene. The B3LYP/LANL2MB calculation showed that the Li+ ion is most stabilized around central position of F-graphene, and the energy was gradually instabilized for the edge region. The direct MO-MD calculations showed that the Li+ ion diffuses on the bulk surface region of F-graphite at 300 K. The nature of the interaction between Li+ and F-graphene was discussed on the basis of theoretical results.

Computing by physical interaction in neurons.

PubMed

Aur, Dorian; Jog, Mandar; Poznanski, Roman R

2011-12-01

The electrodynamics of action potentials represents the fundamental level where information is integrated and processed in neurons. The Hodgkin-Huxley model cannot explain the non-stereotyped spatial charge density dynamics that occur during action potential propagation. Revealed in experiments as spike directivity, the non-uniform charge density dynamics within neurons carry meaningful information and suggest that fragments of information regarding our memories are endogenously stored in structural patterns at a molecular level and are revealed only during spiking activity. The main conceptual idea is that under the influence of electric fields, efficient computation by interaction occurs between charge densities embedded within molecular structures and the transient developed flow of electrical charges. This process of computation underlying electrical interactions and molecular mechanisms at the subcellular level is dissimilar from spiking neuron models that are completely devoid of physical interactions. Computation by interaction describes a more powerful continuous model of computation than the one that consists of discrete steps as represented in Turing machines.

Ultrafast fluorescent decay induced by metal-mediated dipole–dipole interaction in two-dimensional molecular aggregates

DOE PAGES

Hu, Qing; Jin, Dafei; Xiao, Jun; ...

2017-09-05

Two-dimensional molecular aggregate (2DMA), a thin sheet of strongly interacting dipole molecules self-assembled at close distance on an ordered lattice, is a fascinating fluorescent material. It is distinctively different from the conventional (single or colloidal) dye molecules and quantum dots. Here, in this paper, we verify that when a 2DMA is placed at a nanometric distance from a metallic substrate, the strong and coherent interaction between the dipoles inside the 2DMA dominates its fluorescent decay at a picosecond timescale. Our streak-camera lifetime measurement and interacting lattice–dipole calculation reveal that the metal-mediated dipole–dipole interaction shortens the fluorescent lifetime to about one-halfmore » and increases the energy dissipation rate by 10 times that expected from the noninteracting single-dipole picture. In conclusion, our finding can enrich our understanding of nanoscale energy transfer in molecular excitonic systems and may designate a unique direction for developing fast and efficient optoelectronic devices.« less

Investigation of the heparin-thrombin interaction by dynamic force spectroscopy.

PubMed

Wang, Congzhou; Jin, Yingzi; Desai, Umesh R; Yadavalli, Vamsi K

2015-06-01

The interaction between heparin and thrombin is a vital step in the blood (anti)coagulation process. Unraveling the molecular basis of the interactions is therefore extremely important in understanding the mechanisms of this complex biological process. In this study, we use a combination of an efficient thiolation chemistry of heparin, a self-assembled monolayer-based single molecule platform, and a dynamic force spectroscopy to provide new insights into the heparin-thrombin interaction from an energy viewpoint at the molecular scale. Well-separated single molecules of heparin covalently attached to mixed self-assembled monolayers are demonstrated, whereby interaction forces with thrombin can be measured via atomic force microscopy-based spectroscopy. Further these interactions are studied at different loading rates and salt concentrations to directly obtain kinetic parameters. An increase in the loading rate shows a higher interaction force between the heparin and thrombin, which can be directly linked to the kinetic dissociation rate constant (koff). The stability of the heparin/thrombin complex decreased with increasing NaCl concentration such that the off-rate was found to be driven primarily by non-ionic forces. These results contribute to understanding the role of specific and nonspecific forces that drive heparin-thrombin interactions under applied force or flow conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

Probing Silica-Biomolecule Interactions by Solid-State NMR and Molecular Dynamics Simulations.

PubMed

Brückner, Stephan Ingmar; Donets, Sergii; Dianat, Arezoo; Bobeth, Manfred; Gutiérrez, Rafael; Cuniberti, Gianaurelio; Brunner, Eike

2016-11-08

Understanding the molecular interactions between inorganic phases such as silica and organic material is fundamental for chromatographic applications, for tailoring silica-enzyme interactions, and for elucidating the mechanisms of biomineralization. The formation, structure, and properties of the organic/inorganic interface is crucial in this context. Here, we investigate the interaction of selectively 13 C-labeled choline with 29 Si-labeled monosilicic acid/silica at the molecular level. Silica/choline nanocomposites were analyzed by solid-state NMR spectroscopy in combination with extended molecular dynamics (MD) simulations to understand the silica/organic interface. Cross-polarization magic angle spinning (CP MAS)-based NMR experiments like 1 H- 13 C CP-REDOR (rotational-echo double resonance), 1 H- 13 C HETCOR (heteronuclear correlation), and 1 H- 29 Si- 1 H double CP are employed to determine spatial parameters. The measurement of 29 Si- 13 C internuclear distances for selectively 13 C-labeled choline provides an experimental parameter that allows the direct verification of MD simulations. Atomistic modeling using classical MD methodologies is performed using the INTERFACE force field. The modeling results are in excellent agreement with the experimental data and reveal the relevant molecular conformations as well as the nature and interplay of the interactions between the choline cation and the silica surface. Electrostatic interactions and hydrogen bonding are both important and depend strongly on the hydration level as well as the charge state of the silica surface.

Multitargeting by curcumin as revealed by molecular interaction studies

PubMed Central

Gupta, Subash C.; Prasad, Sahdeo; Kim, Ji Hye; Patchva, Sridevi; Webb, Lauren J.; Priyadarsini, Indira K.

2012-01-01

Curcumin (diferuloylmethane), the active ingredient in turmeric (Curcuma longa), is a highly pleiotropic molecule with anti-inflammatory, anti-oxidant, chemopreventive, chemosensitization, and radiosensitization activities. The pleiotropic activities attributed to curcumin come from its complex molecular structure and chemistry, as well as its ability to influence multiple signaling molecules. Curcumin has been shown to bind by multiple forces directly to numerous signaling molecules, such as inflammatory molecules, cell survival proteins, protein kinases, protein reductases, histone acetyltransferase, histone deacetylase, glyoxalase I, xanthine oxidase, proteasome, HIV1 integrase, HIV1 protease, sarco (endo) plasmic reticulum Ca2+ ATPase, DNA methyltransferases 1, FtsZ protofilaments, carrier proteins, and metal ions. Curcumin can also bind directly to DNA and RNA. Owing to its β-diketone moiety, curcumin undergoes keto–enol tautomerism that has been reported as a favorable state for direct binding. The functional groups on curcumin found suitable for interaction with other macromolecules include the α, β-unsaturated β-diketone moiety, carbonyl and enolic groups of the β-diketone moiety, methoxy and phenolic hydroxyl groups, and the phenyl rings. Various biophysical tools have been used to monitor direct interaction of curcumin with other proteins, including absorption, fluorescence, Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopy, surface plasmon resonance, competitive ligand binding, Forster type fluorescence resonance energy transfer (FRET), radiolabeling, site-directed mutagenesis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), immunoprecipitation, phage display biopanning, electron microscopy, 1-anilino-8-naphthalene-sulfonate (ANS) displacement, and co-localization. Molecular docking, the most commonly employed computational tool for calculating binding affinities and predicting binding sites, has also been used to further characterize curcumin’s binding sites. Furthermore, the ability of curcumin to bind directly to carrier proteins improves its solubility and bioavailability. In this review, we focus on how curcumin directly targets signaling molecules, as well as the different forces that bind the curcumin–protein complex and how this interaction affects the biological properties of proteins. We will also discuss various analogues of curcumin designed to bind selective targets with increased affinity. PMID:21979811

Molecular dynamics simulation studies of the interactions between ionic liquids and amino acids in aqueous solution.

PubMed

Tomé, Luciana I N; Jorge, Miguel; Gomes, José R B; Coutinho, João A P

2012-02-16

Although the understanding of the influence of ionic liquids (ILs) on the solubility behavior of biomolecules in aqueous solutions is relevant for the design and optimization of novel biotechnological processes, the underlying molecular-level mechanisms are not yet consensual or clearly elucidated. In order to contribute to the understanding of the molecular interactions established between amino acids and ILs in aqueous media, classical molecular dynamics (MD) simulations were performed for aqueous solutions of five amino acids with different structural characteristics (glycine, alanine, valine, isoleucine, and glutamic acid) in the presence of 1-butyl-3-methylimidazolium bis(trifluoromethyl)sulfonyl imide. The results from MD simulations enable to relate the properties of the amino acids, namely their hydrophobicity, to the type and strength of their interactions with ILs in aqueous solutions and provide an explanation for the direction and magnitude of the solubility phenomena observed in [IL + amino acid + water] systems by a mechanism governed by a balance between competitive interactions of the IL cation, IL anion, and water with the amino acids.

Chemotaxis of Molecular Dyes in Polymer Gradients in Solution.

PubMed

Guha, Rajarshi; Mohajerani, Farzad; Collins, Matthew; Ghosh, Subhadip; Sen, Ayusman; Velegol, Darrell

2017-11-08

Chemotaxis provides a mechanism for directing the transport of molecules along chemical gradients. Here, we show the chemotactic migration of dye molecules in response to the gradients of several different neutral polymers. The magnitude of chemotactic response depends on the structure of the monomer, polymer molecular weight and concentration, and the nature of the solvent. The mechanism involves cross-diffusion up the polymer gradient, driven by favorable dye-polymer interaction. Modeling allows us to quantitatively evaluate the strength of the interaction and the effect of the various parameters that govern chemotaxis.

Inhomogeneity of PAGs in resist film studied by molecular-dynamics simulations for EUV lithography

NASA Astrophysics Data System (ADS)

Toriumi, Minoru; Itani, Toshiro

2014-03-01

EUV resist materials are requested simultaneously to improve the resolution, line-edge roughness (LER), and sensitivity (RLS). In a resist film inhomogeneous structures in nanometer region may have large effects on directly the resolution and LER and indirectly on sensitivity. Inhomogeneity of PAGs in a hybrid resist for EUV lithography was investigated using molecular dynamics simulations. The hybrid resist film showed the inhomogeneous positions and motions of PAG cations and anions. Free volumes in resist matrix influence the motions of PAGs. Molecular structure such as bulky phenyl groups of a PAG cation localize the positions and reduce the motion of a cation. Chemical properties such as ionic interactions and lone-pair interaction also play an important role to determine the inhomogeneity of PAGs. Fluorine interaction enables active motions of PAG anions.

Dynamic molecular oxygen production in cometary comae.

PubMed

Yao, Yunxi; Giapis, Konstantinos P

2017-05-08

Abundant molecular oxygen was discovered in the coma of comet 67P/Churyumov-Gerasimenko. Its origin was ascribed to primordial gaseous O 2 incorporated into the nucleus during the comet's formation. This thesis was put forward after discounting several O 2 production mechanisms in comets, including photolysis and radiolysis of water, solar wind-surface interactions and gas-phase collisions. Here we report an original Eley-Rideal reaction mechanism, which permits direct O 2 formation in single collisions of energetic water ions with oxidized cometary surface analogues. The reaction proceeds by H 2 O + abstracting a surface O-atom, then forming an excited precursor state, which dissociates to produce O 2 - . Subsequent photo-detachment leads to molecular O 2 , whose presence in the coma may thus be linked directly to water molecules and their interaction with the solar wind. This abiotic O 2 production mechanism is consistent with reported trends in the 67P coma and raises awareness of the role of energetic negative ions in comets.

Dynamic molecular oxygen production in cometary comae

NASA Astrophysics Data System (ADS)

Yao, Yunxi; Giapis, Konstantinos P.

2017-05-01

Abundant molecular oxygen was discovered in the coma of comet 67P/Churyumov-Gerasimenko. Its origin was ascribed to primordial gaseous O2 incorporated into the nucleus during the comet's formation. This thesis was put forward after discounting several O2 production mechanisms in comets, including photolysis and radiolysis of water, solar wind-surface interactions and gas-phase collisions. Here we report an original Eley-Rideal reaction mechanism, which permits direct O2 formation in single collisions of energetic water ions with oxidized cometary surface analogues. The reaction proceeds by H2O+ abstracting a surface O-atom, then forming an excited precursor state, which dissociates to produce O2-. Subsequent photo-detachment leads to molecular O2, whose presence in the coma may thus be linked directly to water molecules and their interaction with the solar wind. This abiotic O2 production mechanism is consistent with reported trends in the 67P coma and raises awareness of the role of energetic negative ions in comets.

Molecular recognition in gas sensing: Results from acoustic wave and in-situ FTIR measurements

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

Hierlemann, A.; Ricco, A.J.; Bodenhoefer, K.

Surface acoustic wave (SAW) measurements were combined with direct, in-situ molecular spectroscopy to understand the interactions of surface-confined sensing films with gas-phase analytes. This was accomplished by collecting Fourier-transform infrared external-reflectance spectra (FTIR-ERS) on operating SAW devices during dosing of their specifically coated surfaces with key analytes.

Effect of molecular weight profile of sorghum proanthocyanidins on resistant starch formation.

PubMed

Barros, Frederico; Awika, Joseph; Rooney, Lloyd W

2014-04-01

There is a growing interest to increase resistant starch (RS) in foods through natural modification of starch. Sorghum tannins (proanthocyanidins, PAs) were recently reported to interact with starch, increasing RS. However, there is no information about how the molecular weight profile of PAs affects RS formation. This study investigated how different-molecular-weight PAs from sorghum affected RS formation in different starch models. The levels of RS were higher (331-437 mg g(-1)) when high-amylose starch was cooked with phenolic extracts containing mostly high-molecular-weight PAs compared with extracts containing lower-molecular-weight PAs or monomeric catechin (249-285 mg g(-1)). In general, binding capacity of PAs with amylose increased proportionally with molecular weight. For example, the percentage of PAs bound to amylose increased from 45% (PAs with degree of polymerization (DP) = 6) to 94% (polymeric PAs, DP > 10). The results demonstrate that molecular weight of the PAs directly affects their interaction with starch: the higher the molecular weight, the stronger the binding to amylose and the higher the RS formation. Polymeric PAs from sorghum can naturally modify starch by interacting strongly with amylose and are thus most suitable to produce foods with higher RS. © 2013 Society of Chemical Industry.

High molecular weight kininogen regulates platelet-leukocyte interactions by bridging Mac-1 and glycoprotein Ib.

PubMed

Chavakis, Triantafyllos; Santoso, Sentot; Clemetson, Kenneth J; Sachs, Ulrich J H; Isordia-Salas, Irma; Pixley, Robin A; Nawroth, Peter P; Colman, Robert W; Preissner, Klaus T

2003-11-14

Leukocyte-platelet interaction is important in mediating leukocyte adhesion to a thrombus and leukocyte recruitment to a site of vascular injury. This interaction is mediated at least in part by the beta2-integrin Mac-1 (CD11b/CD18) and its counter-receptor on platelets, glycoprotein Ibalpha (GPIbalpha). High molecular weight kininogen (HK) was previously shown to interact with both GPIbalpha and Mac-1 through its domains 3 and 5, respectively. In this study we investigated the ability of HK to interfere with the leukocyte-platelet interaction. In a purified system, HK binding to GPIbalpha was inhibited by HK domain 3 and the monoclonal antibody (mAb) SZ2, directed against the epitope 269-282 of GPIbalpha, whereas mAb AP1, directed to the region 201-268 of GPIbalpha had no effect. In contrast, mAb AP1 inhibited the Mac-1-GPIbalpha interaction. Binding of GPIbalpha to Mac-1 was enhanced 2-fold by HK. This effect of HK was abrogated in the presence of HK domains 3 or 5 or peptides from the 475-497 region of the carboxyl terminus of domain 5 as well as in the presence of mAb SZ2 but not mAb AP1. Whereas no difference in the affinity of the Mac-1-GPIbalpha interaction was observed in the absence or presence of HK, maximal binding of GPIbalpha to Mac-1 doubled in the presence of HK. Moreover, HK/HKa increased the Mac-1-dependent adhesion of myelomonocytic U937 cells and K562 cells transfected with Mac-1 to immobilized GPIbalpha or to GPIbalpha-transfected Chinese hamster ovary cells. Finally, Mac-1-dependent adhesion of neutrophils to surface-adherent platelets was enhanced by HK. Thus, HK can bridge leukocytes with platelets by interacting via its domain 3 with GPIbalpha and via its domain 5 with Mac-1 thereby augmenting the Mac-1-GPIbalpha interaction. These distinct molecular interactions of HK with leukocytes and platelets contribute to the regulation of the adhesive behavior of vascular cells and provide novel molecular targets for reducing atherothrombotic pathologies.

Assembling oppositely charged lock and key responsive colloids: A mesoscale analog of adaptive chemistry

PubMed Central

Mihut, Adriana M.; Stenqvist, Björn; Lund, Mikael; Schurtenberger, Peter; Crassous, Jérôme J.

2017-01-01

We have seen a considerable effort in colloid sciences to copy Nature’s successful strategies to fabricate complex functional structures through self-assembly. This includes attempts to design colloidal building blocks and their intermolecular interactions, such as creating the colloidal analogs of directional molecular interactions, molecular recognition, host-guest systems, and specific binding. We show that we can use oppositely charged thermoresponsive particles with complementary shapes, such as spherical and bowl-shaped particles, to implement an externally controllable lock-and-key self-assembly mechanism. The use of tunable electrostatic interactions combined with the temperature-dependent size and shape and van der Waals interactions of these building blocks provides an exquisite control over the selectivity and specificity of the interactions and self-assembly process. The dynamic nature of the mechanism allows for reversibly cycling through various structures that range from weakly structured dense liquids to well-defined molecule-shaped clusters with different configurations through variations in temperature and ionic strength. We link this complex and dynamic self-assembly behavior to the relevant molecular interactions, such as screened Coulomb and van der Waals forces and the geometrical complementarity of the two building blocks, and discuss our findings in the context of the concepts of adaptive chemistry recently introduced to molecular systems. PMID:28929133

The ER stress sensor PERK luminal domain functions as a molecular chaperone to interact with misfolded proteins

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

Wang, Peng; Li, Jingzhi; Sha, Bingdong

2016-11-29

PERK is one of the major sensor proteins which can detect the protein-folding imbalance generated by endoplasmic reticulum (ER) stress. It remains unclear how the sensor protein PERK is activated by ER stress. It has been demonstrated that the PERK luminal domain can recognize and selectively interact with misfolded proteins but not native proteins. Moreover, the PERK luminal domain may function as a molecular chaperone to directly bind to and suppress the aggregation of a number of misfolded model proteins. The data strongly support the hypothesis that the PERK luminal domain can interact directly with misfolded proteins to induce ERmore » stress signaling. To illustrate the mechanism by which the PERK luminal domain interacts with misfolded proteins, the crystal structure of the human PERK luminal domain was determined to 3.2 Å resolution. Two dimers of the PERK luminal domain constitute a tetramer in the asymmetric unit. Superimposition of the PERK luminal domain molecules indicated that the β-sandwich domain could adopt multiple conformations. It is hypothesized that the PERK luminal domain may utilize its flexible β-sandwich domain to recognize and interact with a broad range of misfolded proteins.« less

The ER stress sensor PERK luminal domain functions as a molecular chaperone to interact with misfolded proteins.

PubMed

Wang, Peng; Li, Jingzhi; Sha, Bingdong

2016-12-01

PERK is one of the major sensor proteins which can detect the protein-folding imbalance generated by endoplasmic reticulum (ER) stress. It remains unclear how the sensor protein PERK is activated by ER stress. It has been demonstrated that the PERK luminal domain can recognize and selectively interact with misfolded proteins but not native proteins. Moreover, the PERK luminal domain may function as a molecular chaperone to directly bind to and suppress the aggregation of a number of misfolded model proteins. The data strongly support the hypothesis that the PERK luminal domain can interact directly with misfolded proteins to induce ER stress signaling. To illustrate the mechanism by which the PERK luminal domain interacts with misfolded proteins, the crystal structure of the human PERK luminal domain was determined to 3.2 Å resolution. Two dimers of the PERK luminal domain constitute a tetramer in the asymmetric unit. Superimposition of the PERK luminal domain molecules indicated that the β-sandwich domain could adopt multiple conformations. It is hypothesized that the PERK luminal domain may utilize its flexible β-sandwich domain to recognize and interact with a broad range of misfolded proteins.

Isotope separation apparatus and method

DOEpatents

Feldman, Barry J.

1985-01-01

The invention relates to an improved method and apparatus for laser isotope separation by photodeflection. A molecular beam comprising at least two isotopes to be separated intersects, preferably substantially perpendicular to one broad side of the molecular beam, with a laser beam traveling in a first direction. The laser beam is reflected back through the molecular beam, preferably in a second direction essentially opposite to the first direction. Because the molecules in the beam occupy various degenerate energy levels, if the laser beam comprises chirped pulses comprising selected wavelengths, the laser beam will very efficiently excite substantially all unexcited molecules and will cause stimulated emission of substantially all excited molecules of a selected one of the isotopes in the beam which such pulses encounter. Excitation caused by first direction chirped pulses moves molecules of the isotope excited thereby in the first direction. Stimulated emission of excited molecules of the isotope is brought about by returning chirped pulses traveling in the second direction. Stimulated emission moves emitting molecules in a direction opposite to the photon emitted. Because emitted photons travel in the second direction, emitting molecules move in the first direction. Substantial molecular movement of essentially all the molecules containing the one isotope is accomplished by a large number of chirped pulse-molecule interactions. A beam corer collects the molecules in the resulting enriched divergent portions of the beam.

Direct induction of molecular alignment in liquid crystal polymer network film by photopolymerization

NASA Astrophysics Data System (ADS)

Hisano, K.; Aizawa, M.; Ishizu, M.; Kurata, Y.; Shishido, A.

2016-09-01

Liquid crystal (LC) is the promising material for the fabrication of high-performance soft, flexible devices. The fascinating and useful properties arise from their cooperative effect that inherently allows the macroscopic integration and control of molecular alignment through various external stimuli. To date, light-matter interaction is the most attractive stimuli and researchers developed photoalignment through photochemical or photophysical reactions triggered by linearly polarized light. Here we show the new choice based on molecular diffusion by photopolymerization. We found that photopolymerization of a LC monomer and a crosslinker through a photomask enables to direct molecular alignment in the resultant LC polymer network film. The key generating the molecular alignment is molecular diffusion due to the difference of chemical potentials between irradiated and unirradiated regions. This concept is applicable to various shapes of photomask and two-dimensional molecular alignments can be fabricated depending on the spatial design of photomask. By virtue of the inherent versatility of molecular diffusion in materials, the process would shed light on the fabrication of various high-performance flexible materials with molecular alignment having controlled patterns.

Optimization of a polymer composite employing molecular mechanic simulations and artificial neural networks for a novel intravaginal bioadhesive drug delivery device.

PubMed

Ndesendo, Valence M K; Pillay, Viness; Choonara, Yahya E; du Toit, Lisa C; Kumar, Pradeep; Buchmann, Eckhart; Meyer, Leith C R; Khan, Riaz A

2012-01-01

This study aimed at elucidating an optimal synergistic polymer composite for achieving a desirable molecular bioadhesivity and Matrix Erosion of a bioactive-loaded Intravaginal Bioadhesive Polymeric Device (IBPD) employing Molecular Mechanic Simulations and Artificial Neural Networks (ANN). Fifteen lead caplet-shaped devices were formulated by direct compression with the model bioactives zidovudine and polystyrene sulfonate. The Matrix Erosion was analyzed in simulated vaginal fluid to assess the critical integrity. Blueprinting the molecular mechanics of bioadhesion between vaginal epithelial glycoprotein (EGP), mucin (MUC) and the IBPD were performed on HyperChem 8.0.8 software (MM+ and AMBER force fields) for the quantification and characterization of correlative molecular interactions during molecular bioadhesion. Results proved that the IBPD bioadhesivity was pivoted on the conformation, orientation, and poly(acrylic acid) (PAA) composition that interacted with EGP and MUC present on the vaginal epithelium due to heterogeneous surface residue distributions (free energy= -46.33 kcalmol(-1)). ANN sensitivity testing as a connectionist model enabled strategic polymer selection for developing an IBPD with an optimally prolonged Matrix Erosion and superior molecular bioadhesivity (ME = 1.21-7.68%; BHN = 2.687-4.981 N/mm(2)). Molecular modeling aptly supported the EGP-MUC-PAA molecular interaction at the vaginal epithelium confirming the role of PAA in bioadhesion of the IBPD once inserted into the posterior fornix of the vagina.

Sorting nexin 9 recruits clathrin heavy chain to the mitotic spindle for chromosome alignment and segregation.

PubMed

Ma, Maggie P C; Robinson, Phillip J; Chircop, Megan

2013-01-01

Sorting nexin 9 (SNX9) and clathrin heavy chain (CHC) each have roles in mitosis during metaphase. Since the two proteins directly interact for their other cellular function in endocytosis we investigated whether they also interact for metaphase and operate on the same pathway. We report that SNX9 and CHC functionally interact during metaphase in a specific molecular pathway that contributes to stabilization of mitotic spindle kinetochore (K)-fibres for chromosome alignment and segregation. This function is independent of their endocytic role. SNX9 residues in the clathrin-binding low complexity domain are required for CHC association and for targeting both CHC and transforming acidic coiled-coil protein 3 (TACC3) to the mitotic spindle. Mutation of these sites to serine increases the metaphase plate width, indicating inefficient chromosome congression. Therefore SNX9 and CHC function in the same molecular pathway for chromosome alignment and segregation, which is dependent on their direct association.

Sorting Nexin 9 Recruits Clathrin Heavy Chain to the Mitotic Spindle for Chromosome Alignment and Segregation

PubMed Central

Ma, Maggie P. C.; Robinson, Phillip J.; Chircop, Megan

2013-01-01

Sorting nexin 9 (SNX9) and clathrin heavy chain (CHC) each have roles in mitosis during metaphase. Since the two proteins directly interact for their other cellular function in endocytosis we investigated whether they also interact for metaphase and operate on the same pathway. We report that SNX9 and CHC functionally interact during metaphase in a specific molecular pathway that contributes to stabilization of mitotic spindle kinetochore (K)-fibres for chromosome alignment and segregation. This function is independent of their endocytic role. SNX9 residues in the clathrin-binding low complexity domain are required for CHC association and for targeting both CHC and transforming acidic coiled-coil protein 3 (TACC3) to the mitotic spindle. Mutation of these sites to serine increases the metaphase plate width, indicating inefficient chromosome congression. Therefore SNX9 and CHC function in the same molecular pathway for chromosome alignment and segregation, which is dependent on their direct association. PMID:23861900

Vacancy–Vacancy Interaction Induced Oxygen Diffusivity Enhancement in Undoped Nonstoichiometric Ceria

DOE PAGES

Yuan, Fenglin; Zhang, Yanwen; Weber, William J.

2015-05-19

In this paper, molecular dynamics simulations and molecular static calculations have been used to systematically study oxygen vacancy transport in undoped nonstoichiometric ceria. A strong oxygen diffusivity enhancement appears in the vacancy concentration range of 2–4% over the temperature range from 1000 to 2000 K. An Arrhenius ion diffusion mechanism by vacancy hopping along the (100) direction is unambiguously identified, and an increasing trend of both the oxygen migration barrier and the prefactor with increasing vacancy concentration is observed. Within the framework of classical diffusion theory, a weak concentration dependence of the prefactor in oxygen vacancy migration is shown tomore » be crucial for explaining the unusual fast oxygen ion migration in the low concentration range and consequently the appearance of a maximum in oxygen diffusivity. Finally, a representative (100) direction interaction model is constructed to identify long-range vacancy–vacancy interaction as the structural origin of the positive correlation between oxygen migration barrier and vacancy concentration.« less

Molecular dynamics approaches to the design and synthesis of PCB targeting molecularly imprinted polymers: interference to monomer-template interactions in imprinting of 1,2,3-trichlorobenzene.

PubMed

Cleland, Dougal; Olsson, Gustaf D; Karlsson, Björn C G; Nicholls, Ian A; McCluskey, Adam

2014-02-07

The interactions between each component of the pre-polymerisation mixtures used in the synthesis of molecularly imprinted polymers (MIP) specific for 1,2,3,4,5-pentachlorobenzene (1) and 1,2,3-trichlorobenzene (2) were examined in four molecular dynamics simulations. These simulations revealed that the relative frequency of functional monomer-template (FM-T) interactions was consistent with results obtained by the synthesis and evaluation of the actual MIPs. The higher frequency of 1 interaction with trimethylstyrene (TMS; 54.7%) than 1 interaction with pentafluorostyrene (PFS; 44.7%) correlated with a higher imprinting factor (IF) of 2.1 vs. 1.7 for each functional monomer respectively. The higher frequency of PFS interactions with 2 (29.6%) than TMS interactions with 2 (1.9%) also correlated well with the observed differences in IF (3.7) of 2 MIPs imprinted using PFS as the FM than the IF (2.8) of 2 MIPs imprinted using TMS as the FM. The TMS-1 interaction dominated the molecular simulation due to high interaction energies, but the weaker TMS-2 resulted in low interaction maintenance, and thus lower IF values. Examination of the other pre-polymerisation mixture components revealed that the low levels of TMS-2 interaction was, in part, due to interference caused by the cross linker (CL) ethyleneglycol dimethylacrylate (EGDMA) interactions with TMS. The main reason was, however, attributed to MeOH interactions with TMS in both a hydrogen bond and perpendicular configuration. This positioned a MeOH directly above the π-orbital of all TMS for an average of 63.8% of MD2 creating significant interference to π-π stacking interactions between 2 and TMS. These findings are consistent with the deviation from the 'normal' molecularly imprinted polymer synthesis ratio of 1 : 4 : 20 (T : FM : CL) of 20 : 1 : 29 and 15 : 6 : 29 observed with 2 and TMS and PFS respectively. Our molecular dynamics simulations correctly predicted the high level of interference from other MIP synthesis components. The effect on PFS-1 interaction by MeOH was significantly lower and thus this system was not adversely affected.

Optically (solar) pumped oxygen-iodine lasers

NASA Astrophysics Data System (ADS)

Danilov, O. B.; Zhevlakov, A. P.; Yur'ev, M. S.

2014-07-01

We present the results of theoretical and experimental studies demonstrating the possibility of developing an oxygen-iodine laser (OIL) with direct optical pumping of molecular oxygen involving inter-molecular interaction with charge transfer from donor molecule (buffer gas) to acceptor molecule (oxygen). This interaction lifts degeneracy of the lower energy states of molecular oxygen and increases its absorption cross section in the visible spectral region and the UV Herzberg band, where high quantum yield of singlet oxygen is achieved (QY ˜ 1 and QY ˜ 2, respectively) at the same time. A pulse-periodic optical pump sources with pulse energy of ˜50 kJ, pulse duration of ˜25 μs, and repetition rate of ˜10 Hz, which are synchronized with the mechanism of singlet oxygen generation, are developed. This allows implementation of a pulse-periodic oxygen-iodine laser with an efficiency of ˜25%, optical efficiency of ˜40%, and parameter L/ T ˜ 1/1.5, where T is the thermal energy released in the laser active medium upon generation of energy L. It is demonstrated that, under direct solar pumping of molecular oxygen, the efficiency parameter of the OIL can reach L/ T ˜ 1/0.8 in a wide range of scaling factors.

Fibrin-based biomaterials: Modulation of macroscopic properties through rational design at the molecular level

PubMed Central

Brown, Ashley C.; Barker, Thomas H.

2013-01-01

Fibrinogen is one of the primary components of the coagulation cascade and rapidly forms an insoluble matrix following tissue injury. In addition to its important role in hemostasis, fibrin acts as a scaffold for tissue repair and provides important cues for directing cell phenotype following injury. Because of these properties and the ease of polymerization of the material, fibrin has been widely utilized as a biomaterial for over a century. Modifying the macroscopic properties of fibrin, such as elasticity and porosity, has been somewhat elusive until recently, yet with a molecular-level rational design approach can now be somewhat easily modified through alterations of molecular interactions key to the protein’s polymerization process. This review outlines the biochemistry of fibrin and discusses methods for modification of molecular interactions and their application to fibrin based biomaterials. PMID:24056097

Heat shock protein 47 and 65-kDa FK506-binding protein weakly but synergistically interact during collagen folding in the endoplasmic reticulum.

PubMed

Ishikawa, Yoshihiro; Holden, Paul; Bächinger, Hans Peter

2017-10-20

Collagen is the most abundant protein in the extracellular matrix in humans and is critical to the integrity and function of many musculoskeletal tissues. A molecular ensemble comprising more than 20 molecules is involved in collagen biosynthesis in the rough endoplasmic reticulum. Two proteins, heat shock protein 47 (Hsp47/ SERPINH1 ) and 65-kDa FK506-binding protein (FKBP65/ FKBP10 ), have been shown to play important roles in this ensemble. In humans, autosomal recessive mutations in both genes cause similar osteogenesis imperfecta phenotypes. Whereas it has been proposed that Hsp47 and FKBP65 interact in the rough endoplasmic reticulum, there is neither clear evidence for this interaction nor any data regarding their binding affinities for each other. In this study using purified endogenous proteins, we examined the interaction between Hsp47, FKBP65, and collagen and also determined their binding affinities and functions in vitro Hsp47 and FKBP65 show a direct but weak interaction, and FKBP65 prefers to interact with Hsp47 rather than type I collagen. Our results suggest that a weak interaction between Hsp47 and FKBP65 confers mutual molecular stability and also allows for a synergistic effect during collagen folding. We also propose that Hsp47 likely acts as a hub molecule during collagen folding and secretion by directing other molecules to reach their target sites on collagens. Our findings may explain why osteogenesis imperfecta-causing mutations in both genes result in similar phenotypes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Gene-Environment Interactions in Schizophrenia: Review of Epidemiological Findings and Future Directions

PubMed Central

van Os, Jim; Rutten, Bart PF; Poulton, Richie

2008-01-01

Concern is building about high rates of schizophrenia in large cities, and among immigrants, cannabis users, and traumatized individuals, some of which likely reflects the causal influence of environmental exposures. This, in combination with very slow progress in the area of molecular genetics, has generated interest in more complicated models of schizophrenia etiology that explicitly posit gene-environment interactions (EU-GEI. European Network of Schizophrenia Networks for the Study of Gene Environment Interactions. Schizophrenia aetiology: do gene-environment interactions hold the key? [published online ahead of print April 25, 2008] Schizophr Res; S0920-9964(08) 00170–9). Although findings of epidemiological gene-environment interaction (G × E) studies are suggestive of widespread gene-environment interactions in the etiology of schizophrenia, numerous challenges remain. For example, attempts to identify gene-environment interactions cannot be equated with molecular genetic studies with a few putative environmental variables “thrown in”: G × E is a multidisciplinary exercise involving epidemiology, psychology, psychiatry, neuroscience, neuroimaging, pharmacology, biostatistics, and genetics. Epidemiological G × E studies using indirect measures of genetic risk in genetically sensitive designs have the advantage that they are able to model the net, albeit nonspecific, genetic load. In studies using direct molecular measures of genetic variation, a hypothesis-driven approach postulating synergistic effects between genes and environment impacting on a final common pathway, such as “sensitization” of mesolimbic dopamine neurotransmission, while simplistic, may provide initial focus and protection against the numerous false-positive and false-negative results that these investigations engender. Experimental ecogenetic approaches with randomized assignment may help to overcome some of the limitations of observational studies and allow for the additional elucidation of underlying mechanisms using a combination of functional enviromics and functional genomics. PMID:18791076

Molecular Mediators Governing Iron-Copper Interactions

PubMed Central

Gulec, Sukru; Collins, James F.

2015-01-01

Given their similar physiochemical properties, it is a logical postulate that iron and copper metabolism are intertwined. Indeed, iron-copper interactions were first documented over a century ago, but the homeostatic effects of one on the other has not been elucidated at a molecular level to date. Recent experimental work has, however, begun to provide mechanistic insight into how copper influences iron metabolism. During iron deficiency, elevated copper levels are observed in the intestinal mucosa, liver, and blood. Copper accumulation and/or redistribution within enterocytes may influence iron transport, and high hepatic copper may enhance biosynthesis of a circulating ferroxidase, which potentiates iron release from stores. Moreover, emerging evidence has documented direct effects of copper on the expression and activity of the iron-regulatory hormone hepcidin. This review summarizes current experimental work in this field, with a focus on molecular aspects of iron-copper interplay and how these interactions relate to various disease states. PMID:24995690

Bimolecular fluorescence complementation: visualization of molecular interactions in living cells.

PubMed

Kerppola, Tom K

2008-01-01

A variety of experimental methods have been developed for the analysis of protein interactions. The majority of these methods either require disruption of the cells to detect molecular interactions or rely on indirect detection of the protein interaction. The bimolecular fluorescence complementation (BiFC) assay provides a direct approach for the visualization of molecular interactions in living cells and organisms. The BiFC approach is based on the facilitated association between two fragments of a fluorescent protein when the fragments are brought together by an interaction between proteins fused to the fragments. The BiFC approach has been used for visualization of interactions among a variety of structurally diverse interaction partners in many different cell types. It enables detection of transient complexes as well as complexes formed by a subpopulation of the interaction partners. It is essential to include negative controls in each experiment in which the interface between the interaction partners has been mutated or deleted. The BiFC assay has been adapted for simultaneous visualization of multiple protein complexes in the same cell and the competition for shared interaction partners. A ubiquitin-mediated fluorescence complementation assay has also been developed for visualization of the covalent modification of proteins by ubiquitin family peptides. These fluorescence complementation assays have a great potential to illuminate a variety of biological interactions in the future.

4-[(1-Benzyl-1H-1,2,3-triazol-4-yl)meth-oxy]benzene-1,2-dicarbo-nitrile: crystal structure, Hirshfeld surface analysis and energy-minimization calculations.

PubMed

Shamsudin, Norzianah; Tan, Ai Ling; Young, David J; Jotani, Mukesh M; Otero-de-la-Roza, A; Tiekink, Edward R T

2016-04-01

In the solid state, the title compound, C18H13N5O, adopts a conformation whereby the phenyl ring and meth-oxy-benzene-1,2-dicarbo-nitrile residue (r.m.s. deviation of the 12 non-H atoms = 0.041 Å) lie to opposite sides of the central triazolyl ring, forming dihedral angles of 79.30 (13) and 64.59 (10)°, respectively; the dihedral angle between the outer rings is 14.88 (9)°. This conformation is nearly 7 kcal mol(-1) higher in energy than the energy-minimized structure which has a syn disposition of the outer rings, enabling intra-molecular π-π inter-actions. In the crystal, methyl-ene-C-H⋯N(triazol-yl) and carbo-nitrile-N⋯π(benzene) inter-actions lead to supra-molecular chains along the a axis. Supra-molecular layers in the ab plane arise as the chains are connected by benzene-C-H⋯N(carbo-nitrile) inter-actions; layers stack with no directional inter-actions between them. The specified inter-molecular contacts along with other, weaker contributions to the supra-molecular stabilization are analysed in a Hirshfeld surface analysis.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

NASA Astrophysics Data System (ADS)

Mrugalla, Florian; Kast, Stefan M.

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory.

PubMed

Mrugalla, Florian; Kast, Stefan M

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Recent experimental advances on hydrophobic interactions at solid/water and fluid/water interfaces.

PubMed

Zeng, Hongbo; Shi, Chen; Huang, Jun; Li, Lin; Liu, Guangyi; Zhong, Hong

2015-03-15

Hydrophobic effects play important roles in a wide range of natural phenomena and engineering processes such as coalescence of oil droplets in water, air flotation of mineral particles, and folding and assembly of proteins and biomembranes. In this work, the authors highlight recent experimental attempts to reveal the physical origin of hydrophobic effects by directly quantifying the hydrophobic interaction on both solid/water and fluid/water interfaces using state-of-art nanomechanical techniques such as surface forces apparatus and atomic force microscopy (AFM). For solid hydrophobic surfaces of different hydrophobicity, the range of hydrophobic interaction was reported to vary from ∼10 to >100 nm. With various characterization techniques, the very long-ranged attraction (>100 nm) has been demonstrated to be mainly attributed to nonhydrophobic interaction mechanisms such as pre-existing nanobubbles and molecular rearrangement. By ruling out these factors, intrinsic hydrophobic interaction was measured to follow an exponential law with decay length of 1-2 nm with effective range less than 20 nm. On the other hand, hydrophobic interaction measured at fluid interfaces using AFM droplet/bubble probe technique was found to decay with a much shorter length of ∼0.3 nm. This discrepancy of measured decay lengths is proposed to be attributed to inherent physical distinction between solid and fluid interfaces, which impacts the structure of interface-adjacent water molecules. Direct measurement of hydrophobic interaction on a broader range of interfaces and characterization of interfacial water molecular structure using spectroscopic techniques are anticipated to help unravel the origin of this rigidity-related mismatch of hydrophobic interaction and hold promise to uncover the physical nature of hydrophobic effects. With improved understanding of hydrophobic interaction, intrinsic interaction mechanisms of many biological and chemical pathways can be better elucidated, and novel devices/processes can be developed with capacity to modulate and control the hydrophobic effects from the molecular to the macroscopic scale.

Conjugation of antibodies to gold nanorods through Fc portion: synthesis and molecular specific imaging

PubMed Central

Joshi, Pratixa P.; Yoon, Soon Joon; Hardin, William G.; Emelianov, Stanislav; Sokolov, Konstantin V.

2013-01-01

Anisotropic gold nanorods provide a convenient combination of properties, such as tunability of plasmon resonances and strong extinction cross-sections in the near-infrared to red spectral region. These properties have created significant interest in the development of antibody conjugation methods for synthesis of targeted nanorods for a number of biomedical applications, including molecular specific imaging and therapy. Previously published conjugation approaches have achieved molecular specificity. However, the current conjugation methods have several downsides including low stability and potential cytotoxicity of bioconjugates that are produced by electrostatic interactions as well as lack of control over antibody orientation during covalent conjugation. Here we addressed these shortcomings by introducing directional antibody conjugation to the gold nanorod surface. The directional conjugation is achieved through the carbohydrate moiety, which is located on one of the heavy chains of the Fc portion of most antibodies. The carbohydrate is oxidized under mild conditions to a hydrazide reactive aldehyde group. Then, a heterofunctional linker with hydrazide and dithiol groups is used to attach antibodies to gold nanorods. The directional conjugation approach was characterized using electron microscopy, zeta potential and extinction spectra. We also determined spectral changes associated with nanorod aggregation; these spectral changes can be used as a convenient quality control of nanorod bioconjugates. Molecular specificity of the synthesized antibody targeted nanorods was demonstrated using hyperspectral optical and photoacoustic imaging of cancer cell culture models. Additionally, we observed characteristic changes in optical spectra of molecular specific nanorods after their interactions with cancer cells; the observed spectral signatures can be explored for sensitive cancer detection. PMID:23631707

A turbulent wake as a tracer of 30,000 years of Mira's mass loss history.

PubMed

Martin, D Christopher; Seibert, Mark; Neill, James D; Schiminovich, David; Forster, Karl; Rich, R Michael; Welsh, Barry Y; Madore, Barry F; Wheatley, Jonathan M; Morrissey, Patrick; Barlow, Tom A

2007-08-16

Mira is one of the first variable stars ever discovered and it is the prototype (and also the nearest example) of a class of low-to-intermediate-mass stars in the late stages of stellar evolution. These stars are relatively common and they return a large fraction of their original mass to the interstellar medium (ISM) (ref. 2) through a processed, dusty, molecular wind. Thus stars in Mira's stage of evolution have a direct impact on subsequent star and planet formation in their host galaxy. Previously, the only direct observation of the interaction between Mira-type stellar winds and the ISM was in the infrared. Here we report the discovery of an ultraviolet-emitting bow shock and turbulent wake extending over 2 degrees on the sky, arising from Mira's large space velocity and the interaction between its wind and the ISM. The wake is visible only in the far ultraviolet and is consistent with an unusual emission mechanism whereby molecular hydrogen is excited by turbulent mixing of cool molecular gas and shock-heated gas. This wind wake is a tracer of the past 30,000 years of Mira's mass-loss history and provides an excellent laboratory for studying turbulent stellar wind-ISM interactions.

Simulation of wave packet tunneling of interacting identical particles

NASA Astrophysics Data System (ADS)

Lozovik, Yu. E.; Filinov, A. V.; Arkhipov, A. S.

2003-02-01

We demonstrate a different method of simulation of nonstationary quantum processes, considering the tunneling of two interacting identical particles, represented by wave packets. The used method of quantum molecular dynamics (WMD) is based on the Wigner representation of quantum mechanics. In the context of this method ensembles of classical trajectories are used to solve quantum Wigner-Liouville equation. These classical trajectories obey Hamiltonian-like equations, where the effective potential consists of the usual classical term and the quantum term, which depends on the Wigner function and its derivatives. The quantum term is calculated using local distribution of trajectories in phase space, therefore, classical trajectories are not independent, contrary to classical molecular dynamics. The developed WMD method takes into account the influence of exchange and interaction between particles. The role of direct and exchange interactions in tunneling is analyzed. The tunneling times for interacting particles are calculated.

Design and Implementation of a Self-Directed Stereochemistry Lesson Using Embedded Virtual Three-Dimensional Images in a Portable Document Format

ERIC Educational Resources Information Center

Cody, Jeremy A.; Craig, Paul A.; Loudermilk, Adam D.; Yacci, Paul M.; Frisco, Sarah L.; Milillo, Jennifer R.

2012-01-01

A novel stereochemistry lesson was prepared that incorporated both handheld molecular models and embedded virtual three-dimensional (3D) images. The images are fully interactive and eye-catching for the students; methods for preparing 3D molecular images in Adobe Acrobat are included. The lesson was designed and implemented to showcase the 3D…

Molecular level in silico studies for oncology. Direct models review

NASA Astrophysics Data System (ADS)

Psakhie, S. G.; Tsukanov, A. A.

2017-09-01

The combination of therapy and diagnostics in one process "theranostics" is a trend in a modern medicine, especially in oncology. Such an approach requires development and usage of multifunctional hybrid nanoparticles with a hierarchical structure. Numerical methods and mathematical models play a significant role in the design of the hierarchical nanoparticles and allow looking inside the nanoscale mechanisms of agent-cell interactions. The current position of in silico approach in biomedicine and oncology is discussed. The review of the molecular level in silico studies in oncology, which are using the direct models, is presented.

The changing world of G protein-coupled receptors: from monomers to dimers and receptor mosaics with allosteric receptor-receptor interactions.

PubMed

Fuxe, Kjell; Marcellino, Daniel; Borroto-Escuela, Dasiel Oscar; Frankowska, Malgorzata; Ferraro, Luca; Guidolin, Diego; Ciruela, Francisco; Agnati, Luigi F

2010-10-01

Based on indications of direct physical interactions between neuropeptide and monoamine receptors in the early 1980s, the term receptor-receptor interactions was introduced and later on the term receptor heteromerization in the early 1990s. Allosteric mechanisms allow an integrative activity to emerge either intramolecularly in G protein-coupled receptor (GPCR) monomers or intermolecularly via receptor-receptor interactions in GPCR homodimers, heterodimers, and receptor mosaics. Stable heteromers of Class A receptors may be formed that involve strong high energy arginine-phosphate electrostatic interactions. These receptor-receptor interactions markedly increase the repertoire of GPCR recognition, signaling and trafficking in which the minimal signaling unit in the GPCR homomers appears to be one receptor and one G protein. GPCR homomers and GPCR assemblies are not isolated but also directly interact with other proteins to form horizontal molecular networks at the plasma membrane.

Molecular interaction of 2-mercaptobenzimidazole with catalase reveals a potentially toxic mechanism of the inhibitor.

PubMed

Teng, Yue; Zou, Luyi; Huang, Ming; Zong, Wansong

2014-12-01

2-Mercaptobenzimidazole (MBI) is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment possesses a potential risk to human health. In this work, the toxic interaction of MBI with the important antioxidant enzyme catalase (CAT) was investigated using spectroscopic and molecular docking methods under physiological conditions. MBI can spontaneously bind with CAT with one binding site through hydrogen bonds and van der Waals forces to form MBI-CAT complex. The molecular docking study revealed that MBI bound into the CAT interface of chains B and C, which led to some conformational and microenvironmental changes of CAT and further resulted in the inhibition of CAT activity. This present study provides direct evidence at a molecular level to show that exposure to MBI could induce changes in the structure and function of the enzyme CAT. Copyright © 2014 Elsevier B.V. All rights reserved.

Metabolism of 4-Aminopiperidine Drugs by Cytochrome P450s: Molecular and Quantum Mechanical Insights into Drug Design

PubMed Central

2011-01-01

4-Aminopiperidines are a variety of therapeutic agents that are extensively metabolized by cytochrome P450s with CYP3A4 as a major isoform catalyzing their N-dealkylation reaction. However, its catalytic mechanism has not been fully elucidated in a molecular interaction level. Here, we applied theoretical approaches including the molecular mechanics-based docking to study the binding patterns and quantum mechanics-based reactivity calculations. They were supported by the experimental human liver microsomal clearance and P450 isoform phenotyping data. Our results herein suggested that the molecular interactions between substrates and CYP3A4 active site residues are essential for the N-dealkylation of 4-aminopiperidines. We also found that the serine 119 residue of CYP3A4 may serve as a key hydrogen-bonding partner to interact with the 4-amino groups of the studied drugs. The reactivity of the side chain α-carbon hydrogens drives the direction of catalysis as well. As a result, structure-based drug design approaches look promising to guide drug discovery programs into the optimized drug metabolism space. PMID:21841964

Molecular hydrogen interacts more strongly when rotationally excited at low temperatures leading to faster reactions.

PubMed

Shagam, Yuval; Klein, Ayelet; Skomorowski, Wojciech; Yun, Renjie; Averbukh, Vitali; Koch, Christiane P; Narevicius, Edvardas

2015-11-01

The role of internal molecular degrees of freedom, such as rotation, has scarcely been explored experimentally in low-energy collisions despite their significance to cold and ultracold chemistry. Particularly important to astrochemistry is the case of the most abundant molecule in interstellar space, hydrogen, for which two spin isomers have been detected, one of which exists in its rotational ground state whereas the other is rotationally excited. Here we demonstrate that quantization of molecular rotation plays a key role in cold reaction dynamics, where rotationally excited ortho-hydrogen reacts faster due to a stronger long-range attraction. We observe rotational state-dependent non-Arrhenius universal scaling laws in chemi-ionization reactions of para-H2 and ortho-H2 by He(2(3)P2), spanning three orders of magnitude in temperature. Different scaling laws serve as a sensitive gauge that enables us to directly determine the exact nature of the long-range intermolecular interactions. Our results show that the quantum state of the molecular rotor determines whether or not anisotropic long-range interactions dominate cold collisions.

Molecular imaging of prostate cancer: translating molecular biology approaches into the clinical realm.

PubMed

Vargas, Hebert Alberto; Grimm, Jan; F Donati, Olivio; Sala, Evis; Hricak, Hedvig

2015-05-01

The epidemiology of prostate cancer has dramatically changed since the introduction of prostate-specific antigen (PSA) screening in the 1980's. Most prostate cancers today are detected at early stages of the disease and are considered 'indolent'; however, some patients' prostate cancers demonstrate a more aggressive behaviour which leads to rapid progression and death. Increasing understanding of the biology underlying the heterogeneity that characterises this disease has led to a continuously evolving role of imaging in the management of prostate cancer. Functional and metabolic imaging techniques are gaining importance as the impact on the therapeutic paradigm has shifted from structural tumour detection alone to distinguishing patients with indolent tumours that can be managed conservatively (e.g., by active surveillance) from patients with more aggressive tumours that may require definitive treatment with surgery or radiation. In this review, we discuss advanced imaging techniques that allow direct visualisation of molecular interactions relevant to prostate cancer and their potential for translation to the clinical setting in the near future. The potential use of imaging to follow molecular events during drug therapy as well as the use of imaging agents for therapeutic purposes will also be discussed. • Advanced imaging techniques allow direct visualisation of molecular interactions in prostate cancer. • MRI/PET, optical and Cerenkov imaging facilitate the translation of molecular biology. • Multiple compounds targeting PSMA expression are currently undergoing clinical translation. • Other targets (e.g., PSA, prostate-stem cell antigen, GRPR) are in development.

Hadronic molecular states from the Kbar{K}^{ast} interaction

NASA Astrophysics Data System (ADS)

Lü, Pei-Liang; He, Jun

2016-12-01

In this work, the Kbar{K}^{ast} interaction is studied in a quasipotential Bethe-Salpeter equation approach combined with the one-boson-exchange model. With the help of the hidden-gauge Lagrangian, the exchanges of pseudoscalar mesons (π and η) and vector mesons (ρ, ω and φ) are considered to describe the Kbar{K}^{ast} interaction. Besides the direct vector-meson exchange which can be related to the Weinberg-Tomozawa term, pseudoscalar-meson exchanges also play important roles in the mechanism of the Kbar{K}^{ast} interaction. The poles of scattering amplitude are searched to find the molecular states produced from the Kbar{K}^{ast} interaction. In the case of quantum number IG(J^{PC}) = 0+(1^{++}), a pole is found with a reasonable cutoff, which can be related to the f1(1285) in experiment. Another bound state with 0-(1^{+-}) is also produced from the Kbar{K}^{ast} interaction, which can be related to the h1(1380). In the isovector sector, the interaction is much weaker and a bound state with 1+(1+) relevant to the b1(1235) is produced but at a larger cutoff. Our results suggest that in the hadronic molecular state picture the f1(1285) and b1(1235) are the strange partners of the X(3872) and Zc(3900), respectively.

Interaction of toluene with two-color asymmetric laser fields: Controlling the directional emission of molecular hydrogen fragments

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

Kaziannis, S.; Kotsina, N.; Kosmidis, C.

The interaction of toluene with strong asymmetric two-color laser irradiation of 40 fs duration is studied by means of Time of flight mass spectrometry. Highly energetic H{sub 2}{sup +} and H{sub 3}{sup +} fragment ions are produced through an isomerization process taking place within transient multiply charged parent ions. Comparative study of deuterium labeled toluene isotopes enables the discrimination between molecular hydrogen fragments formed exclusively within the CH{sub 3}- part from those that require hydrogen atom exchange between the former and the phenyl moiety. It is demonstrated that by manipulating the relative phase of the ω/2ω field components the selectivemore » ionization of oriented toluene molecules can be used as a tool to control the directional emission of the H{sub 2}{sup +}, H{sub 3}{sup +} species.« less

Mesoscale Thermodynamic Analysis of Atomic-Scale Dislocation-Obstacle Interactions Simulated by Molecular Dynamics

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

Monet, Giath; Bacon, David J; Osetskiy, Yury N

2010-01-01

Given the time and length scales in molecular dynamics (MD) simulations of dislocation-defect interactions, quantitative MD results cannot be used directly in larger scale simulations or compared directly with experiment. A method to extract fundamental quantities from MD simulations is proposed here. The first quantity is a critical stress defined to characterise the obstacle resistance. This mesoscopic parameter, rather than the obstacle 'strength' designed for a point obstacle, is to be used for an obstacle of finite size. At finite temperature, our analyses of MD simulations allow the activation energy to be determined as a function of temperature. The resultsmore » confirm the proportionality between activation energy and temperature that is frequently observed by experiment. By coupling the data for the activation energy and the critical stress as functions of temperature, we show how the activation energy can be deduced at a given value of the critical stress.« less

p53 inhibits autophagy by interacting with the human ortholog of yeast Atg17, RB1CC1/FIP200.

PubMed

Morselli, Eugenia; Shen, Shensi; Ruckenstuhl, Christoph; Bauer, Maria Anna; Mariño, Guillermo; Galluzzi, Lorenzo; Criollo, Alfredo; Michaud, Mickael; Maiuri, Maria Chiara; Chano, Tokuhiro; Madeo, Frank; Kroemer, Guido

2011-08-15

The tumor suppressor protein p53 tonically suppresses autophagy when it is present in the cytoplasm. This effect is phylogenetically conserved from mammals to nematodes, and human p53 can inhibit autophagy in yeast, as we show here. Bioinformatic investigations of the p53 interactome in relationship to the autophagy-relevant protein network underscored the possible relevance of a direct molecular interaction between p53 and the mammalian ortholog of the essential yeast autophagy protein Atg17, namely RB1-inducible coiled-coil protein 1 (RB1CC1), also called FAK family kinase-interacting protein of 200 KDa (FIP200). Mutational analyses revealed that a single point mutation in p53 (K382R) abolished its capacity to inhibit autophagy upon transfection into p53-deficient human colon cancer or yeast cells. In conditions in which wild-type p53 co-immunoprecipitated with RB1CC1/FIP200, p53 (K382R) failed to do so, underscoring the importance of the physical interaction between these proteins for the control of autophagy. In conclusion, p53 regulates autophagy through a direct molecular interaction with RB1CC1/FIP200, a protein that is essential for the very apical step of autophagy initiation.

Revealing interaction between sulfobutylether-β-cyclodextrin and reserpine by chemiluminescence and site-directed molecular docking.

PubMed

Xiong, Xunyu; Wu, Min; Zhao, Xinfeng; Song, Zhenghua

2014-09-01

The host-guest interaction between sulfobutylether-β-cyclodextrin (SBE-β-CD) and reserpine (RSP) is described using flow injection-chemiluminescence (FI-CL) and site-directed molecular docking methods. It was found that RSP could inhibit the CL intensity produced by a luminol/SBE-β-CD system. The decrease in CL intensity was logarithmic over an RSP concentration range of 0.03 to 700.0 nM, giving a regression equation of ∆I = 107.1lgCRES  + 186.1 with a detection limit of 10 pM (3σ). The CL assay was successfully applied in the determination of RSP in injection, saliva and urine samples with recoveries in the range 93.5-106.1%. Using the proposed CL model, the binding constant (KCD-R ) and the stoichiometric ratio of SBE-β-CD/RSP were calculated to be 7.4 × 10(6)  M(-1) and 1 : 1, respectively. Using molecular docking, it was confirmed that luminol binds to the small cavity of SBE-β-CD with a nonpolar interaction, while RSP targeted the larger cavity of SBE-β-CD and formed a 1 : 1 complex with hydrogen bonds. The proposed new CL method has the potential to become a powerful tool for revealing the host-guest interaction between CDs and drugs, as well as monitoring drugs with high sensitivity. Copyright © 2013 John Wiley & Sons, Ltd.

Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly

PubMed Central

Cook, Jeremy D.; Kondapalli, Kalyan C.; Rawat, Swati; Childs, William C.; Murugesan, Yogapriya; Dancis, Andrew; Stemmler, Timothy L.

2010-01-01

Frataxin, a conserved nuclear encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich’s ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two: Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone n the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to better understand the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry (ITC). Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into a Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly. PMID:20815377

Molecular Details of the Yeast Frataxin-Isu1 Interaction during Mitochondrial Fe-S Cluster Assembly

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

Cook, J.; Kondapalli, K; Rawat, S

2010-01-01

Frataxin, a conserved nuclear-encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich's ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two, Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural modulemore » to improve our understanding of the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry. Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into an Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly.« less

Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly.

PubMed

Cook, Jeremy D; Kondapalli, Kalyan C; Rawat, Swati; Childs, William C; Murugesan, Yogapriya; Dancis, Andrew; Stemmler, Timothy L

2010-10-12

Frataxin, a conserved nuclear-encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich's ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two, Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to improve our understanding of the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry. Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into an Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly.

Imaging HIV-1 Tat Trafficking and Interactions by Engineered Green-Fluorescent-Protein Tagging

NASA Astrophysics Data System (ADS)

Beltram, Fabio

2002-03-01

The direct monitoring of protein function in live cells under physiologically relevant conditions is one of the most powerful and innovative methodologies for proteomics. Efficient florescent probes fully compatible with human-cell expression are the fundamental tools for these studies and their optimization opens the way to resolution at the single-protein level. Biological events involving protein pairs are also directly accessible thanks to tuning of protein-tag spectral properties and production of complementary pairs. Such pairs are characterized by overlapping absorption (for the acceptor tag) and emission (for the donor tag) spectra. By tagging the proteins of interest with acceptor and donor molecules, protein interaction can be directly visualized by FRET, fluorescent resonant energy transfer. In this talk we shall present the design by molecular dynamics calculations and the application of optimized green fluorescent proteins to the study of the human immunodeficiency virus HIV-1 proteomics. In particular trafficking and cellular interactions of HIV-1 transactivator protein Tat in live human cells will be presented. Tat localization and complex internalization pathways of exogenous molecules will be presented thanks to the peculiar optical properties of mutated GFPs. Cellular protein partners and subcellular interaction sites will be identified and directly visualized. The relevance of such results and of advanced spectroscopic and imaging techniques for a new level of understanding of biological processes and its significance for advancement in molecular biology will be underlined. A. Marcello et al., J. Biol. Chem. 276, 39220 (2001). R. Cinelli et al., Appl. Phys. Lett. 79, 3353 (2001).

Halogen bonding (X-bonding): A biological perspective

PubMed Central

Scholfield, Matthew R; Zanden, Crystal M Vander; Carter, Megan; Ho, P Shing

2013-01-01

The concept of the halogen bond (or X-bond) has become recognized as contributing significantly to the specificity in recognition of a large class of halogenated compounds. The interaction is most easily understood as primarily an electrostatically driven molecular interaction, where an electropositive crown, or σ-hole, serves as a Lewis acid to attract a variety of electron-rich Lewis bases, in analogous fashion to a classic hydrogen bonding (H-bond) interaction. We present here a broad overview of X-bonds from the perspective of a biologist who may not be familiar with this recently rediscovered class of interactions and, consequently, may be interested in how they can be applied as a highly directional and specific component of the molecular toolbox. This overview includes a discussion for where X-bonds are found in biomolecular structures, and how their structure–energy relationships are studied experimentally and modeled computationally. In total, our understanding of these basic concepts will allow X-bonds to be incorporated into strategies for the rational design of new halogenated inhibitors against biomolecular targets or toward molecular engineering of new biological-based materials. PMID:23225628

Emergence and evolution of an interaction between intrinsically disordered proteins

PubMed Central

Hultqvist, Greta; Åberg, Emma; Camilloni, Carlo; Sundell, Gustav N; Andersson, Eva; Dogan, Jakob; Chi, Celestine N; Vendruscolo, Michele; Jemth, Per

2017-01-01

Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. However, it is not clear how such interactions emerge and evolve on a molecular level. We performed phylogenetic reconstruction, resurrection and biophysical characterization of two interacting disordered protein domains, CID and NCBD. CID appeared after the divergence of protostomes and deuterostomes 450–600 million years ago, while NCBD was present in the protostome/deuterostome ancestor. The most ancient CID/NCBD formed a relatively weak complex (Kd∼5 µM). At the time of the first vertebrate-specific whole genome duplication, the affinity had increased (Kd∼200 nM) and was maintained in further speciation. Experiments together with molecular modeling using NMR chemical shifts suggest that new interactions involving intrinsically disordered proteins may evolve via a low-affinity complex which is optimized by modulating direct interactions as well as dynamics, while tolerating several potentially disruptive mutations. DOI: http://dx.doi.org/10.7554/eLife.16059.001 PMID:28398197

Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression.

PubMed

Danno, Hiroki; Michiue, Tatsuo; Hitachi, Keisuke; Yukita, Akira; Ishiura, Shoichi; Asashima, Makoto

2008-04-08

The neural-related genes Sox2, Pax6, Otx2, and Rax have been associated with severe ocular malformations such as anophthalmia and microphthalmia, but it remains unclear as to how these genes are linked functionally. We analyzed the upstream signaling of Xenopus Rax (also known as Rx1) and identified the Otx2 and Sox2 proteins as direct upstream regulators of Rax. We revealed that endogenous Otx2 and Sox2 proteins bound to the conserved noncoding sequence (CNS1) located approximately 2 kb upstream of the Rax promoter. This sequence is conserved among vertebrates and is required for potent transcriptional activity. Reporter assays showed that Otx2 and Sox2 synergistically activated transcription via CNS1. Furthermore, the Otx2 and Sox2 proteins physically interacted with each other, and this interaction was affected by the Sox2-missense mutations identified in these ocular disorders. These results demonstrate that the direct interaction and interdependence between the Otx2 and Sox2 proteins coordinate Rax expression in eye development, providing molecular linkages among the genes responsible for ocular malformation.

Theoretical study of optical activity of 1:1 hydrogen bond complexes of water with S-warfarin

NASA Astrophysics Data System (ADS)

Dadsetani, Mehrdad; Abdolmaleki, Ahmad; Zabardasti, Abedin

2016-11-01

The molecular interaction between S-warfarin (SW) and a single water molecule was investigated using the B3LYP method at 6-311 ++G(d,p) basis set. The vibrational spectra of the optimized complexes have been investigated for stabilization checking. Quantum theories of atoms in molecules, natural bond orbitals, molecular electrostatic potentials and energy decomposition analysis methods have been applied to analyze the intermolecular interactions. The intermolecular charge transfer in the most stable complex is in the opposite direction from those in the other complexes. The optical spectra and the hyperpolarizabilities of SW-water hydrogen bond complexes have been computed.

Isobaric first-principles molecular dynamics of liquid water with nonlocal van der Waals interactions

NASA Astrophysics Data System (ADS)

Miceli, Giacomo; de Gironcoli, Stefano; Pasquarello, Alfredo

2015-01-01

We investigate the structural properties of liquid water at near ambient conditions using first-principles molecular dynamics simulations based on a semilocal density functional augmented with nonlocal van der Waals interactions. The adopted scheme offers the advantage of simulating liquid water at essentially the same computational cost of standard semilocal functionals. Applied to the water dimer and to ice Ih, we find that the hydrogen-bond energy is only slightly enhanced compared to a standard semilocal functional. We simulate liquid water through molecular dynamics in the NpH statistical ensemble allowing for fluctuations of the system density. The structure of the liquid departs from that found with a semilocal functional leading to more compact structural arrangements. This indicates that the directionality of the hydrogen-bond interaction has a diminished role as compared to the overall attractions, as expected when dispersion interactions are accounted for. This is substantiated through a detailed analysis comprising the study of the partial radial distribution functions, various local order indices, the hydrogen-bond network, and the selfdiffusion coefficient. The explicit treatment of the van der Waals interactions leads to an overall improved description of liquid water.

Molecular interactions between tomato and the leaf mold pathogen Cladosporium fulvum.

PubMed

Rivas, Susana; Thomas, Colwyn M

2005-01-01

The interaction between tomato and the leaf mold pathogen Cladosporium fulvum is controlled in a gene-for-gene manner. This interaction has provided useful insights to the molecular basis of recognition specificity in plant disease resistance (R) proteins, disease resistance (R) gene evolution, R-protein mediated signaling, and cellular responses to pathogen attack. Tomato Cf genes encode type I membrane-associated receptor-like proteins (RLPs) comprised predominantly of extracellular leucine-rich repeats (eLRRs) and which are anchored in the plasma membrane. Cf proteins recognize fungal avirulence (Avr) peptides secreted into the leaf apoplast during infection. A direct interaction of Cf proteins with their cognate Avr proteins has not been demonstrated and the molecular mechanism of Avr protein perception is not known. Following ligand perception Cf proteins trigger a hypersensitive response (HR) and the arrest of pathogen development. Cf proteins lack an obvious signaling domain, suggesting that defense response activation is mediated through interactions with other partners. Avr protein perception results in the rapid accumulation of active oxygen species (AOS), changes in cellular ion fluxes, activation of protein kinase cascades, changes in gene expression and, possibly, targeted protein degradation. Here we review our current understanding of Cf-mediated responses in resistance to C. fulvum.

Directly Insight Into the Inter- and Intramolecular Interactions of CL-20/TNT Energetic Cocrystal through the Theoretical Simulations of THz Spectroscopy.

PubMed

Shi, Lu; Duan, Xiao-Hui; Zhu, Li-Guo; Liu, Xun; Pei, Chong-Hua

2016-03-03

Compared with cocrystal coformers, an explosive cocrystal has distinctive packing arrangements and complex intermolecular interactions. Identifying the spectral signatures of an explosive cocrystal and understanding the molecular low-frequency modes by means of the spectrum in the terahertz range are of great worth to the explicit mechanism of cocrystal formation. In this work, on the basis of the joint molecular dynamics (MD) simulations and solid-state density functional theory (DFT) calculations, we have investigated the terahertz (THz) absorption spectra of the CL-20/TNT cocrystal and its different directions as well as cocrystal coformers and determined the systematic and all-sided assignments of corresponding THz vibration modes. The THz spectral comparison of the cocrystal with different directions and the cocrystal coformers indicates that the CL-20/TNT cocrystal has five fresh low-frequency absorption features as unique and discernible peaks for identification, in which 0.25, 0.73, and 0.87 THz are attributed to intensive crystalline vibrations; 0.87 THz is also caused by C-H···O hydrogen-bonding bending vibrations; 1.60 and 1.85 THz features originate from C-H···O hydrogen-bond stretching vibrations. Additionally, the THz spectrum of the (001) direction of the CL-20/TNT cocrystal verifies that the molecular conformation of the CL-20 is the same as that in the β-polymorph, other than the initial conformation of raw material ε-CL-20.

Molecular structure and interactions in the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide.

PubMed

Dhumal, Nilesh R; Noack, Kristina; Kiefer, Johannes; Kim, Hyung J

2014-04-03

Electronic structure theory (density functional and Møller-Plesset perturbation theory) and vibrational spectroscopy (FT-IR and Raman) are employed to study molecular interactions in the room-temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide. Different conformers of a cation-anion pair based on their molecular interactions are simulated in the gas phase and in a dielectric continuum solvent environment. Although the ordering of conformers in energy varies with theoretical methods, their predictions for three lowest energy conformers in the gas phase are similar. Strong C-H---N interactions between the acidic hydrogen atom of the cation imidazole ring and the nitrogen atom of the anion are predicted for either the lowest or second lowest energy conformer. In a continuum solvent, different theoretical methods yield the same ion-pair conformation for the lowest energy state. In both phases, the density functional method predicts that the anion is in a trans conformation in the lowest energy ion pair state. The theoretical results are compared with experimental observations from Raman scattering and IR absorption spectroscopies and manifestations of the molecular interactions in the vibrational spectra are discussed. The directions of the frequency shifts of the characteristic vibrations relative to the free anion and cation are explained by calculating the difference electron density coupled with electron density topography.

Adiabatic quantum simulation of quantum chemistry.

PubMed

Babbush, Ryan; Love, Peter J; Aspuru-Guzik, Alán

2014-10-13

We show how to apply the quantum adiabatic algorithm directly to the quantum computation of molecular properties. We describe a procedure to map electronic structure Hamiltonians to 2-body qubit Hamiltonians with a small set of physically realizable couplings. By combining the Bravyi-Kitaev construction to map fermions to qubits with perturbative gadgets to reduce the Hamiltonian to 2-body, we obtain precision requirements on the coupling strengths and a number of ancilla qubits that scale polynomially in the problem size. Hence our mapping is efficient. The required set of controllable interactions includes only two types of interaction beyond the Ising interactions required to apply the quantum adiabatic algorithm to combinatorial optimization problems. Our mapping may also be of interest to chemists directly as it defines a dictionary from electronic structure to spin Hamiltonians with physical interactions.

Autonomous molecular cascades for evaluation of cell surfaces

NASA Astrophysics Data System (ADS)

Rudchenko, Maria; Taylor, Steven; Pallavi, Payal; Dechkovskaia, Alesia; Khan, Safana; Butler, Vincent P., Jr.; Rudchenko, Sergei; Stojanovic, Milan N.

2013-08-01

Molecular automata are mixtures of molecules that undergo precisely defined structural changes in response to sequential interactions with inputs. Previously studied nucleic acid-based automata include game-playing molecular devices (MAYA automata) and finite-state automata for the analysis of nucleic acids, with the latter inspiring circuits for the analysis of RNA species inside cells. Here, we describe automata based on strand-displacement cascades directed by antibodies that can analyse cells by using their surface markers as inputs. The final output of a molecular automaton that successfully completes its analysis is the presence of a unique molecular tag on the cell surface of a specific subpopulation of lymphocytes within human blood cells.

GATE: software for the analysis and visualization of high-dimensional time series expression data.

PubMed

MacArthur, Ben D; Lachmann, Alexander; Lemischka, Ihor R; Ma'ayan, Avi

2010-01-01

We present Grid Analysis of Time series Expression (GATE), an integrated computational software platform for the analysis and visualization of high-dimensional biomolecular time series. GATE uses a correlation-based clustering algorithm to arrange molecular time series on a two-dimensional hexagonal array and dynamically colors individual hexagons according to the expression level of the molecular component to which they are assigned, to create animated movies of systems-level molecular regulatory dynamics. In order to infer potential regulatory control mechanisms from patterns of correlation, GATE also allows interactive interroga-tion of movies against a wide variety of prior knowledge datasets. GATE movies can be paused and are interactive, allowing users to reconstruct networks and perform functional enrichment analyses. Movies created with GATE can be saved in Flash format and can be inserted directly into PDF manuscript files as interactive figures. GATE is available for download and is free for academic use from http://amp.pharm.mssm.edu/maayan-lab/gate.htm

Identifying Mechanisms of Interfacial Dynamics Using Single-Molecule Tracking

PubMed Central

Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

2012-01-01

The “soft” (i.e. non-covalent) interactions between molecules and surfaces are complex and highly-varied (e.g. hydrophobic, hydrogen bonding, ionic) often leading to heterogeneous interfacial behavior. Heterogeneity can arise either from spatial variation of the surface/interface itself or from molecular configurations (i.e. conformation, orientation, aggregation state, etc.). By observing adsorption, diffusion, and desorption of individual fluorescent molecules, single-molecule tracking can characterize these types of heterogeneous interfacial behavior in ways that are inaccessible to traditional ensemble-averaged methods. Moreover, the fluorescence intensity or emission wavelength (in resonance energy transfer experiments) can be used to simultaneously track molecular configuration and directly relate this to the resulting interfacial mobility or affinity. In this feature article, we review recent advances involving the use of single-molecule tracking to characterize heterogeneous molecule-surface interactions including: multiple modes of diffusion and desorption associated with both internal and external molecular configuration, Arrhenius activated interfacial transport, spatially dependent interactions, and many more. PMID:22716995

Host gene-microbiome interactions: molecular mechanisms in inflammatory bowel disease.

PubMed

Chu, Hiutung

2017-07-24

Recent studies have identified links between host genetic variants and microbial recognition of the microbiome. Defects in host-microbiome interactions in individuals harboring inflammatory bowel disease risk alleles may result in imbalances of the microbial community, impaired pathogen clearance, and failure to sense beneficial commensal microbes. These findings highlight the importance of maintaining bi-directional communication at the mucosal interface during intestinal homeostasis.

Hybrid incompatibility arises in a sequence-based bioenergetic model of transcription factor binding.

PubMed

Tulchinsky, Alexander Y; Johnson, Norman A; Watt, Ward B; Porter, Adam H

2014-11-01

Postzygotic isolation between incipient species results from the accumulation of incompatibilities that arise as a consequence of genetic divergence. When phenotypes are determined by regulatory interactions, hybrid incompatibility can evolve even as a consequence of parallel adaptation in parental populations because interacting genes can produce the same phenotype through incompatible allelic combinations. We explore the evolutionary conditions that promote and constrain hybrid incompatibility in regulatory networks using a bioenergetic model (combining thermodynamics and kinetics) of transcriptional regulation, considering the bioenergetic basis of molecular interactions between transcription factors (TFs) and their binding sites. The bioenergetic parameters consider the free energy of formation of the bond between the TF and its binding site and the availability of TFs in the intracellular environment. Together these determine fractional occupancy of the TF on the promoter site, the degree of subsequent gene expression and in diploids, and the degree of dominance among allelic interactions. This results in a sigmoid genotype-phenotype map and fitness landscape, with the details of the shape determining the degree of bioenergetic evolutionary constraint on hybrid incompatibility. Using individual-based simulations, we subjected two allopatric populations to parallel directional or stabilizing selection. Misregulation of hybrid gene expression occurred under either type of selection, although it evolved faster under directional selection. Under directional selection, the extent of hybrid incompatibility increased with the slope of the genotype-phenotype map near the derived parental expression level. Under stabilizing selection, hybrid incompatibility arose from compensatory mutations and was greater when the bioenergetic properties of the interaction caused the space of nearly neutral genotypes around the stable expression level to be wide. F2's showed higher hybrid incompatibility than F1's to the extent that the bioenergetic properties favored dominant regulatory interactions. The present model is a mechanistically explicit case of the Bateson-Dobzhansky-Muller model, connecting environmental selective pressure to hybrid incompatibility through the molecular mechanism of regulatory divergence. The bioenergetic parameters that determine expression represent measurable properties of transcriptional regulation, providing a predictive framework for empirical studies of how phenotypic evolution results in epistatic incompatibility at the molecular level in hybrids. Copyright © 2014 by the Genetics Society of America.

Specialized Functional Diversity and Interactions of the Na,K-ATPase

PubMed Central

Matchkov, Vladimir V.; Krivoi, Igor I.

2016-01-01

Na,K-ATPase is a protein ubiquitously expressed in the plasma membrane of all animal cells and vitally essential for their functions. A specialized functional diversity of the Na,K-ATPase isozymes is provided by molecular heterogeneity, distinct subcellular localizations, and functional interactions with molecular environment. Studies over the last decades clearly demonstrated complex and isoform-specific reciprocal functional interactions between the Na,K-ATPase and neighboring proteins and lipids. These interactions are enabled by a spatially restricted ion homeostasis, direct protein-protein/lipid interactions, and protein kinase signaling pathways. In addition to its “classical” function in ion translocation, the Na,K-ATPase is now considered as one of the most important signaling molecules in neuronal, epithelial, skeletal, cardiac and vascular tissues. Accordingly, the Na,K-ATPase forms specialized sub-cellular multimolecular microdomains which act as receptors to circulating endogenous cardiotonic steroids (CTS) triggering a number of signaling pathways. Changes in these endogenous cardiotonic steroid levels and initiated signaling responses have significant adaptive values for tissues and whole organisms under numerous physiological and pathophysiological conditions. This review discusses recent progress in the studies of functional interactions between the Na,K-ATPase and molecular microenvironment, the Na,K-ATPase-dependent signaling pathways and their significance for diversity of cell function. PMID:27252653

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

Hu, Qing; Jin, Dafei; Xiao, Jun

Two-dimensional molecular aggregate (2DMA), a thin sheet of strongly interacting dipole molecules self-assembled at close distance on an ordered lattice, is a fascinating fluorescent material. It is distinctively different from the conventional (single or colloidal) dye molecules and quantum dots. Here, in this paper, we verify that when a 2DMA is placed at a nanometric distance from a metallic substrate, the strong and coherent interaction between the dipoles inside the 2DMA dominates its fluorescent decay at a picosecond timescale. Our streak-camera lifetime measurement and interacting lattice–dipole calculation reveal that the metal-mediated dipole–dipole interaction shortens the fluorescent lifetime to about one-halfmore » and increases the energy dissipation rate by 10 times that expected from the noninteracting single-dipole picture. In conclusion, our finding can enrich our understanding of nanoscale energy transfer in molecular excitonic systems and may designate a unique direction for developing fast and efficient optoelectronic devices.« less

Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes.

PubMed

Sonntag, Yonathan; Musgaard, Maria; Olesen, Claus; Schiøtt, Birgit; Møller, Jesper Vuust; Nissen, Poul; Thøgersen, Lea

2011-01-01

The structural elucidation of membrane proteins continues to gather pace, but we know little about their molecular interactions with the lipid environment or how they interact with the surrounding bilayer. Here, with the aid of low-resolution X-ray crystallography, we present direct structural information on membrane interfaces as delineated by lipid phosphate groups surrounding the sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) in its phosphorylated and dephosphorylated Ca(2+)-free forms. The protein-lipid interactions are further analysed using molecular dynamics simulations. We find that SERCA adapts to membranes of different hydrophobic thicknesses by inducing local deformations in the lipid bilayers and by undergoing small rearrangements of the amino-acid side chains and helix tilts. These mutually adaptive interactions allow smooth transitions through large conformational changes associated with the transport cycle of SERCA, a strategy that may be of general nature for many membrane proteins.

A simple molecular orbital treatment of current distributions in quantum transport through molecular junctions

NASA Astrophysics Data System (ADS)

Jhan, Sin-Mu; Jin, Bih-Yaw

2017-11-01

A simple molecular orbital treatment of local current distributions inside single molecular junctions is developed in this paper. Using the first-order perturbation theory and nonequilibrium Green's function techniques in the framework of Hückel theory, we show that the leading contributions to local current distributions are directly proportional to the off-diagonal elements of transition density matrices. Under the orbital approximation, the major contributions to local currents come from a few dominant molecular orbital pairs which are mixed by the interactions between the molecule and electrodes. A few simple molecular junctions consisting of single- and multi-ring conjugated systems are used to demonstrate that local current distributions inside molecular junctions can be decomposed by partial sums of a few leading contributing transition density matrices.

Bioresponsive probes for molecular imaging: concepts and in vivo applications.

PubMed

van Duijnhoven, Sander M J; Robillard, Marc S; Langereis, Sander; Grüll, Holger

2015-01-01

Molecular imaging is a powerful tool to visualize and characterize biological processes at the cellular and molecular level in vivo. In most molecular imaging approaches, probes are used to bind to disease-specific biomarkers highlighting disease target sites. In recent years, a new subset of molecular imaging probes, known as bioresponsive molecular probes, has been developed. These probes generally benefit from signal enhancement at the site of interaction with its target. There are mainly two classes of bioresponsive imaging probes. The first class consists of probes that show direct activation of the imaging label (from "off" to "on" state) and have been applied in optical imaging and magnetic resonance imaging (MRI). The other class consists of probes that show specific retention of the imaging label at the site of target interaction and these probes have found application in all different imaging modalities, including photoacoustic imaging and nuclear imaging. In this review, we present a comprehensive overview of bioresponsive imaging probes in order to discuss the various molecular imaging strategies. The focus of the present article is the rationale behind the design of bioresponsive molecular imaging probes and their potential in vivo application for the detection of endogenous molecular targets in pathologies such as cancer and cardiovascular disease. Copyright © 2015 John Wiley & Sons, Ltd.

Interaction of AR and iNOS in lens epithelial cell: A new pathogenesis and potential therapeutic targets of diabetic cataract.

PubMed

Li, Xue; Liu, Wenping; Huang, Xinduo; Xiong, Jianping; Wei, Xiaoyong

2017-02-01

Although there is significant interest in revealing the role of aldose reductase (AR) and inducible nitric oxide synthase (iNOS) in diabetic cataract (DC), the interaction of AR and iNOS remains unknown. The aim of this study is to investigate the pathogenesis mechanisms and explore as a new potential therapeutic targets for DC. This study investigated the interaction of AR-iNOS through the methods of enzyme kinetics, molecular docking and molecular dynamics simulation, co-immunoprecipitation and fluorescence resonance energy transfer (FRET). The IC50 of AR for inhibition of iNOS activity is 0.04 μM, and the IC50 of iNOS for inhibition of AR activity is 0.042 μM through enzyme kinetics; the interface showed that ARG99 on AR and GLU317 on iNOS played the key roles in the interaction of AR-iNOS predicted by molecular docking and molecular dynamics simulation. Co-immunoprecipitation of protein complexes in human lens epithelial cell (HLEC) demonstrated that AR could association with iNOS in cell; and the interaction distance of AR-iNOS was 6.50 ± 0.22 nm detected by FRET. This study exhibited a direct inhibition interaction between AR and iNOS in HLECs. It is the first report of inhibition interaction between AR and iNOS, suggesting a new pathophysiological mechanism and providing a new insight into the therapeutic mechanism of DC. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular modelling of protein-protein/protein-solvent interactions

NASA Astrophysics Data System (ADS)

Luchko, Tyler

The inner workings of individual cells are based on intricate networks of protein-protein interactions. However, each of these individual protein interactions requires a complex physical interaction between proteins and their aqueous environment at the atomic scale. In this thesis, molecular dynamics simulations are used in three theoretical studies to gain insight at the atomic scale about protein hydration, protein structure and tubulin-tubulin (protein-protein) interactions, as found in microtubules. Also presented, in a fourth project, is a molecular model of solvation coupled with the Amber molecular modelling package, to facilitate further studies without the need of explicitly modelled water. Basic properties of a minimally solvated protein were calculated through an extended study of myoglobin hydration with explicit solvent, directly investigating water and protein polarization. Results indicate a close correlation between polarization of both water and protein and the onset of protein function. The methodology of explicit solvent molecular dynamics was further used to study tubulin and microtubules. Extensive conformational sampling of the carboxy-terminal tails of 8-tubulin was performed via replica exchange molecular dynamics, allowing the characterisation of the flexibility, secondary structure and binding domains of the C-terminal tails through statistical analysis methods. Mechanical properties of tubulin and microtubules were calculated with adaptive biasing force molecular dynamics. The function of the M-loop in microtubule stability was demonstrated in these simulations. The flexibility of this loop allowed constant contacts between the protofilaments to be maintained during simulations while the smooth deformation provided a spring-like restoring force. Additionally, calculating the free energy profile between the straight and bent tubulin configurations was used to test the proposed conformational change in tubulin, thought to cause microtubule destabilization. No conformational change was observed but a nucleotide dependent 'softening' of the interaction was found instead, suggesting that an entropic force in a microtubule configuration could be the mechanism of microtubule collapse. Finally, to overcome much of the computational costs associated with explicit soIvent calculations, a new combination of molecular dynamics with the 3D-reference interaction site model (3D-RISM) of solvation was integrated into the Amber molecular dynamics package. Our implementation of 3D-RISM shows excellent agreement with explicit solvent free energy calculations. Several optimisation techniques, including a new multiple time step method, provide a nearly 100 fold performance increase, giving similar computational performance to explicit solvent.

Dependence of Interaction Free Energy between Solutes on an External Electrostatic Field

PubMed Central

Yang, Pei-Kun

2013-01-01

To explore the athermal effect of an external electrostatic field on the stabilities of protein conformations and the binding affinities of protein-protein/ligand interactions, the dependences of the polar and hydrophobic interactions on the external electrostatic field, −Eext, were studied using molecular dynamics (MD) simulations. By decomposing Eext into, along, and perpendicular to the direction formed by the two solutes, the effect of Eext on the interactions between these two solutes can be estimated based on the effects from these two components. Eext was applied along the direction of the electric dipole formed by two solutes with opposite charges. The attractive interaction free energy between these two solutes decreased for solutes treated as point charges. In contrast, the attractive interaction free energy between these two solutes increased, as observed by MD simulations, for Eext = 40 or 60 MV/cm. Eext was applied perpendicular to the direction of the electric dipole formed by these two solutes. The attractive interaction free energy was increased for Eext = 100 MV/cm as a result of dielectric saturation. The force on the solutes along the direction of Eext computed from MD simulations was greater than that estimated from a continuum solvent in which the solutes were treated as point charges. To explore the hydrophobic interactions, Eext was applied to a water cluster containing two neutral solutes. The repulsive force between these solutes was decreased/increased for Eext along/perpendicular to the direction of the electric dipole formed by these two solutes. PMID:23852018

Med5(Nut1) and Med17(Srb4) Are Direct Targets of Mediator Histone H4 Tail Interactions

PubMed Central

Liu, Zhongle; Myers, Lawrence C.

2012-01-01

The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. In addition to its canonical role in transcriptional activation, recent studies have demonstrated that S. cerevisiae Mediator can interact directly with nucleosomes, and their histone tails. Mutations in Mediator subunits have shown that Mediator and certain chromatin structures mutually impact each other structurally and functionally in vivo. We have taken a UV photo cross-linking approach to further delineate the molecular basis of Mediator chromatin interactions and help determine whether the impact of certain Mediator mutants on chromatin is direct. Specifically, by using histone tail peptides substituted with an amino acid analog that is a UV activatible crosslinker, we have identified specific subunits within Mediator that participate in histone tail interactions. Using Mediator purified from mutant yeast strains we have evaluated the impact of these subunits on histone tail binding. This analysis has identified the Med5 subunit of Mediator as a target for histone tail interactions and suggests that the previously observed effect of med5 mutations on telomeric heterochromatin and silencing is direct. PMID:22693636

Saturn Magnetospheric Impact on Surface Molecular Chemistry and Astrobiological Potential of Enceladus

NASA Technical Reports Server (NTRS)

Cooper, Paul D.; Cooper, John F.; Sittler, Edward C.; Burger, Matthew H.; Sturner, Steven J.; Rymer, Abigail M.

2008-01-01

The active south polar surface of Enceladus is exposed to strong chemical processing by direct interaction with charged plasma and energetic particles in the local magnetospheric environment of this icy moon. Chemical oxidation activity is suggested by detection of H202 at the surface in this region and less directly by substantial presence of C02, CO, and N2 in the plume gases. Molecular composition of the uppermost surface, including ejecta from plume activity, is radiolytically transformed mostly by penetrating energetic electrons with lesser effects from more depleted populations of energetic protons. The main sources of molecular plasma ions and E-ring dust grains in the magnetospheric environment are the cryovolcanic plume emissions from Enceladus. These molecular ions and the dust grains are chemically processed by magnetospheric interactions that further impact surface chemistry on return to Enceladus. For example, H20 neutrals dominating the emitted plume gas return to the surface mostly as H30+ ions after magnetospheric processing. Surface oxidant loading is further increased by return of radiolytically processed ice grains from the E-ring. Plume frost deposition and micrometeoroid gardening protect some fraction of newly produced molecular species from destruction by further irradiation. The evident horizontal and vertical mobility of surface ices in the south polar region drive mixing of these processed materials into the moon interior with potential impacts on deep ice molecular chemistry and plume gas production. Similarly as suggested previously for Europa, the externally driven source of radiolytic oxidants could affect evolution of life in any subsurface liquid water environments of Enceladus.

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

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

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived frommore » fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.« less

Small Talk: Children's Everyday `Molecule' Ideas

NASA Astrophysics Data System (ADS)

Jakab, Cheryl

2013-08-01

This paper reports on 6-11-year-old children's `sayings and doings' (Harré 2002) as they explore molecule artefacts in dialectical-interactive teaching interviews (Fleer, Cultural Studies of Science Education 3:781-786, 2008; Hedegaard et al. 2008). This sociocultural study was designed to explore children's everyday awareness of and meaning-making with cultural molecular artefacts. Our everyday world is populated with an ever increasing range of molecular or nanoworld words, symbols, images, and games. What do children today say about these artefacts that are used to represent molecular world entities? What are the material and social resources that can influence a child's everyday and developing scientific ideas about `molecules'? How do children interact with these cognitive tools when given expert assistance? What meaning-making is afforded when children are socially and materially assisted in using molecular tools in early chemical and nanoworld thinking? Tool-dependent discursive studies show that provision of cultural artefacts can assist and direct developmental thinking across many domains of science (Schoultz et al., Human Development 44:103-118, 2001; Siegal 2008). Young children's use of molecular artefacts as cognitive tools has not received much attention to date (Jakab 2009a, b). This study shows 6-11-year-old children expressing everyday ideas of molecular artefacts and raising their own questions about the artefacts. They are seen beginning to domesticate (Erneling 2010) the words, symbols, and images to their own purposes when given the opportunity to interact with such artefacts in supported activity. Discursive analysis supports the notion that using `molecules' as cultural tools can help young children to begin `putting on molecular spectacles' (Kind 2004). Playing with an interactive game (ICT) is shown to be particularly helpful in assisting children's early meaning-making with representations of molecules, atoms, and their chemical symbols.

An automated method for finding molecular complexes in large protein interaction networks

PubMed Central

Bader, Gary D; Hogue, Christopher WV

2003-01-01

Background Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks. Initial mapping efforts have already produced a wealth of data. As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery. Results This paper describes a novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes. The method is based on vertex weighting by local neighborhood density and outward traversal from a locally dense seed protein to isolate the dense regions according to given parameters. The algorithm has the advantage over other graph clustering methods of having a directed mode that allows fine-tuning of clusters of interest without considering the rest of the network and allows examination of cluster interconnectivity, which is relevant for protein networks. Protein interaction and complex information from the yeast Saccharomyces cerevisiae was used for evaluation. Conclusion Dense regions of protein interaction networks can be found, based solely on connectivity data, many of which correspond to known protein complexes. The algorithm is not affected by a known high rate of false positives in data from high-throughput interaction techniques. The program is available from . PMID:12525261

DSMC Simulation and Experimental Validation of Shock Interaction in Hypersonic Low Density Flow

PubMed Central

2014-01-01

Direct simulation Monte Carlo (DSMC) of shock interaction in hypersonic low density flow is developed. Three collision molecular models, including hard sphere (HS), variable hard sphere (VHS), and variable soft sphere (VSS), are employed in the DSMC study. The simulations of double-cone and Edney's type IV hypersonic shock interactions in low density flow are performed. Comparisons between DSMC and experimental data are conducted. Investigation of the double-cone hypersonic flow shows that three collision molecular models can predict the trend of pressure coefficient and the Stanton number. HS model shows the best agreement between DSMC simulation and experiment among three collision molecular models. Also, it shows that the agreement between DSMC and experiment is generally good for HS and VHS models in Edney's type IV shock interaction. However, it fails in the VSS model. Both double-cone and Edney's type IV shock interaction simulations show that the DSMC errors depend on the Knudsen number and the models employed for intermolecular interaction. With the increase in the Knudsen number, the DSMC error is decreased. The error is the smallest in HS compared with those in the VHS and VSS models. When the Knudsen number is in the level of 10−4, the DSMC errors, for pressure coefficient, the Stanton number, and the scale of interaction region, are controlled within 10%. PMID:24672360

Crankshafts: using simple, flat C2h-symmetric molecules to direct the assembly of chiral 2D nanopatterns.

PubMed

Zhou, Hui; Wuest, James D

2013-06-18

Linear D2h-symmetric bisisophthalic acids 1 and 2 and related substances have well-defined flattened structures, high affinities for graphite, and strong abilities to engage in specific intermolecular interactions. Their adsorption produces characteristic nanopatterns that reveal how 2D molecular organization can be controlled by reliable interadsorbate interactions such as hydrogen bonds when properly oriented by molecular geometry. In addition, the behavior of these compounds shows how large-scale organization can be obstructed by programming molecules to associate strongly according to competing motifs that have similar stability and can coexist smoothly without creating significant defects. Analogous new bisisophthalic acids 3a and 4a have similar associative properties, and their unique C2h-symmetric crankshaft geometry gives them the added ability to probe the poorly understood effect of chirality on molecular organization. Their adsorption shows how nanopatterns composed predictably of a single enantiomer can be obtained by depositing molecules that can respect established rules of association only by accepting neighbors of the same configuration. In addition, an analysis of the adsorption of crankshaft compounds 3a and 4a and their derivatives by STM reveals directly on the molecular level how kinetics and thermodynamics compete to control the crystallization of chiral compounds. In such ways, detailed studies of the adsorption of properly designed compounds on surfaces are proving to be a powerful way to discover and test rules that broadly govern molecular organization in both 2D and 3D.

Molecular biomimetics: utilizing nature's molecular ways in practical engineering.

PubMed

Tamerler, Candan; Sarikaya, Mehmet

2007-05-01

In nature, proteins are the machinery that accomplish many functions through their specific recognition and interactions in biological systems from single-celled to multicellular organisms. Biomolecule-material interaction is accomplished via molecular specificity, leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, molecular recognition and, consequently, functions developed through successive cycles of mutation and selection. Using biology as a guide, we can now understand, engineer and control peptide-material interactions and exploit these to tailor novel materials and systems for practical applications. We adapted combinatorial biology protocols to display peptide libraries, either on the cell surface or on phages, to select short peptides specific to a variety of practical materials systems. Following the selection step, we determined the kinetics and stability of peptide binding experimentally to understand the bound peptide structure via modeling and its assembly via atomic force microscopy. The peptides were further engineered to have multiple repeats or their amino acid sequences varied to tailor their function. Both nanoparticles and flat inorganic substrates containing multimaterials patterned at the nano- and microscales were used for self-directed immobilization of molecular constructs. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems with wide ranging applications, from tissue engineering, drug delivery and biosensors, to nanotechnology and bioremediation. Here we give examples of protein-mediated functional materials in biology, peptide selection and engineering with affinity to inorganics, demonstrate potential utilizations in materials science, engineering and medicine, and describe future prospects.

Insight into the Putative Specific Interactions between Cholesterol, Sphingomyelin, and Palmitoyl-Oleoyl Phosphatidylcholine

PubMed Central

Aittoniemi, Jussi; Niemelä, Perttu S.; Hyvönen, Marja T.; Karttunen, Mikko; Vattulainen, Ilpo

2007-01-01

The effects of cholesterol (Chol) on phospholipid bilayers include ordering of the fatty acyl chains, condensing of the lipids in the bilayer plane, and promotion of the liquid-ordered phase. These effects depend on the type of phospholipids in the bilayer and are determined by the nature of the underlying molecular interactions. As for Chol, it has been shown to interact more favorably with sphingomyelin than with most phosphatidylcholines, which in given circumstances leads to formation of lateral domains. However, the exact origin and nature of Chol-phospholipid interactions have recently been subjects of speculation. We examine interactions between Chol, palmitoylsphingomyelin (PSM) and palmitoyl-oleoyl-phosphatidylcholine (POPC) in hydrated lipid bilayers by extensive atom-scale molecular dynamics simulations. We employ a tailored lipid configuration: Individual PSM and Chol monomers, as well as PSM-Chol dimers, are embedded in a POPC lipid bilayer in the liquid crystalline phase. Such a setup allows direct comparison of dimeric and monomeric PSMs and Chol, which ultimately shows how the small differences in PSM and POPC structure can lead to profoundly different interactions with Chol. Our analysis shows that direct hydrogen bonding between PSM and Chol does not provide an adequate explanation for their putative specific interaction. Rather, a combination of charge-pairing, hydrophobic, and van der Waals interactions leads to a lower tilt in PSM neighboring Chol than in Chol with only POPC neighbors. This implies improved Chol-induced ordering of PSM's chains over POPC's chains. These findings are discussed in the context of the hydrophobic mismatch concept suggested recently. PMID:17114220

Physics Division annual review, 1 April 1980-31 March 1981

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

Not Available

1982-06-01

Progress in nuclear physics research is reported in the following areas: medium-energy physics (pion reaction mechanisms, high-resolution studies and nuclear structure, and two-nucleon physics with pions and electrons); heavy-ion research at the tandem and superconducting linear accelerator (resonant structure in heavy-ion reactions, fusion cross sections, high angular momentum states in nuclei, and reaction mechanisms and distributions of reaction strengths); charged-particle research; neutron and photonuclear physics; theoretical physics (heavy-ion direct-reaction theory, nuclear shell theory and nuclear structure, nuclear matter and nuclear forces, intermediate-energy physics, microscopic calculations of high-energy collisions of heavy ions, and light ion direct reactions); the superconducting linac; acceleratormore » operations; and GeV electron linac. Progress in atomic and molecular physics research is reported in the following areas: dissociation and other interactions of energetic molecular ions in solid and gaseous targets, beam-foil research and collision dynamics of heavy ions, photoionization- photoelectron research, high-resolution laser rf spectroscopy with atomic and molecular beams, moessbauer effect research, and theoretical atomic physics. Studies on interactions of energetic particles with solids are also described. Publications are listed. (WHK)« less

[Motivation and Emotional States: Structural Systemic, Neurochemical, Molecular and Cellular Mechanisms].

PubMed

Bazyan, A S

2016-01-01

The structural, systemic, neurochemical, molecular and cellular mechanisms of organization and coding motivation and emotional states are describe. The GABA and glutamatergic synaptic systems of basal ganglia form a neural network and participate in the implementation of voluntary behavior. Neuropeptides, neurohormones and paracrine neuromodulators involved in the organization of motivation and emotional states, integrated with synaptic systems, controlled by neural networks and organizing goal-directed behavior. Structural centers for united and integrated of information in voluntary and goal-directed behavior are globus pallidus. Substantia nigra pars reticulata switches the information from corticobasal networks to thalamocortical networks, induces global dopaminergic (DA) signal and organize interaction of mesolimbic and nigostriatnoy DA systems controlled by prefrontal and motor cortex. Together with the motor cortex, substantia nigra displays information in the brainstem and spinal cord to implementation of behavior. Motivation states are formed in the interaction of neurohormonal and neuropeptide systems by monoaminergic systems of brain. Emotional states are formed by monoaminergic systems of the mid-brain, where the leading role belongs to the mesolimbic DA system. The emotional and motivation state of the encoded specific epigenetic molecular and chemical pattern of neuron.

Cell-Cell Interactions during pollen tube guidance

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

Daphne Preuss

The long-term goal of this research is to identify the signaling molecules that mediate plant cell-cell interactions during pollination. The immediate goals of this project are to perform genetic and molecular analysis of pollen tube guidance. Specifically, we proposed to: 1. Characterize the pistil components that direct pollen tube navigation using the Arabidopsis thaliana in vitro pollen tube guidance system 2. Identify pistil signals that direct pollen tube guidance by a) using microarrays to profile gene expression in developing pistils, and b) employing proteomics and metabolomics to isolate pollen tube guidance signals. 3. Explore the genetic basis of natural variationmore » in guidance signals, comparing the in vitro interactions between pollen and pistils from A. thaliana and its close relatives.« less

Conformational analysis of GT1B ganglioside and its interaction with botulinum neurotoxin type B: a study by molecular modeling and molecular dynamics.

PubMed

Venkateshwari, Sureshkumar; Veluraja, Kasinadar

2012-01-01

The conformational property of oligosaccharide GT1B in aqueous environment was studied by molecular dynamics (MD) simulation using all-atom model. Based on the trajectory analysis, three prominent conformational models were proposed for GT1B. Direct and water-mediated hydrogen bonding interactions stabilize these structures. The molecular modeling and 15 ns MD simulation of the Botulinum Neuro Toxin/B (BoNT/B) - GT1B complex revealed that BoNT/B can accommodate the GT1B in the single binding mode. Least mobility was seen for oligo-GT1B in the binding pocket. The bound conformation of GT1B obtained from the MD simulation of the BoNT/B-GT1B complex bear a close conformational similarity with the crystal structure of BoNT/A-GT1B complex. The mobility noticed for Arg 1268 in the dynamics was accounted for its favorable interaction with terminal NeuNAc. The internal NeuNAc1 tends to form 10 hydrogen bonds with BoNT/B, hence specifying this particular site as a crucial space for the therapeutic design that can restrict the pathogenic activity of BoNT/B.

Arginine 26 and aspartic acid 69 of the regulatory subunit are key residues of subunits interaction of acetohydroxyacid synthase isozyme III from E. coli.

PubMed

Zhao, Yuefang; Wen, Xin; Niu, Congwei; Xi, Zhen

2012-11-05

Acetohydroxyacid synthase (AHAS), which catalyzes the first step in the biosynthesis of branched-chain amino acids, is composed of catalytic and regulatory subunits. The enzyme exhibits full activity only when the regulatory subunit (RSU) binds to the catalytic subunit (CSU). However, the crystal structure of the holoenzyme has not been reported yet, and the molecular interaction between the CSU and RSU is also unknown. Herein, we introduced a global-surface, site-directed labeling scanning method to determine the potential interaction region of the RSU. This approach relies on the insertion of a bulky fluorescent probe at the designated site on the surface of the RSU to cause a dramatic change in holoenzyme activity by perturbing subunit interaction. Then, the key amino acid residues in the potential interaction regions were identified by site-directed mutagenesis. Compared to the wild-type, the single-point mutants R26A and D69A showed 54 and 64 % activity, respectively, whereas the double mutant (R26A+D69A) gave 14 %, thus suggesting that residues Arg26 and Asp69 are the key residues of subunit interaction with cooperative action. Additionally, the results of GST pull-down assays and pH-dependence experiments suggested that polar interaction is the main force for subunits interaction. A plausible protein-protein interaction model of the holoenzyme of Escherichia coli AHAS III is proposed, based on the mutagenesis and protein docking studies. The protocol established here should be useful for the identification of the molecular interactions between proteins. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Anisotropic forces from spatially constrained focal adhesions mediate contact guidance directed cell migration

PubMed Central

Ray, Arja; Lee, Oscar; Win, Zaw; Edwards, Rachel M.; Alford, Patrick W.; Kim, Deok-Ho; Provenzano, Paolo P.

2017-01-01

Directed migration by contact guidance is a poorly understood yet vital phenomenon, particularly for carcinoma cell invasion on aligned collagen fibres. We demonstrate that for single cells, aligned architectures providing contact guidance cues induce constrained focal adhesion maturation and associated F-actin alignment, consequently orchestrating anisotropic traction stresses that drive cell orientation and directional migration. Consistent with this understanding, relaxing spatial constraints to adhesion maturation either through reduction in substrate alignment density or reduction in adhesion size diminishes the contact guidance response. While such interactions allow single mesenchymal-like cells to spontaneously ‘sense' and follow topographic alignment, intercellular interactions within epithelial clusters temper anisotropic cell–substratum forces, resulting in substantially lower directional response. Overall, these results point to the control of contact guidance by a balance of cell–substratum and cell–cell interactions, modulated by cell phenotype-specific cytoskeletal arrangements. Thus, our findings elucidate how phenotypically diverse cells perceive ECM alignment at the molecular level. PMID:28401884

A recipe for free-energy functionals of polarizable molecular fluids

NASA Astrophysics Data System (ADS)

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T. A.

2014-04-01

Classical density-functional theory is the most direct approach to equilibrium structures and free energies of inhomogeneous liquids, but requires the construction of an approximate free-energy functional for each liquid of interest. We present a general recipe for constructing functionals for small-molecular liquids based only on bulk experimental properties and ab initio calculations of a single solvent molecule. This recipe combines the exact free energy of the non-interacting system with fundamental measure theory for the repulsive contribution and a weighted density functional for the short-ranged attractive interactions. We add to these ingredients a weighted polarization functional for the long-range correlations in both the rotational and molecular-polarizability contributions to the dielectric response. We also perform molecular dynamics calculations for the free energy of cavity formation and the high-field dielectric response, and show that our free-energy functional adequately describes these properties (which are key for accurate solvation calculations) for all three solvents in our study: water, chloroform, and carbon tetrachloride.

Molecular simulations enlighten the binding mode of quercetin to lipoxygenase-3.

PubMed

Fiorucci, Sébastien; Golebiowski, Jérôme; Cabrol-Bass, Daniel; Antonczak, Serge

2008-11-01

Inhibition of lipoxygenases (LOXs) by flavonoid compounds is now well documented, but the description of the associated mechanism remains controversial due to a lack of information at the molecular level. For instance, X-ray determination of quercetin/LOX-3 system has led to a structure where the enzyme was cocrystallized with a degradation product of the substrate, which rendered the interpretation of the reported interactions between this flavonoid compound and the enzyme difficult. Molecular modeling simulations can in principle allow obtaining precious insights that could fill this lack of structural information. Thus, in this study, we have investigated various binding modes of quercetin to LOX-3 enzyme in order to understand the first step of the inhibition process, that is the association of the two entities. Molecular dynamics simulations and free energy calculations suggest that quercetin binds the metal center via its 3-hydroxychromone function. Moreover, enzyme/substrate interactions within the cavity impose steric hindrances to quercetin that may activate a direct dioxygen addition on the substrate. (c) 2008 Wiley-Liss, Inc.

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin.

PubMed

Fuchs, Julian E; Huber, Roland G; Waldner, Birgit J; Kahler, Ursula; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

2015-01-01

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm "dynamics govern specificity" might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.

Adiabatic Quantum Simulation of Quantum Chemistry

PubMed Central

Babbush, Ryan; Love, Peter J.; Aspuru-Guzik, Alán

2014-01-01

We show how to apply the quantum adiabatic algorithm directly to the quantum computation of molecular properties. We describe a procedure to map electronic structure Hamiltonians to 2-body qubit Hamiltonians with a small set of physically realizable couplings. By combining the Bravyi-Kitaev construction to map fermions to qubits with perturbative gadgets to reduce the Hamiltonian to 2-body, we obtain precision requirements on the coupling strengths and a number of ancilla qubits that scale polynomially in the problem size. Hence our mapping is efficient. The required set of controllable interactions includes only two types of interaction beyond the Ising interactions required to apply the quantum adiabatic algorithm to combinatorial optimization problems. Our mapping may also be of interest to chemists directly as it defines a dictionary from electronic structure to spin Hamiltonians with physical interactions. PMID:25308187

Chirality in molecular collision dynamics

NASA Astrophysics Data System (ADS)

Lombardi, Andrea; Palazzetti, Federico

2018-02-01

Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies. Here we review some ideas and recent advances about the role of chirality in molecular collisions, designing and illustrating molecular beam experiments for the demonstration of chiral effects and suggesting a scenario for a stereo-directional origin of chiral selection.

How to examine soil sorption of ionizable organic compounds and avoid varying pH?

NASA Astrophysics Data System (ADS)

Borisover, Mikhail

2017-04-01

Multiple natural and anthropogenic organic compounds including new and emerging pollutants undergo ionization in aqueous solutions, and their sorption by soils and sediments is contributed by presence of both molecular and ionized species. Better understanding of environmental fate of organic chemicals requires taking into account interactions of molecular and ionized species with environmental sorbents. A "standard" (and undoubtedly important) procedure for differentiating contributions of molecular and ionized species into the overall soil sorption of an organic compound involves varying pH of solution in batch sorption experiments. However, varying pH is (1) often not possible, without destroying a sorbent, e.g., due to the buffer capacity of soils containing carbonates, (2) difficult for further interpretation, since it changes not only the ionization status of a solute in a solution but also the sorbent structure, e.g., a conformation of organic matter, and/or ionization of surface functional groups, (3) making difficult (or even impossible) to explicitly evaluate the role of dissolved species-bulk water interactions, directly affecting the affinity of a sorbate to distribute between water and a sorbent. Indeed, both molecular and ionized species undergo interactions with the solvent bulk and, at least in the case of the ionized ones, there was no a simple way to quantify organic ion-water interactions and their role in organic ion distribution between soil and water phases. This paper presents a "counter-intuitive" approach to examine sorption interactions of an ionizable compound, without experimenting with varied pH. The approach is based on an idea of replacing an initial state in sorption transfer of an ionizable compound from the solvent bulk to a solvated (hydrated) sorbed state: a traditional coefficient describing distribution of a partially ionized compound between a hydrated sorbent and a co-equilibrated aqueous phase is converted to the coefficient describing the transfer of the sorbing compound from its initial molecular (non-ionized) state (in a solution or in the gas phase) to the final hydrated sorbed state equilibrated with the actual aqueous solution of this ionizable compound. In this way, any contributions from the bulk solvent-organic ion interactions into the sorption transfer may be excluded; in addition, further any solute-solvent interactions may be taken out of the consideration. Therefore, compound's sorption characteristics "cleared" of solute-solvent interactions may be obtained, and a better understanding of relations between interactions in a sorbed phase and a molecular structure of organic sorbates can be reached. The approach is illustrated by examining sorption of variously ionized organic compounds, i.e., those belonging to the pharmaceuticals and personal care products (triclosan, gemfibrozil, galaxolide), and aliphatic organic acids on natural and organic amendment-enriched soils. Specifically, it is demonstrated how the greater H-donating ability of trifluoroacetic acid, as compared with acetic acid, strengthens the acid interactions in the soil phase. In another series of examples, it is shown how hydrophobic and non-ionizing galaxolide interacts weakly with soils, as compared with partially ionized triclosan and almost fully ionized gemfibrozil, i.e., leading to the conclusions not reachable based only on the direct comparison of experimentally measured distribution coefficients.

Mechanisms that Underlie Co-variation of the Brain and Face

PubMed Central

Marcucio, Ralph S.; Young, Nathan M.; Hu, Diane; Hallgrimsson, Benedikt

2011-01-01

The effect of the brain on the morphology of the face has long been recognized in both evolutionary biology and clinical medicine. In this paper we describe factors that are active between development of the brain and face and how these might impact craniofacial variation. First, there is the physical influence of the brain, which contributes to overall growth and morphology of the face through direct structural interactions. Second, there is the molecular influence of the brain, which signals to facial tissues to establish signaling centers that regulate patterned growth. Importantly, subtle alterations to these physical or molecular interactions may contribute to both normal and abnormal variation. These interactions are therefore critical to our understanding of how a diversity of facial morphologies can be generated both within species and across evolutionary time. PMID:21381182

The IntAct molecular interaction database in 2012

PubMed Central

Kerrien, Samuel; Aranda, Bruno; Breuza, Lionel; Bridge, Alan; Broackes-Carter, Fiona; Chen, Carol; Duesbury, Margaret; Dumousseau, Marine; Feuermann, Marc; Hinz, Ursula; Jandrasits, Christine; Jimenez, Rafael C.; Khadake, Jyoti; Mahadevan, Usha; Masson, Patrick; Pedruzzi, Ivo; Pfeiffenberger, Eric; Porras, Pablo; Raghunath, Arathi; Roechert, Bernd; Orchard, Sandra; Hermjakob, Henning

2012-01-01

IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from September 2011, IntAct contains approximately 275 000 curated binary interaction evidences from over 5000 publications. The IntAct website has been improved to enhance the search process and in particular the graphical display of the results. New data download formats are also available, which will facilitate the inclusion of IntAct's data in the Semantic Web. IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact. PMID:22121220

The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

NASA Astrophysics Data System (ADS)

Štambuk, Nikola

The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

Elucidation of the glucose transport pathway in glucose transporter 4 via steered molecular dynamics simulations.

PubMed

Sheena, Aswathy; Mohan, Suma S; Haridas, Nidhina Pachakkil A; Anilkumar, Gopalakrishnapillai

2011-01-01

GLUT4 is a predominant insulin regulated glucose transporter expressed in major glucose disposal tissues such as adipocytes and muscles. Under the unstimulated state, GLUT4 resides within intracellular vesicles. Various stimuli such as insulin translocate this protein to the plasma membrane for glucose transport. In the absence of a crystal structure for GLUT4, very little is known about the mechanism of glucose transport by this protein. Earlier we proposed a homology model for GLUT4 and performed a conventional molecular dynamics study revealing the conformational rearrangements during glucose and ATP binding. However, this study could not explain the transport of glucose through the permeation tunnel. To elucidate the molecular mechanism of glucose transport and its energetic, a steered molecular dynamics study (SMD) was used. Glucose was pulled from the extracellular end of GLUT4 to the cytoplasm along the pathway using constant velocity pulling method. We identified several key residues within the tunnel that interact directly with either the backbone ring or the hydroxyl groups of glucose. A rotation of glucose molecule was seen near the sugar binding site facilitating the sugar recognition process at the QLS binding site. This study proposes a possible glucose transport pathway and aids the identification of several residues that make direct interactions with glucose during glucose transport. Mutational studies are required to further validate the observation made in this study.

Use of gold nanoparticles as crosslink agent to form chitosan nanocapsules: study of the direct interaction in aqueous solutions.

PubMed

Prado-Gotor, R; López-Pérez, G; Martín, M J; Cabrera-Escribano, F; Franconetti, A

2014-06-01

A systematic study of the interaction between free anionic gold nanoparticles and chitosan in a solution is presented. A spectroscopic study of the interaction between 10nm gold nanoparticles and low molecular weight chitosan is reported as a function of the concentration and pH of the polymer in a solution. Zeta potential measurements and TEM images indicate the effective aggregation of the nanoparticles in the presence of chitosan. At the same time, anionic gold nanoparticles act as crosslink agents to form chitosan nanocapsules with an average molecular size of 260nm. The changes of the surface plasmon band due to the adsorption of the polymer on the nanoparticle surface allow using of the citrate gold nanoparticles as sensors of the polymer for analytical purposes. The limit of detection for chitosan biopolymer is 69nM. The optimum pH for the interaction between the biopolymer and the nanoparticles is found at a value of 6.4, obtained from spectrophotometric measurements and applying a deconvolution analysis of the experimental data. A simple model based on molecular surface electrostatic interactions is proposed to understand the pH dependence of the investigated system. Copyright © 2014 Elsevier Inc. All rights reserved.

Science review: Mechanisms of impaired adrenal function in sepsis and molecular actions of glucocorticoids

PubMed Central

Prigent, Hélène; Maxime, Virginie; Annane, Djillali

2004-01-01

This review describes current knowledge on the mechanisms that underlie glucocorticoid insufficiency in sepsis and the molecular action of glucocorticoids. In patients with severe sepsis, numerous factors predispose to glucocorticoid insufficiency, including drugs, coagulation disorders and inflammatory mediators. These factors may compromise the hypothalamic–pituitary axis (i.e. secondary adrenal insufficiency) or the adrenal glands (i.e. primary adrenal failure), or may impair glucocorticoid access to target cells (i.e. peripheral tissue resistance). Irreversible anatomical damages to the hypothalamus, pituitary, or adrenal glands rarely occur. Conversely, transient functional impairment in hormone synthesis may be a common complication of severe sepsis. Glucocorticoids interact with a specific cytosolic glucocorticoid receptor, which undergoes conformational changes, sheds heat shock proteins and translocates to the nucleus. Glucocorticoids may also interact with membrane binding sites at the surface of the cells. The molecular action of glucocorticoids results in genomic and nongenomic effects. Direct and indirect transcriptional and post-transcriptional effects related to the cytosolic glucocorticoid receptor account for the genomic effects. Nongenomic effects are probably subsequent to cytosolic interaction between the glucocorticoid receptor and proteins, or to interaction between glucocorticoids and specific membrane binding sites. PMID:15312206

TYCHO SN 1572: A NAKED Ia SUPERNOVA REMNANT WITHOUT AN ASSOCIATED AMBIENT MOLECULAR CLOUD

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

Tian, W. W.; Leahy, D. A., E-mail: tww@bao.ac.cn

The historical supernova remnant (SNR) Tycho SN 1572 originates from the explosion of a normal Type Ia supernova that is believed to have originated from a carbon-oxygen white dwarf in a binary system. We analyze the 21 cm continuum, H I, and {sup 12}CO-line data from the Canadian Galactic Plane Survey in the direction of SN 1572 and the surrounding region. We construct H I absorption spectra to SN 1572 and three nearby compact sources. We conclude that SN 1572 has no molecular cloud interaction, which argues against previous claims that a molecular cloud is interacting with the SNR. Thismore » new result does not support a recent claim that dust, newly detected by AKARI, originates from such an SNR-cloud interaction. We suggest that the SNR has a kinematic distance of 2.5-3.0 kpc based on a nonlinear rotational curve model. Very high energy {gamma}-ray emission from the remnant has been detected by the VERITAS telescope, so our result shows that its origin should not be an SNR-cloud interaction. Both radio and X-ray observations support that SN 1572 is an isolated Type Ia SNR.« less

Bacterial-fungal interactions: ecology, mechanisms and challenges.

PubMed

Deveau, Aurélie; Bonito, Gregory; Uehling, Jessie; Paoletti, Mathieu; Becker, Matthias; Bindschedler, Saskia; Hacquard, Stéphane; Hervé, Vincent; Labbé, Jessy; Lastovetsky, Olga A; Mieszkin, Sophie; Millet, Larry J; Vajna, Balázs; Junier, Pilar; Bonfante, Paola; Krom, Bastiaan P; Olsson, Stefan; van Elsas, Jan Dirk; Wick, Lukas Y

2018-05-01

Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.

Light-operated machines based on threaded molecular structures.

PubMed

Credi, Alberto; Silvi, Serena; Venturi, Margherita

2014-01-01

Rotaxanes and related species represent the most common implementation of the concept of artificial molecular machines, because the supramolecular nature of the interactions between the components and their interlocked architecture allow a precise control on the position and movement of the molecular units. The use of light to power artificial molecular machines is particularly valuable because it can play the dual role of "writing" and "reading" the system. Moreover, light-driven machines can operate without accumulation of waste products, and photons are the ideal inputs to enable autonomous operation mechanisms. In appropriately designed molecular machines, light can be used to control not only the stability of the system, which affects the relative position of the molecular components but also the kinetics of the mechanical processes, thereby enabling control on the direction of the movements. This step forward is necessary in order to make a leap from molecular machines to molecular motors.

In Silico Identification of Novel APRIL Peptide Antagonists and Binding Insights by Molecular Modeling and Immunosorbent Assays.

PubMed

Silva, Joao H M da; Calmon-Hamaty, Flavia; Savino, Wilson; Hahne, Michael; Caffarena, Ernesto R

2015-01-01

The "A proliferation inducing ligand" protein (APRIL) is a cytokine over-expressed in many transformed and tumoral cells acting onto two distinct receptors of the Tumoral Necrosis Factor B cell maturation antigen (BCMA) and the transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI). We herein describe, through a detailed computational approach, the molecular interactions between TACI and its ligands APRIL and another structurally similar protein called B-cell activating factor (BAFF) by means of molecular dynamics. Dynamical analysis suggests R84 and D85 residues from TACI as possible mutation candidates, yielding increased affinity between TACI and APRIL. The association of computational simulations, site directed mutagenesis and peptide design could be a powerful tool, driving to better in vitro experiments. Our results contribute to the elucidation of APRIL signaling and help clarify the effects of blocking interaction between APRIL and its receptors through the use of particular peptides.

Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression

PubMed Central

Danno, Hiroki; Michiue, Tatsuo; Hitachi, Keisuke; Yukita, Akira; Ishiura, Shoichi; Asashima, Makoto

2008-01-01

The neural-related genes Sox2, Pax6, Otx2, and Rax have been associated with severe ocular malformations such as anophthalmia and microphthalmia, but it remains unclear as to how these genes are linked functionally. We analyzed the upstream signaling of Xenopus Rax (also known as Rx1) and identified the Otx2 and Sox2 proteins as direct upstream regulators of Rax. We revealed that endogenous Otx2 and Sox2 proteins bound to the conserved noncoding sequence (CNS1) located ≈2 kb upstream of the Rax promoter. This sequence is conserved among vertebrates and is required for potent transcriptional activity. Reporter assays showed that Otx2 and Sox2 synergistically activated transcription via CNS1. Furthermore, the Otx2 and Sox2 proteins physically interacted with each other, and this interaction was affected by the Sox2-missense mutations identified in these ocular disorders. These results demonstrate that the direct interaction and interdependence between the Otx2 and Sox2 proteins coordinate Rax expression in eye development, providing molecular linkages among the genes responsible for ocular malformation. PMID:18385377

σ-Hole Bond vs π-Hole Bond: A Comparison Based on Halogen Bond.

PubMed

Wang, Hui; Wang, Weizhou; Jin, Wei Jun

2016-05-11

The σ-hole and π-hole are the regions with positive surface electrostatic potential on the molecule entity; the former specifically refers to the positive region of a molecular entity along extension of the Y-Ge/P/Se/X covalent σ-bond (Y = electron-rich group; Ge/P/Se/X = Groups IV-VII), while the latter refers to the positive region in the direction perpendicular to the σ-framework of the molecular entity. The directional noncovalent interactions between the σ-hole or π-hole and the negative or electron-rich sites are named σ-hole bond or π-hole bond, respectively. The contributions from electrostatic, charge transfer, and other terms or Coulombic interaction to the σ-hole bond and π-hole bond were reviewed first followed by a brief discussion on the interplay between the σ-hole bond and the π-hole bond as well as application of the two types of noncovalent interactions in the field of anion recognition. It is expected that this review could stimulate further development of the σ-hole bond and π-hole bond in theoretical exploration and practical application in the future.

A molecular dynamics study of the binary complexes of APP, JIP1, and the cargo binding domain of KLC.

PubMed

Taylor, Cooper A; Miller, Bill R; Shah, Soleil S; Parish, Carol A

2017-02-01

Mutations in the amyloid precursor protein (APP) are responsible for the formation of amyloid-β peptides. These peptides play a role in Alzheimer's and other dementia-related diseases. The cargo binding domain of the kinesin-1 light chain motor protein (KLC1) may be responsible for transporting APP either directly or via interaction with C-jun N-terminal kinase-interacting protein 1 (JIP1). However, to date there has been no direct experimental or computational assessment of such binding at the atomistic level. We used molecular dynamics and free energy estimations to gauge the affinity for the binary complexes of KLC1, APP, and JIP1. We find that all binary complexes (KLC1:APP, KLC1:JIP1, and APP:JIP1) contain conformations with favorable binding free energies. For KLC1:APP the inclusion of approximate entropies reduces the favorability. This is likely due to the flexibility of the 42-residue APP protein. In all cases we analyze atomistic/residue driving forces for favorable interactions. Proteins 2017; 85:221-234. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Alcohol action on a neuronal membrane receptor: evidence for a direct interaction with the receptor protein.

PubMed Central

Li, C; Peoples, R W; Weight, F F

1994-01-01

For almost a century, alcohols have been thought to produce their effects by actions on the membrane lipids of central nervous system neurons--the well known "lipid theory" of alcohol action. The rationale for this theory is the correlation of potency with oil/water or membrane/buffer partition coefficient. Although a number of recent studies have shown that alcohols can affect the function of certain neuronal neurotransmitter receptors, there is no evidence that the alcohols interact directly with these membrane proteins. In the present study, we report that inhibition of a neuronal neurotransmitter receptor, an ATP-gated ion channel, by a series of alcohols exhibits a distinct cutoff effect. For alcohols with a molecular volume of < or = 42.2 ml/mol, potency for inhibiting ATP-activated current was correlated with lipid solubility (order of potency: 1-propanol = trifluoroethanol > monochloroethanol > ethanol > methanol). However, despite increased lipid solubility, alcohols with a molecular volume of > or = 46.1 ml/mol (1-butanol, 1-pentanol, trichloroethanol, and dichloroethanol) were without effect on the ATP-activated current. The results suggest that alcohols inhibit the function of this neurotransmitter receptor by interacting with a small hydrophobic pocket on the receptor protein. PMID:8058780

Regulatory function of Arabidopsis lipid transfer protein 1 (LTP1) in ethylene response and signaling.

PubMed

Wang, Honglin; Sun, Yue; Chang, Jianhong; Zheng, Fangfang; Pei, Haixia; Yi, Yanjun; Chang, Caren; Dong, Chun-Hai

2016-07-01

Ethylene as a gaseous plant hormone is directly involved in various processes during plant growth and development. Much is known regarding the ethylene receptors and regulatory factors in the ethylene signal transduction pathway. In Arabidopsis thaliana, REVERSION-TO-ETHYLENE SENSITIVITY1 (RTE1) can interact with and positively regulates the ethylene receptor ETHYLENE RESPONSE1 (ETR1). In this study we report the identification and characterization of an RTE1-interacting protein, a putative Arabidopsis lipid transfer protein 1 (LTP1) of unknown function. Through bimolecular fluorescence complementation, a direct molecular interaction between LTP1 and RTE1 was verified in planta. Analysis of an LTP1-GFP fusion in transgenic plants and plasmolysis experiments revealed that LTP1 is localized to the cytoplasm. Analysis of ethylene responses showed that the ltp1 knockout is hypersensitive to 1-aminocyclopropanecarboxylic acid (ACC), while LTP1 overexpression confers insensitivity. Analysis of double mutants etr1-2 ltp1 and rte1-3 ltp1 demonstrates a regulatory function of LTP1 in ethylene receptor signaling through the molecular association with RTE1. This study uncovers a novel function of Arabidopsis LTP1 in the regulation of ethylene response and signaling.

Elucidation of Lipid Binding Sites on Lung Surfactant Protein A Using X-ray Crystallography, Mutagenesis, and Molecular Dynamics Simulations.

PubMed

Goh, Boon Chong; Wu, Huixing; Rynkiewicz, Michael J; Schulten, Klaus; Seaton, Barbara A; McCormack, Francis X

2016-07-05

Surfactant protein A (SP-A) is a collagenous C-type lectin (collectin) that is critical for pulmonary defense against inhaled microorganisms. Bifunctional avidity of SP-A for pathogen-associated molecular patterns (PAMPs) such as lipid A and for dipalmitoylphosphatidylcholine (DPPC), the major component of surfactant membranes lining the air-liquid interface of the lung, ensures that the protein is poised for first-line interactions with inhaled pathogens. To improve our understanding of the motifs that are required for interactions with microbes and surfactant structures, we explored the role of the tyrosine-rich binding surface on the carbohydrate recognition domain of SP-A in the interaction with DPPC and lipid A using crystallography, site-directed mutagenesis, and molecular dynamics simulations. Critical binding features for DPPC binding include a three-walled tyrosine cage that binds the choline headgroup through cation-π interactions and a positively charged cluster that binds the phosphoryl group. This basic cluster is also critical for binding of lipid A, a bacterial PAMP and target for SP-A. Molecular dynamics simulations further predict that SP-A binds lipid A more tightly than DPPC. These results suggest that the differential binding properties of SP-A favor transfer of the protein from surfactant DPPC to pathogen membranes containing appropriate lipid PAMPs to effect key host defense functions.

Carbohydrate binding specificity of pea lectin studied by NMR spectroscopy and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Cheong, Youngjoo; Shim, Gyuchang; Kang, Dongil; Kim, Yangmee

1999-02-01

The conformational details of Man( α1,6)Man( α)OMe are investigated through NMR spectroscopy in conjunction with molecular modeling. The lowest energy structure (M1) in the adiabatic energy map calculated with a dielectric constant of 50 has glycosidic dihedral angles of φ=-60°, ψ=180° and ω=180°. The other low energy structure (M2) has glycosidic dihedral angles of φ=-60°, ψ=180° and ω=-60°. Molecular dynamics simulations and NMR experiments prove that Man( α1,6)Man( α)OMe in the free form exists with conformational averaging of M1 and M2 conformers predominantly. Molecular dynamics simulations of the pea lectin-carbohydrate complex with explicit water molecules starting from the X-ray crystallographic structure of pea lectin show that the protein-carbohydrate interaction centers mainly on the hydrogen bonds and van der Waals interactions between protein and carbohydrate. From the molecular dynamics simulation, it is found that the M1 structure can bind to pea lectin better than the M2 structure. The origin of this selectivity is the water- mediated hydrogen bond interactions between the remote mannose and the binding site of pea lectin as well as the direct hydrogen bond interaction between the terminal mannose and pea lectin. Extensive networks of interactions in the carbohydrate binding site and the metal binding site are important in maintaining the carbohydrate binding properties of pea lectin. Especially, the predominant factors of mannose binding specificity of pea lectin are the hydrogen bond interactions between the 4th hydroxyl groups of the terminal sugar ring and the side chains of Asp-81 and Asn-125 in the carbohydrate binding site, and the additional interactions between these side chains of Asp-81 and Asn-125 and the calcium ion in the metal binding site of pea lectin.

HPIDB 2.0: a curated database for host–pathogen interactions

PubMed Central

Ammari, Mais G.; Gresham, Cathy R.; McCarthy, Fiona M.; Nanduri, Bindu

2016-01-01

Identification and analysis of host–pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host–pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB 2.0 (http://www.agbase.msstate.edu/hpi/main.html) is a resource for HPI data, and contains 45, 238 manually curated entries in the current release. Since the first description of the database in 2010, multiple enhancements to HPIDB data and interface services were made that are described here. Notably, HPIDB 2.0 now provides targeted biocuration of molecular interaction data. As a member of the International Molecular Exchange consortium, annotations provided by HPIDB 2.0 curators meet community standards to provide detailed contextual experimental information and facilitate data sharing. Moreover, HPIDB 2.0 provides access to rapidly available community annotations that capture minimum molecular interaction information to address immediate researcher needs for HPI network analysis. In addition to curation, HPIDB 2.0 integrates HPI from existing external sources and contains tools to infer additional HPI where annotated data are scarce. Compared to other interaction databases, our data collection approach ensures HPIDB 2.0 users access the most comprehensive HPI data from a wide range of pathogens and their hosts (594 pathogen and 70 host species, as of February 2016). Improvements also include enhanced search capacity, addition of Gene Ontology functional information, and implementation of network visualization. The changes made to HPIDB 2.0 content and interface ensure that users, especially agricultural researchers, are able to easily access and analyse high quality, comprehensive HPI data. All HPIDB 2.0 data are updated regularly, are publically available for direct download, and are disseminated to other molecular interaction resources. Database URL: http://www.agbase.msstate.edu/hpi/main.html PMID:27374121

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

PubMed Central

Fantini, Jacques; Yahi, Nouara; Garmy, Nicolas

2013-01-01

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

Mapping the Small Molecule Interactome by Mass Spectrometry.

PubMed

Flaxman, Hope A; Woo, Christina M

2018-01-16

Mapping small molecule interactions throughout the proteome provides the critical structural basis for functional analysis of their impact on biochemistry. However, translation of mass spectrometry-based proteomics methods to directly profile the interaction between a small molecule and the whole proteome is challenging because of the substoichiometric nature of many interactions, the diversity of covalent and noncovalent interactions involved, and the subsequent computational complexity associated with their spectral assignment. Recent advances in chemical proteomics have begun fill this gap to provide a structural basis for the breadth of small molecule-protein interactions in the whole proteome. Innovations enabling direct characterization of the small molecule interactome include faster, more sensitive instrumentation coupled to chemical conjugation, enrichment, and labeling methods that facilitate detection and assignment. These methods have started to measure molecular interaction hotspots due to inherent differences in local amino acid reactivity and binding affinity throughout the proteome. Measurement of the small molecule interactome is producing structural insights and methods for probing and engineering protein biochemistry. Direct structural characterization of the small molecule interactome is a rapidly emerging area pushing new frontiers in biochemistry at the interface of small molecules and the proteome.

Direct Nanoscale Characterization of Submolecular Mobility in Complex Organic Non-linear Optical Systems

NASA Astrophysics Data System (ADS)

Knorr, Daniel; Gray, Tomoko; Kim, Tae-Dong; Luo, Jingdong; Jen, Alex; Overney, Rene

2008-03-01

For organic non-linear optical (NLO) materials composed of intricate molecular building blocks, the challenge is to deduce meaningful molecular scale mobility information to understand complex relaxation and phase behavior. This is crucial, as the process of achieving a robust acentric alignment strongly depends on the availability of inter- and intra-molecular mobilities outside the temperature range of the device operation window. Here, we introduce a nanoscale methodology based on scanning probe microscopy that provides direct insight into structural relaxations and shows great potential to direct material design of sophisticated macromolecules. It also offers a means by which mesoscale dynamics and cooperativity involved in relaxation processes can be quantified in terms of dynamic entropy and enthalpy. This study demonstrates this methodology to describe the mesocale dynamics of two systems (1) organic networking dendronized NLO molecular glasses that self-assemble into physically linked polymers due to quadrupolar phenyl-perfluorophenyl interactions and (2) dendronized side-chain electro-optic (EO) polymers. For the self assembling glasses, the degree of intermolecular cooperativity can be deduced using this methodology, while for the dendronized side-chain polymers, specific side chain mobilities are exploited to improve EO properties.

Direct Photolithography on Molecular Crystals for High Performance Organic Optoelectronic Devices.

PubMed

Yao, Yifan; Zhang, Lei; Leydecker, Tim; Samorì, Paolo

2018-05-23

Organic crystals are generated via the bottom-up self-assembly of molecular building blocks which are held together through weak noncovalent interactions. Although they revealed extraordinary charge transport characteristics, their labile nature represents a major drawback toward their integration in optoelectronic devices when the use of sophisticated patterning techniques is required. Here we have devised a radically new method to enable the use of photolithography directly on molecular crystals, with a spatial resolution below 300 nm, thereby allowing the precise wiring up of multiple crystals on demand. Two archetypal organic crystals, i.e., p-type 2,7-diphenyl[1]benzothieno[3,2- b][1]benzothiophene (Dph-BTBT) nanoflakes and n-type N, N'-dioctyl-3,4,9,10-perylenedicarboximide (PTCDI-C8) nanowires, have been exploited as active materials to realize high-performance top-contact organic field-effect transistors (OFETs), inverter and p-n heterojunction photovoltaic devices supported on plastic substrate. The compatibility of our direct photolithography technique with organic molecular crystals is key for exploiting the full potential of organic electronics for sophisticated large-area devices and logic circuitries, thus paving the way toward novel applications in plastic (opto)electronics.

Estrogen Receptor Folding Modulates cSrc Kinase SH2 Interaction via a Helical Binding Mode.

PubMed

Nieto, Lidia; Tharun, Inga M; Balk, Mark; Wienk, Hans; Boelens, Rolf; Ottmann, Christian; Milroy, Lech-Gustav; Brunsveld, Luc

2015-11-20

The estrogen receptors (ERs) feature, next to their transcriptional role, important nongenomic signaling actions, with emerging clinical relevance. The Src Homology 2 (SH2) domain mediated interaction between cSrc kinase and ER plays a key role in this; however the molecular determinants of this interaction have not been elucidated. Here, we used phosphorylated ER peptide and semisynthetic protein constructs in a combined biochemical and structural study to, for the first time, provide a quantitative and structural characterization of the cSrc SH2-ER interaction. Fluorescence polarization experiments delineated the SH2 binding motif in the ER sequence. Chemical shift perturbation analysis by nuclear magnetic resonance (NMR) together with molecular dynamics (MD) simulations allowed us to put forward a 3D model of the ER-SH2 interaction. The structural basis of this protein-protein interaction has been compared with that of the high affinity SH2 binding sequence GpYEEI. The ER features a different binding mode from that of the "two-pronged plug two-hole socket" model in the so-called specificity determining region. This alternative binding mode is modulated via the folding of ER helix 12, a structural element directly C-terminal of the key phosphorylated tyrosine. The present findings provide novel molecular entries for understanding nongenomic ER signaling and targeting the corresponding disease states.

Molecular interactions between the olive and the fruit fly Bactrocera oleae

PubMed Central

2012-01-01

Background The fruit fly Bactrocera oleae is the primary biotic stressor of cultivated olives, causing direct and indirect damages that significantly reduce both the yield and the quality of olive oil. To study the olive-B. oleae interaction, we conducted transcriptomic and proteomic investigations of the molecular response of the drupe. The identifications of genes and proteins involved in the fruit response were performed using a Suppression Subtractive Hybridisation technique and a combined bi-dimensional electrophoresis/nanoLC-ESI-LIT-MS/MS approach, respectively. Results We identified 196 ESTs and 26 protein spots as differentially expressed in olives with larval feeding tunnels. A bioinformatic analysis of the identified non-redundant EST and protein collection indicated that different molecular processes were affected, such as stress response, phytohormone signalling, transcriptional control and primary metabolism, and that a considerable proportion of the ESTs could not be classified. The altered expression of 20 transcripts was also analysed by real-time PCR, and the most striking differences were further confirmed in the fruit of a different olive variety. We also cloned the full-length coding sequences of two genes, Oe-chitinase I and Oe-PR27, and showed that these are wound-inducible genes and activated by B. oleae punctures. Conclusions This study represents the first report that reveals the molecular players and signalling pathways involved in the interaction between the olive fruit and its most damaging biotic stressor. Drupe response is complex, involving genes and proteins involved in photosynthesis as well as in the production of ROS, the activation of different stress response pathways and the production of compounds involved in direct defence against phytophagous larvae. Among the latter, trypsin inhibitors should play a major role in drupe resistance reaction. PMID:22694925

Emergence of chirality in hexagonally packed monolayers of hexapentyloxytriphenylene on Au(111): a joint experimental and theoretical study.

PubMed

Sleczkowski, Piotr; Katsonis, Nathalie; Kapitanchuk, Oleksiy; Marchenko, Alexandr; Mathevet, Fabrice; Croset, Bernard; Lacaze, Emmanuelle

2014-11-11

We investigate the expression of chirality in a monolayer formed spontaneously by 2,3,6,7,10,11-pentyloxytriphenylene (H5T) on Au(111). We resolve its interface morphology by combining scanning tunneling microscopy (STM) with theoretical calculations of intermolecular and interfacial interaction potentials. We observe two commensurate structures. While both of them belong to a hexagonal space group, analogical to the triangular symmetry of the molecule and the hexagonal symmetry of the substrate surface, they surprisingly reveal a 2D chiral character. The corresponding breaking of symmetry arises for two reasons. First it is due to the establishment of a large molecular density on the substrate, which leads to a rotation of the molecules with respect to the molecular network crystallographic axes to avoid steric repulsion between neighboring alkoxy chains. Second it is due to the molecule-substrate interactions, leading to commensurable large crystallographic cells associated with the large size of the molecule. As a consequence, molecular networks disoriented with respect to the high symmetry directions of the substrate are induced. The high simplicity of the intermolecular and molecule-substrate van der Waals interactions leading to these observations suggests a generic character for this kind of symmetry breaking. We demonstrate that, for similar molecular densities, only two kinds of molecular networks are stabilized by the molecule-substrate interactions. The most stable network favors the interfacial interactions between terminal alkoxy tails and Au(111). The metastable one favors a specific orientation of the triphenylene core with its symmetry axes collinear to the Au⟨110⟩. This specific orientation of the triphenylene cores with respect to Au(111) appears associated with an energy advantage larger by at least 0.26 eV with respect to the disoriented core.

Quantifying the Molecular Origins of Opposite Solvent Effects on Protein-Protein Interactions

PubMed Central

Vagenende, Vincent; Han, Alvin X.; Pek, Han B.; Loo, Bernard L. W.

2013-01-01

Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments. PMID:23696727

Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

PubMed

Vagenende, Vincent; Han, Alvin X; Pek, Han B; Loo, Bernard L W

2013-01-01

Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.

Bio-Mimetic Sensors Based on Molecularly Imprinted Membranes

PubMed Central

Algieri, Catia; Drioli, Enrico; Guzzo, Laura; Donato, Laura

2014-01-01

An important challenge for scientific research is the production of artificial systems able to mimic the recognition mechanisms occurring at the molecular level in living systems. A valid contribution in this direction resulted from the development of molecular imprinting. By means of this technology, selective molecular recognition sites are introduced in a polymer, thus conferring it bio-mimetic properties. The potential applications of these systems include affinity separations, medical diagnostics, drug delivery, catalysis, etc. Recently, bio-sensing systems using molecularly imprinted membranes, a special form of imprinted polymers, have received the attention of scientists in various fields. In these systems imprinted membranes are used as bio-mimetic recognition elements which are integrated with a transducer component. The direct and rapid determination of an interaction between the recognition element and the target analyte (template) was an encouraging factor for the development of such systems as alternatives to traditional bio-assay methods. Due to their high stability, sensitivity and specificity, bio-mimetic sensors-based membranes are used for environmental, food, and clinical uses. This review deals with the development of molecularly imprinted polymers and their different preparation methods. Referring to the last decades, the application of these membranes as bio-mimetic sensor devices will be also reported. PMID:25196110

Direct characterization of hydrophobic hydration during cold and pressure denaturation.

PubMed

Das, Payel; Matysiak, Silvina

2012-05-10

Cold and pressure denaturation are believed to have their molecular origin in hydrophobic interactions between nonpolar groups and water. However, the direct characterization of the temperature- and pressure-dependent variations of those interactions with atomistic simulations remains challenging. We investigated the role of solvent in the cold and pressure denaturation of a model hydrophobic 32-mer polymer by performing extensive coarse-grained molecular dynamics simulations including explicit solvation. Our simulations showed that the water-excluded folded state of this polymer is marginally stable and can be unfolded by heating or cooling, as well as by applying pressure, similar to globular proteins. We further detected essential population of a hairpin-like configuration prior to the collapse, which is consistently accompanied by a vapor bubble at the elbow of the kink. Increasing pressure suppresses formation of this vapor bubble by reducing water fluctuations in the hydration shell of the polymer, thus promoting unfolding. Further analysis revealed a slight reduction of water tetrahedrality in the polymer hydration shell compared to the bulk. Cold denaturation is driven by an enhanced tetrahedral ordering of hydration shell water than bulk water. At elevated pressures, the strikingly reduced fluctuations combined with the increase in interstitial water molecules in the polymer hydration shell contribute to weakening of hydrophobic interactions, thereby promoting pressure unfolding. These findings provide critical molecular insights into the changes in hydrophobic hydration during cold and pressure unfolding of a hydrophobic polymer, which is strongly related to the cold and pressure denaturation of globular proteins.

Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms.

PubMed

Bonati, Laura; Corrada, Dario; Tagliabue, Sara Giani; Motta, Stefano

2017-02-01

Molecular modeling has given important contributions to elucidation of the main stages in the AhR signal transduction pathway. Despite the lack of experimentally determined structures of the AhR functional domains, information derived from homologous systems has been exploited for modeling their structure and interactions. Homology models of the AhR PASB domain have provided information on the binding cavity and contributed to elucidate species-specific differences in ligand binding. Molecular Docking simulations of the ligand binding process have given insights into differences in binding of diverse agonists, antagonists, and selective AhR modulators, and their application to virtual screening of large databases of compounds have allowed identification of novel AhR ligands. Recently available structural information on protein-protein and protein-DNA complexes of other bHLH-PAS systems has opened the way for modeling the AhR:ARNT dimer structure and investigating the mechanisms of AhR transformation and DNA binding. Future research directions should include simulation of the protein dynamics to obtain a more reliable description of intermolecular interactions involved in signal transmission.

Lipopolysaccharides in diazotrophic bacteria.

PubMed

Serrato, Rodrigo V

2014-01-01

Biological nitrogen fixation (BNF) is a process in which the atmospheric nitrogen (N2) is transformed into ammonia (NH3) by a select group of nitrogen-fixing organisms, or diazotrophic bacteria. In order to furnish the biologically useful nitrogen to plants, these bacteria must be in constant molecular communication with their host plants. Some of these molecular plant-microbe interactions are very specific, resulting in a symbiotic relationship between the diazotroph and the host. Others are found between associative diazotrophs and plants, resulting in plant infection and colonization of internal tissues. Independent of the type of ecological interaction, glycans, and glycoconjugates produced by these bacteria play an important role in the molecular communication prior and during colonization. Even though exopolysaccharides (EPS) and lipochitooligosaccharides (LCO) produced by diazotrophic bacteria and released onto the environment have their importance in the microbe-plant interaction, it is the lipopolysaccharides (LPS), anchored on the external membrane of these bacteria, that mediates the direct contact of the diazotroph with the host cells. These molecules are extremely variable among the several species of nitrogen fixing-bacteria, and there are evidences of the mechanisms of infection being closely related to their structure.

Direct measurements of intermolecular forces by chemical force microscopy

NASA Astrophysics Data System (ADS)

Vezenov, Dmitri Vitalievich

1999-12-01

Detailed description of intermolecular forces is key to understanding a wide range of phenomena from molecular recognition to materials failure. The unique features of atomic force microscopy (AFM) to make point contact force measurements with ultra high sensitivity and to generate spatial maps of surface topography and forces have been extended to include measurements between well-defined organic molecular groups. Chemical modification of AFM probes with self-assembled monolayers (SAMs) was used to make them sensitive to specific molecular interactions. This novel chemical force microscopy (CFM) technique was used to probe forces between different molecular groups in a range of environments (vacuum, organic liquids and aqueous solutions); measure surface energetics on a nanometer scale; determine pK values of the surface acid and base groups; measure forces to stretch and unbind a short synthetic DNA duplex and map the spatial distribution of specific functional groups and their ionization state. Studies of adhesion forces demonstrated the important contribution of hydrogen bonding to interactions between simple organic functionalities. The chemical identity of the tip and substrate surfaces as well as the medium had a dramatic effect on adhesion between model monolayers. A direct correlation between surface free energy and adhesion forces was established. The adhesion between epoxy polymer and model mixed SAMs varied with the amount of hydrogen bonding component in the monolayers. A consistent interpretation of CFM measurements in polar solvents was provided by contact mechanics models and intermolecular force components theory. Forces between tips and surfaces functionalized with SAMs terminating in acid or base groups depended on their ionization state. A novel method of force titration was introduced for highly local characterization of the pK's of surface functional groups. The pH-dependent changes in friction forces were exploited to map spatially the changes in ionization state on SAM surfaces. The phase contrast in tapping mode AFM between chemically distinct monolayer regions and corresponding adhesion forces were found to be directly correlated. Thus, both friction and intermittent contact CFM images could be interpreted in terms of the strength of intermolecular interactions. CFM was also used to probe biomolecular interactions. Separation forces between complementary oligonucleotide strands were significantly larger than the forces measured between noncomplementary strands and were consistent with the unbinding of a single DNA duplex. CFM data provided a direct measure of the forces required to elastically deform, structurally-transform and separate well-defined, synthetic duplexes into single strand oligonucleotides.

μ-Carbonato-bis-(bis-{2-[(diethyl-amino)-meth-yl]phen-yl}bis-muth(III)).

PubMed

Soran, Albert P; Nema, Mihai G; Breunig, Hans J; Silvestru, Cristian

2011-01-12

The mol-ecular structure of the title compound, [Bi(2)(C(11)H(16)N)(4)(CO(3))], consists of a symmetrically bridging carbonato group which binds two [2-Et(2)NCH(2)C(6)H(4)](2)Bi units that are crystallographically related via a twofold rotation axis bis-ecting the carbonate group. The two Bi atoms and two of the C atoms directly bonded to bis-muth are quasi-planar [deviations of 0.323 (1) and 0.330 (9)Å for the Bi and C atoms, respectively] with the carbonate group. The remaining two ligands are in a trans arrangement relative to the quasi-planar (CBi)(2)CO(3) system. The metal atom is strongly coordinated by the N atom of one pendant arm [Bi-N = 2.739 (6) Å], almost trans to the O atom, while the N atom of the other pendant arm exhibits a weaker intra-molecular inter-action [Bi⋯N = 3.659 (7) Å] almost trans to a C atom. If both these intra-molecular N→Bi inter-actions per metal atom are considered, the overall coordination geometry at bis-muth becomes distorted square-pyramidal [(C,N)(2)BiO cores] and the compound can be described as a hypervalent 12-Bi-5 species. Additional quite short intra-molecular Bi⋯O inter-actions are also present [3.796 (8)-4.020 (9) Å]. Inter-molecular associations through weak η(6)⋯Bi inter-actions [Bi⋯centroid of benzene ring = 3.659 (1) Å] lead to a ribbon-like supra-molecular association.

Binding of Bisphenol-F, a bisphenol analogue, to calf thymus DNA by multi-spectroscopic and molecular docking studies.

PubMed

Usman, Afia; Ahmad, Masood

2017-08-01

BPF (Bisphenol-F), a member of the bisphenol family, having a wide range of industrial applications is gradually replacing Bisphenol-A. It is a recognized endocrine disrupting chemical (EDC). EDCs have been implicated in increased incidences of breast, prostate and testis cancers besides diabetes, obesity and decreased fertility. Due to the adverse effects of EDCs on human health, attempts have been directed towards their mechanism of toxicity especially at the molecular level. Hence, to understand the mechanism at the DNA level, interaction of BPF with calf thymus DNA was studied employing multi-spectroscopic, voltammetric and molecular docking techniques. Fluorescence spectra, cyclic voltammetry (CV), circular dichroism (CD) and molecular docking studies of BPF with DNA were suggestive of minor groove binding of BPF. UV-visible absorption and fluorescence spectra suggested static quenching due to complex formation between BPF and ctDNA. Hoechst 33258 (HO) and ethidium bromide (EB) displacement studies further confirmed such mode of BPF interaction. Thermodynamic and molecular docking parameters revealed the mechanism of binding of BPF with ctDNA to be favorable and spontaneous due to negative ΔG and occurring through hydrogen bonds and van der waals interactions. BPF induced DNA cleavage under in vitro conditions by plasmid nicking assay suggested it to be genotoxic. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (Oryza sativa L.): insights from molecular dynamics simulations.

PubMed

Dehury, Budheswar; Maharana, Jitendra; Sahoo, Bikash Ranjan; Sahu, Jagajjit; Sen, Priyabrata; Modi, Mahendra Kumar; Barooah, Madhumita

2015-04-01

The avirulence gene avrxa5 of bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) recognized by the resistant rice lines having corresponding resistance (xa5) gene in a gene-for-gene manner. We used a combinatorial approach involving protein-protein docking, molecular dynamics (MD) simulations and binding free energy calculations to gain novel insights into the gene-for-gene mechanism that governs the direct interaction of R-Avr protein. From the best three binding poses predicted by molecular docking, MD simulations were performed to explore the dynamic binding mechanism of xa5 and avrxa5. Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) techniques were employed to calculate the binding free energy and to uncover the thriving force behind the molecular recognition of avrxa5 by eukaryotic transcription factor xa5. Binding free energy analysis revealed van der Waals term as the most constructive component that favors the xa5 and avrxa5 interaction. In addition, hydrogen bonds (H-bonds) and essential electrostatic interactions analysis highlighted amino acid residues Lys54/Asp870, Lys56/Ala868, Lys56/Ala866, Lys56/Glu871, Ile59/His862, Gly61/Phe858, His62/Arg841, His62/Leu856, Ser101/Ala872 and Ser105/Asp870 plays pivotal role for the energetically stability of the R-Avr complex. Insights gained from the present study are expected to unveil the molecular mechanisms that define the transcriptional activator mediated transcriptome modification in host plants. Copyright © 2015 Elsevier Inc. All rights reserved.

Nanohashtag structures based on carbon nanotubes and molecular linkers

NASA Astrophysics Data System (ADS)

Frye, Connor W.; Rybolt, Thomas R.

2018-03-01

Molecular mechanics was used to study the noncovalent interactions between single-walled carbon nanotubes and molecular linkers. Groups of nanotubes have the tendency to form tight, parallel bundles (||||). Molecular linkers were introduced into our models to stabilize nanostructures with carbon nanotubes held in perpendicular orientations. Molecular mechanics makes it possible to estimate the strength of noncovalent interactions holding these structures together and to calculate the overall binding energy of the structures. A set of linkers were designed and built around a 1,3,5,7-cyclooctatetraene tether with two corannulene containing pincers that extend in opposite directions from the central cyclooctatetraene portion. Each pincer consists of a pairs of "arms." These molecular linkers were modified so that the "hand" portions of each pair of "arms" could close together to grab and hold two carbon nanotubes in a perpendicular arrangement. To illustrate the possibility of more complicated and open perpendicular CNTs structures, our primary goal was to create a model of a nanohashtag (#) CNT conformation that is more stable than any parallel CNT arrangements with bound linker molecules forming clumps of CNTs and linkers in non-hashtag arrangements. This goal was achieved using a molecular linker (C280H96) that utilizes van der Waals interactions to two perpendicular oriented CNTs. Hydrogen bonding was then added between linker molecules to augment the stability of the hashtag structure. In the hashtag structure with hydrogen bonding, four (5,5) CNTs of length 4.46 nm (18 rings) and four linkers (C276H92N8O8) stabilized the hashtag so that the average binding energy per pincer was 118 kcal/mol.

Solid-State Solvation and Enhanced Exciton Diffusion in Doped Organic Thin Films under Mechanical Pressure.

PubMed

Chang, Wendi; Akselrod, Gleb M; Bulović, Vladimir

2015-04-28

Direct modification of exciton energy has been previously used to optimize the operation of organic optoelectronic devices. One demonstrated method for exciton energy modification is through the use of the solvent dielectric effects in doped molecular films. To gain a deeper appreciation of the underlying physical mechanisms, in this work we test the solid-state solvation effect in molecular thin films under applied external pressure. We observe that external mechanical pressure increases dipole-dipole interactions, leading to shifts in the Frenkel exciton energy and enhancement of the time-resolved spectral red shift associated with the energy-transfer-mediated exciton diffusion. Measurements are performed on host:dopant molecular thin films, which show bathochromic shifts in photoluminescence (PL) under increasing pressure. This is in agreement with a simple solvation theory model of exciton energetics with a fitting parameter based on the mechanical properties of the host matrix material. We measure no significant change in exciton lifetime with increasing pressure, consistent with unchanged aggregation in molecular films under compression. However, we do observe an increase in exciton spectral thermalization rate for compressed molecular films, indicating enhanced exciton diffusion for increased dipole-dipole interactions under pressure. The results highlight the contrast between molecular energy landscapes obtained when dipole-dipole interactions are increased by the pressure technique versus the conventional dopant concentration variation methods, which can lead to extraneous effects such as aggregation at higher doping concentrations. The present work demonstrates the use of pressure-probing techniques in studying energy disorder and exciton dynamics in amorphous molecular thin films.

Solid-State Solvation and Enhanced Exciton Diffusion in Doped Organic Thin Films under Mechanical Pressure

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

Chang, Wendi; Akselrod, Gleb M.; Bulović, Vladimir

2015-04-28

Direct modification of exciton energy has been previously used to optimize the operation of organic optoelectronic devices. One demonstrated method for exciton energy modification is through the use of the solvent dielectric effects in doped molecular films. To gain a deeper appreciation of the underlying physical mechanisms, in this work we test the solid-state solvation effect in molecular thin films under applied external pressure. We observe that external mechanical pressure increases dipole–dipole interactions, leading to shifts in the Frenkel exciton energy and enhancement of the time-resolved spectral red shift associated with the energy-transfer-mediated exciton diffusion. Measurements are performed on host:dopantmore » molecular thin films, which show bathochromic shifts in photoluminescence (PL) under increasing pressure. This is in agreement with a simple solvation theory model of exciton energetics with a fitting parameter based on the mechanical properties of the host matrix material. We measure no significant change in exciton lifetime with increasing pressure, consistent with unchanged aggregation in molecular films under compression. However, we do observe an increase in exciton spectral thermalization rate for compressed molecular films, indicating enhanced exciton diffusion for increased dipole–dipole interactions under pressure. The results highlight the contrast between molecular energy landscapes obtained when dipole–dipole interactions are increased by the pressure technique versus the conventional dopant concentration variation methods, which can lead to extraneous effects such as aggregation at higher doping concentrations. The present work demonstrates the use of pressure-probing techniques in studying energy disorder and exciton dynamics in amorphous molecular thin films.« less

Testing a structural model for viral DNA packaging motor function by optical tweezers measurements, site directed mutagenesis, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Keller, Nicholas A.; Migliori, Amy D.; Arya, Gaurav; Rao, Venigalla B.; Smith, Douglas E.

2013-09-01

Many double-stranded DNA viruses employ a molecular motor to package DNA into preformed capsid shells. Based on structures of phage T4 motor proteins determined by X-ray crystallography and cryo-electron microscopy, Rao, Rossmann and coworkers recently proposed a structural model for motor function. They proposed that DNA is ratcheted by a large conformational change driven by electrostatic interactions between charged residues at an interface between two globular domains of the motor protein. We have conducted experiments to test this model by studying the effect on packaging under applied load of site-directed changes altering these residues. We observe significant impairment of packaging activity including reductions in packaging rate, percent time packaging, and time active under high load. We show that these measured impairments correlate well with alterations in free energies associated with the conformational change predicted by molecular dynamics simulations.

Stereodynamics in state-resolved scattering at the gas–liquid interface

PubMed Central

Perkins, Bradford G.; Nesbitt, David J.

2008-01-01

Stereodynamics at the gas–liquid interface provides insight into the important physical interactions that directly influence heterogeneous chemistry at the surface and within the bulk liquid. We investigate molecular beam scattering of CO2 from a liquid perfluoropolyether (PFPE) surface in vacuum [incident energy Einc = 10.6(8) kcal/mol, incident angle θinc = 60°] to specifically reveal rotational angular-momentum directions for scattered molecules. Experimentally, internal quantum state populations and MJ distributions are probed by high-resolution polarization-modulated infrared laser spectroscopy. Analysis of J-state populations reveals dual-channel scattering dynamics characterized by a two-temperature Boltzmann distribution for trapping–desorption and impulsive scattering. In addition, molecular dynamics simulations of CO2 + fluorinated self-assembled monolayers have been used to model CO2 + PFPE dynamics. Experimental results and molecular dynamics simulations reveal highly oriented CO2 distributions that preferentially scatter with “top spin” as a strongly increasing function of J state. PMID:18678907

Specificity in cationic interaction with poly(N-isopropylacrylamide).

PubMed

Du, Hongbo; Wickramasinghe, Sumith Ranil; Qian, Xianghong

2013-05-02

Classical molecular dynamics (MD) simulations were conducted for PNIPAM in 1 M monovalent alkali chloride salt solutions as well as in 0.5 M divalent Mg(2+) and Ca(2+) chloride salt solutions. It was found that the strength for the direct alkali ion-amide O binding is strongly correlated with the size of the ionic radius. The smallest Li(+) ion binds strongest to amide O, and the largest Cs(+) ion has the weakest interaction with the amide bond. For the divalent Mg(2+) and Ca(2+) ions, their interactions with the amide bond are weak and appear to be mediated by the water molecules, particularly in the case of Mg(2+), resulting from their strong hydration. The direct binding between the cations and amide O requires partial desovlation of the ions that is energetically unfavorable for Mg(2+) and also to a great extent for Ca(2+). The higher cation charge makes the electrostatic interaction more favorable but the dehydration process less favorable. This competition between electrostatic interaction and the dehydration process largely dictates whether the direct binding between the cation and amide O is energetically preferred or not. For monovalent alkali ions, it is energetically preferred to bind directly with the amide O. Moreover, Li(+) ion is also found to associate strongly with the hydrophobic residues on PNIPAM.

An interactive computer lab of the galvanic cell for students in biochemistry.

PubMed

Ahlstrand, Emma; Buetti-Dinh, Antoine; Friedman, Ran

2018-01-01

We describe an interactive module that can be used to teach basic concepts in electrochemistry and thermodynamics to first year natural science students. The module is used together with an experimental laboratory and improves the students' understanding of thermodynamic quantities such as Δ r G, Δ r H, and Δ r S that are calculated but not directly measured in the lab. We also discuss how new technologies can substitute some parts of experimental chemistry courses, and improve accessibility to course material. Cloud computing platforms such as CoCalc facilitate the distribution of computer codes and allow students to access and apply interactive course tools beyond the course's scope. Despite some limitations imposed by cloud computing, the students appreciated the approach and the enhanced opportunities to discuss study questions with their classmates and instructor as facilitated by the interactive tools. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):58-65, 2018. © 2017 The International Union of Biochemistry and Molecular Biology.

Effects of macromolecular crowding on biochemical reaction equilibria: a molecular thermodynamic perspective.

PubMed

Hu, Zhongqiao; Jiang, Jianwen; Rajagopalan, Raj

2007-09-01

A molecular thermodynamic model is developed to investigate the effects of macromolecular crowding on biochemical reactions. Three types of reactions, representing protein folding/conformational isomerization, coagulation/coalescence, and polymerization/association, are considered. The reactants, products, and crowders are modeled as coarse-grained spherical particles or as polymer chains, interacting through hard-sphere interactions with or without nonbonded square-well interactions, and the effects of crowder size and chain length as well as product size are examined. The results predicted by this model are consistent with experimentally observed crowding effects based on preferential binding or preferential exclusion of the crowders. Although simple hard-core excluded-volume arguments do in general predict the qualitative aspects of the crowding effects, the results show that other intermolecular interactions can substantially alter the extent of enhancement or reduction of the equilibrium and can even change the direction of the shift. An advantage of the approach presented here is that competing reactions can be incorporated within the model.

Dynamic and coordinated single-molecular interactions at TM4SF5-enriched microdomains guide invasive behaviors in 2- and 3-dimensional environments.

PubMed

Kim, Hye-Jin; Kwon, Sojung; Nam, Seo Hee; Jung, Jae Woo; Kang, Minkyung; Ryu, Jihye; Kim, Ji Eon; Cheong, Jin-Gyu; Cho, Chang Yun; Kim, Somi; Song, Dae-Geun; Kim, Yong-Nyun; Kim, Tai Young; Jung, Min-Kyo; Lee, Kyung-Min; Pack, Chan-Gi; Lee, Jung Weon

2017-04-01

Membrane proteins sense extracellular cues and transduce intracellular signaling to coordinate directionality and speed during cellular migration. They are often localized to specific regions, as with lipid rafts or tetraspanin-enriched microdomains; however, the dynamic interactions of tetraspanins with diverse receptors within tetraspanin-enriched microdomains on cellular surfaces remain largely unexplored. Here, we investigated effects of tetraspan(in) TM4SF5 (transmembrane 4 L6 family member 5)-enriched microdomains (T 5 ERMs) on the directionality of cell migration. Physical association of TM4SF5 with epidermal growth factor receptor (EGFR) and integrin α5 was visualized by live fluorescence cross-correlation spectroscopy and higher-resolution microscopy at the leading edge of migratory cells, presumably forming TM4SF5-enriched microdomains. Whereas TM4SF5 and EGFR colocalized at the migrating leading region more than at the rear, TM4SF5 and integrin α5 colocalized evenly throughout cells. Cholesterol depletion and disruption in TM4SF5 post-translational modifications, including N -glycosylation and palmitoylation, altered TM4SF5 interactions and cellular localization, which led to less cellular migration speed and directionality in 2- or 3-dimensional conditions. TM4SF5 controlled directional cell migration and invasion, and importantly, these TM4SF5 functions were dependent on cholesterol, TM4SF5 post-translational modifications, and EGFR and integrin α5 activity. Altogether, we showed that TM4SF5 dynamically interacted with EGFR and integrin α5 in migratory cells to control directionality and invasion.-Kim, H.-J., Kwon, S., Nam, S. H., Jung, J. W., Kang, M., Ryu, J., Kim, J. E., Cheong, J.-G., Cho, C. Y., Kim, S., Song, D.-G., Kim, Y.-N., Kim, T. Y., Jung, M.-K., Lee, K.-M., Pack, C.-G., Lee, J. W. Dynamic and coordinated single-molecular interactions at TM4SF5-enriched microdomains guide invasive behaviors in 2- and 3-dimensional environments. © FASEB.

Phototropism: at the crossroads of light-signaling pathways.

PubMed

Goyal, Anupama; Szarzynska, Bogna; Fankhauser, Christian

2013-07-01

Phototropism enables plants to orient growth towards the direction of light and thereby maximizes photosynthesis in low-light environments. In angiosperms, blue-light photoreceptors called phototropins are primarily involved in sensing the direction of light. Phytochromes and cryptochromes (sensing red/far-red and blue light, respectively) also modulate asymmetric hypocotyl growth, leading to phototropism. Interactions between different light-signaling pathways regulating phototropism occur in cryptogams and angiosperms. In this review, we focus on the molecular mechanisms underlying the co-action between photosensory systems in the regulation of hypocotyl phototropism in Arabidopsis thaliana. Recent studies have shown that phytochromes and cryptochromes enhance phototropism by controlling the expression of important regulators of phototropin signaling. In addition, phytochromes may also regulate growth towards light via direct interaction with the phototropins. Copyright © 2013 Elsevier Ltd. All rights reserved.

Ligand-directed targeting of lymphatic vessels uncovers mechanistic insights in melanoma metastasis.

PubMed

Christianson, Dawn R; Dobroff, Andrey S; Proneth, Bettina; Zurita, Amado J; Salameh, Ahmad; Dondossola, Eleonora; Makino, Jun; Bologa, Cristian G; Smith, Tracey L; Yao, Virginia J; Calderone, Tiffany L; O'Connell, David J; Oprea, Tudor I; Kataoka, Kazunori; Cahill, Dolores J; Gershenwald, Jeffrey E; Sidman, Richard L; Arap, Wadih; Pasqualini, Renata

2015-02-24

Metastasis is the most lethal step of cancer progression in patients with invasive melanoma. In most human cancers, including melanoma, tumor dissemination through the lymphatic vasculature provides a major route for tumor metastasis. Unfortunately, molecular mechanisms that facilitate interactions between melanoma cells and lymphatic vessels are unknown. Here, we developed an unbiased approach based on molecular mimicry to identify specific receptors that mediate lymphatic endothelial-melanoma cell interactions and metastasis. By screening combinatorial peptide libraries directly on afferent lymphatic vessels resected from melanoma patients during sentinel lymphatic mapping and lymph node biopsies, we identified a significant cohort of melanoma and lymphatic surface binding peptide sequences. The screening approach was designed so that lymphatic endothelium binding peptides mimic cell surface proteins on tumor cells. Therefore, relevant metastasis and lymphatic markers were biochemically identified, and a comprehensive molecular profile of the lymphatic endothelium during melanoma metastasis was generated. Our results identified expression of the phosphatase 2 regulatory subunit A, α-isoform (PPP2R1A) on the cell surfaces of both melanoma cells and lymphatic endothelial cells. Validation experiments showed that PPP2R1A is expressed on the cell surfaces of both melanoma and lymphatic endothelial cells in vitro as well as independent melanoma patient samples. More importantly, PPP2R1A-PPP2R1A homodimers occur at the cellular level to mediate cell-cell interactions at the lymphatic-tumor interface. Our results revealed that PPP2R1A is a new biomarker for melanoma metastasis and show, for the first time to our knowledge, an active interaction between the lymphatic vasculature and melanoma cells during tumor progression.

A gene network bioinformatics analysis for pemphigoid autoimmune blistering diseases.

PubMed

Barone, Antonio; Toti, Paolo; Giuca, Maria Rita; Derchi, Giacomo; Covani, Ugo

2015-07-01

In this theoretical study, a text mining search and clustering analysis of data related to genes potentially involved in human pemphigoid autoimmune blistering diseases (PAIBD) was performed using web tools to create a gene/protein interaction network. The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database was employed to identify a final set of PAIBD-involved genes and to calculate the overall significant interactions among genes: for each gene, the weighted number of links, or WNL, was registered and a clustering procedure was performed using the WNL analysis. Genes were ranked in class (leader, B, C, D and so on, up to orphans). An ontological analysis was performed for the set of 'leader' genes. Using the above-mentioned data network, 115 genes represented the final set; leader genes numbered 7 (intercellular adhesion molecule 1 (ICAM-1), interferon gamma (IFNG), interleukin (IL)-2, IL-4, IL-6, IL-8 and tumour necrosis factor (TNF)), class B genes were 13, whereas the orphans were 24. The ontological analysis attested that the molecular action was focused on extracellular space and cell surface, whereas the activation and regulation of the immunity system was widely involved. Despite the limited knowledge of the present pathologic phenomenon, attested by the presence of 24 genes revealing no protein-protein direct or indirect interactions, the network showed significant pathways gathered in several subgroups: cellular components, molecular functions, biological processes and the pathologic phenomenon obtained from the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database. The molecular basis for PAIBD was summarised and expanded, which will perhaps give researchers promising directions for the identification of new therapeutic targets.

Hydrogen bonded binary molecular adducts derived from exobidentate N-donor ligand with dicarboxylic acids: Acid⋯imidazole hydrogen-bonding interactions in neutral and ionic heterosynthons

NASA Astrophysics Data System (ADS)

Kathalikkattil, Amal Cherian; Damodaran, Subin; Bisht, Kamal Kumar; Suresh, Eringathodi

2011-01-01

Four new binary molecular compounds between a flexible exobidentate N-heterocycle and a series of dicarboxylic acids have been synthesized. The N-donor 1,4-bis(imidazol-1-ylmethyl)benzene (bix) was reacted with flexible and rigid dicarboxylic acids viz., cyclohexane-1,4-dicarboxylic acid (H 2chdc), naphthalene-1,4-dicarboxylic acid (H 2npdc) and 1H-pyrazole-3,5-dicarboxylic acid (H 2pzdc), generating four binary molecular complexes. X-ray crystallographic investigation of the molecular adducts revealed the primary intermolecular interactions carboxylic acid⋯amine (via O-H⋯N) as well as carboxylate⋯protonated amine (via N-H +⋯O -) within the binary compounds, generating layered and two-dimensional sheet type H-bonded networks involving secondary weak interactions (C-H⋯O) including the solvent of crystallization. Depending on the differences in p Ka values of the selected base/acid (Δp Ka), diverse H-bonded supramolecular assemblies could be premeditated. This study demonstrates the H-bonding interactions between imidazole/imidazolium cation and carboxylic acid/carboxylate anion in providing sufficient driving force for the directed assembly of binary molecular complexes. In the two-component solid form of hetero synthons involving bix and dicarboxylic acid, only H 2chdc exist as cocrystal with bix, while all the other three compounds crystallized exclusively as salt, in agreement with the Δp Ka values predicted for the formation of salts/cocrystals from the base and acid used in the synthesis of supramolecular solids.

Insights into plant plasma membrane aquaporin trafficking.

PubMed

Hachez, Charles; Besserer, Arnaud; Chevalier, Adrien S; Chaumont, François

2013-06-01

Plasma membrane intrinsic proteins (PIPs) are plant aquaporins that facilitate the diffusion of water and small uncharged solutes through the cell membrane. Deciphering the network of interacting proteins that modulate PIP trafficking to and activity in the plasma membrane is essential to improve our knowledge about PIP regulation and function. This review highlights the most recent advances related to PIP subcellular routing and dynamic redistribution, identifies some key molecular interacting proteins, and indicates exciting directions for future research in this field. A better understanding of the mechanisms by which plants optimize water movement might help in identifying new molecular players of agronomical relevance involved in the control of cellular water uptake and drought tolerance. Copyright © 2012 Elsevier Ltd. All rights reserved.

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

PubMed Central

Fuchs, Julian E.; Huber, Roland G.; Waldner, Birgit J.; Kahler, Ursula; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R.

2015-01-01

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm “dynamics govern specificity” might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design. PMID:26496636

Displacement of Drugs from Human Serum Albumin: From Molecular Interactions to Clinical Significance.

PubMed

Rimac, Hrvoje; Debeljak, Željko; Bojić, Mirza; Miller, Larisa

2017-01-01

Human serum albumin (HSA) is the most abundant protein in human serum. It has numerous functions, one of which is transport of small hydrophobic molecules, including drugs, toxins, nutrients, hormones and metabolites. HSA has the ability to interact with a wide variety of structurally different compounds. This promiscuous, nonspecific affinity can lead to sudden changes in concentrations caused by displacement, when two or more compounds compete for binding to the same molecular site. It is important to consider drug combinations and their binding to HSA when defining dosing regimens, as this can directly influence drug's free, active concentration in blood. In present paper we review drug interactions with potential for displacement from HSA, situations in which they are likely to occur and their clinical significance. We also offer guidelines in designing drugs with decreased binding to HSA. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Structure and effect of sarcosine on water and urea by using molecular dynamics simulations: Implications in protein stabilization.

PubMed

Kumar, Narendra; Kishore, Nand

2013-01-01

Sarcosine is one of the most important protecting osmolytes which is also known to counteract the denaturing effect of urea. We used molecular dynamics simulation methods to investigate the mechanism of protein stabilization and counteraction of urea by sarcosine. We found that sarcosine enhanced the tetrahedral structure of water and strengthened its hydrogen bonding network. We also found that sarcosine did not form clusters unlike glycine. Our results show strong interaction between sarcosine and urea molecules. Addition of sarcosine enhanced the urea-water structure and urea-water lifetime indicated an increase in the solvation of urea. These findings suggest that sarcosine indirectly stabilizes protein by enhancing water-water structure thus decreasing the hydrophobic effect and counteracts the effect of urea by increasing the solvation of urea and directly interacting with it leaving urea less available to interact with protein. Copyright © 2012 Elsevier B.V. All rights reserved.

Molecular dynamics simulation of trp-repressor/operator complex: analysis of hydrogen bond patterns of protein DNA interaction

NASA Astrophysics Data System (ADS)

Suenaga, A.; Yatsu, C.; Komeiji, Y.; Uebayasi, M.; Meguro, T.; Yamato, I.

2000-08-01

Molecular dynamics simulation of Escherichia colitrp-repressor/operator complex was performed to elucidate protein-DNA interactions in solution for 800 ps on special-purpose computer MD-GRAPE. The Ewald summation method was employed to treat the electrostatic interaction without cutoff. DNA kept stable conformation in comparison with the result of the conventional cutoff method. Thus, the trajectories obtained were used to analyze the protein-DNA interaction and to understand the role of dynamics of water molecules forming sequence specific recognition interface. The dynamical cross-correlation map showed a significant positive correlation between the helix-turn-helix DNA-binding motifs and the major grooves of operator DNA. The extensive contact surface was stable during the simulation. Most of the contacts consisted of direct interactions between phosphates of DNA and the protein, but several water-mediated polar contacts were also observed. These water-mediated interactions, which were also seen in the crystal structure (Z. Otwinowski, et al., Nature, 335 (1998) 321) emerged spontaneously from the randomized initial configuration of the solvent. This result suggests the importance of the water-mediated interaction in specific recognition of DNA by the trp-repressor, consistent with X-ray structural information.

Structural Elements in the Gαs and Gαq C Termini That Mediate Selective G Protein-coupled Receptor (GPCR) Signaling.

PubMed

Semack, Ansley; Sandhu, Manbir; Malik, Rabia U; Vaidehi, Nagarajan; Sivaramakrishnan, Sivaraj

2016-08-19

Although the importance of the C terminus of the α subunit of the heterotrimeric G protein in G protein-coupled receptor (GPCR)-G protein pairing is well established, the structural basis of selective interactions remains unknown. Here, we combine live cell FRET-based measurements and molecular dynamics simulations of the interaction between the GPCR and a peptide derived from the C terminus of the Gα subunit (Gα peptide) to dissect the molecular mechanisms of G protein selectivity. We observe a direct link between Gα peptide binding and stabilization of the GPCR conformational ensemble. We find that cognate and non-cognate Gα peptides show deep and shallow binding, respectively, and in distinct orientations within the GPCR. Binding of the cognate Gα peptide stabilizes the agonist-bound GPCR conformational ensemble resulting in favorable binding energy and lower flexibility of the agonist-GPCR pair. We identify three hot spot residues (Gαs/Gαq-Gln-384/Leu-349, Gln-390/Glu-355, and Glu-392/Asn-357) that contribute to selective interactions between the β2-adrenergic receptor (β2-AR)-Gαs and V1A receptor (V1AR)-Gαq The Gαs and Gαq peptides adopt different orientations in β2-AR and V1AR, respectively. The β2-AR/Gαs peptide interface is dominated by electrostatic interactions, whereas the V1AR/Gαq peptide interactions are predominantly hydrophobic. Interestingly, our study reveals a role for both favorable and unfavorable interactions in G protein selection. Residue Glu-355 in Gαq prevents this peptide from interacting strongly with β2-AR. Mutagenesis to the Gαs counterpart (E355Q) imparts a cognate-like interaction. Overall, our study highlights the synergy in molecular dynamics and FRET-based approaches to dissect the structural basis of selective G protein interactions. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Species comparisons in molecular and functional attributes of the androgen and estrogen receptor

EPA Science Inventory

While endocrine disrupting compounds (EDCs) have the potential to act via several mechanisms of action, one of the most widely studied is the ability of environmental chemicals to interact directly with either the estrogen (ER) or androgen receptor (AR). In vitro screening assay...

Assembly of bipolar microtubule structures by passive cross-linkers and molecular motors

NASA Astrophysics Data System (ADS)

Johann, D.; Goswami, D.; Kruse, K.

2016-06-01

During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. The spindle contains the midzone, a stable region of overlapping antiparallel microtubules, that is essential for maintaining bipolarity. Although a lot is known about the molecular players involved, the mechanism underlying midzone formation and maintenance is still poorly understood. We study the interaction of polar filaments that are cross-linked by molecular motors moving directionally and by passive cross-linkers diffusing along microtubules. Using a particle-based stochastic model, we find that the interplay of motors and passive cross-linkers can generate a stable finite overlap between a pair of antiparallel polar filaments. We develop a mean-field theory to study this mechanism in detail and investigate the influence of steric interactions between motors and passive cross-linkers on the overlap dynamics. In the presence of interspecies steric interactions, passive cross-linkers mimic the behavior of molecular motors and stable finite overlaps are generated even for non-cross-linking motors. Finally, we develop a mean-field theory for a bundle of aligned polar filaments and show that they can self-organize into a spindlelike pattern. Our work suggests possible ways as to how cells can generate spindle midzones and control their extensions.

Halogen-Adatom Mediated Phase Transition of Two-Dimensional Molecular Self-Assembly on a Metal Surface.

PubMed

Niu, Tianchao; Wu, Jinge; Ling, Faling; Jin, Shuo; Lu, Guanghong; Zhou, Miao

2018-01-09

Construction of tunable and robust two-dimensional (2D) molecular arrays with desirable lattices and functionalities over a macroscopic scale relies on spontaneous and reversible noncovalent interactions between suitable molecules as building blocks. Halogen bonding, with active tunability of direction, strength, and length, is ideal for tailoring supramolecular structures. Herein, by combining low-temperature scanning tunneling microscopy and systematic first-principles calculations, we demonstrate novel halogen bonding involving single halogen atoms and phase engineering in 2D molecular self-assembly. On the Au(111) surface, we observed catalyzed dehalogenation of hexabromobenzene (HBB) molecules, during which negatively charged bromine adatoms (Br δ- ) were generated and participated in assembly via unique C-Br δ+ ···Br δ- interaction, drastically different from HBB assembly on a chemically inert graphene substrate. We successfully mapped out different phases of the assembled superstructure, including densely packed hexagonal, tetragonal, dimer chain, and expanded hexagonal lattices at room temperature, 60 °C, 90 °C, and 110 °C, respectively, and the critical role of Br δ- in regulating lattice characteristics was highlighted. Our results show promise for manipulating the interplay between noncovalent interactions and catalytic reactions for future development of molecular nanoelectronics and 2D crystal engineering.

Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp

DOE PAGES

Liu, Kuanqing; Myers, Angela R.; Pisithkul, Tippapha; ...

2015-02-05

The nucleotide (p)ppGpp mediates bacterial stress responses, but its targets and underlying mechanisms of action vary among bacterial species and remain incompletely understood. In this paper, we characterize the molecular interaction between (p)ppGpp and guanylate kinase (GMK), revealing the importance of this interaction in adaptation to starvation. Combining structural and kinetic analyses, we show that (p)ppGpp binds the GMK active site and competitively inhibits the enzyme. The (p)ppGpp-GMK interaction prevents the conversion of GMP to GDP, resulting in GMP accumulation upon amino acid downshift. Abolishing this interaction leads to excess (p)ppGpp and defective adaptation to amino acid starvation. A surveymore » of GMKs from phylogenetically diverse bacteria shows that the (p)ppGpp-GMK interaction is conserved in members of Firmicutes, Actinobacteria, and Deinococcus-Thermus, but not in Proteobacteria, where (p)ppGpp regulates RNA polymerase (RNAP). Finally, we propose that GMK is an ancestral (p)ppGpp target and RNAP evolved more recently as a direct target in Proteobacteria.« less

PRMT7 Interacts with ASS1 and Citrullinemia Mutations Disrupt the Interaction.

PubMed

Verma, Mamta; Charles, Ramya Chandar M; Chakrapani, Baskar; Coumar, Mohane Selvaraj; Govindaraju, Gayathri; Rajavelu, Arumugam; Chavali, Sreenivas; Dhayalan, Arunkumar

2017-07-21

Protein arginine methyltransferase 7 (PRMT7) catalyzes the introduction of monomethylation marks at the arginine residues of substrate proteins. PRMT7 plays important roles in the regulation of gene expression, splicing, DNA damage, paternal imprinting, cancer and metastasis. However, little is known about the interaction partners of PRMT7. To address this, we performed yeast two-hybrid screening of PRMT7 and identified argininosuccinate synthetase (ASS1) as a potential interaction partner of PRMT7. We confirmed that PRMT7 directly interacts with ASS1 using pull-down studies. ASS1 catalyzes the rate-limiting step of arginine synthesis in urea cycle and citrulline-nitric oxide cycle. We mapped the interface of PRMT7-ASS1 complex through computational approaches and validated the predicted interface in vivo by site-directed mutagenesis. Evolutionary analysis revealed that the ASS1 residues important for PRMT7-ASS1 interaction have co-evolved with PRMT7. We showed that ASS1 mutations linked to type I citrullinemia disrupt the ASS1-PRMT7 interaction, which might explain the molecular pathogenesis of the disease. Copyright © 2017 Elsevier Ltd. All rights reserved.

Direct molecular interactions between Beclin 1 and the canonical NFκB activation pathway.

PubMed

Niso-Santano, Mireia; Criollo, Alfredo; Malik, Shoaib Ahmad; Michaud, Michael; Morselli, Eugenia; Mariño, Guillermo; Lachkar, Sylvie; Galluzzi, Lorenzo; Maiuri, Maria Chaira; Kroemer, Guido

2012-02-01

General (macro)autophagy and the activation of NFκB constitute prominent responses to a large array of intracellular and extracellular stress conditions. The depletion of any of the three subunits of the inhibitor of NFκB (IκB) kinase (IKKα, IKKβ, IKKγ/NEMO), each of which is essential for the canonical NFκB activation pathway, limits autophagy induction by physiological or pharmacological triggers, while constitutive active IKK subunits suffice to stimulate autophagy. The activation of IKK usually relies on TGFβ-activated kinase 1 (TAK1), which is also necessary for the optimal induction of autophagy in multiple settings. TAK1 interacts with two structurally similar co-activators, TAK1-binding proteins 2 and 3 (TAB2 and TAB3). Importantly, in resting conditions both TAB2 and TAB3 bind the essential autophagic factor Beclin 1, but not TAK1. In response to pro-autophagic stimuli, TAB2 and TAB3 dissociate from Beclin 1 and engage in stimulatory interactions with TAK1. The inhibitory interaction between TABs and Beclin 1 is mediated by their coiled-coil domains (CCDs). Accordingly, the overexpression of either TAB2 or TAB3 CCD stimulates Beclin 1- and TAK1-dependent autophagy. These results point to the existence of a direct molecular crosstalk between the canonical NFκB activation pathway and the autophagic core machinery that guarantees the coordinated induction of these processes in response to stress.

A molecular theory of liquid interfaces.

PubMed

Kovalenko, Andriy; Hirata, Fumio

2005-04-21

We propose a site site generalization of the Lovett-Mow-Buff-Wertheim integro-differential equation for the one-particle density distributions to polyatomic fluids. The method provides microscopic description of liquid interfaces of molecular fluids and solutions. It uses the inhomogeneous site-site direct correlation function of molecular fluid consistently constructed by nonlinear interpolation between the homogeneous ones. The site site correlations of the coexisting bulk phases are obtained from the reference interaction site model (RISM) integral equation with our closure approximation. For illustration, we calculated the structure of the planar liquid-vapor as well as liquid-liquid interfaces of n-hexane and methanol at ambient conditions.

Molecular and Cellular Mechanisms of Sperm-Oocyte Interactions Opinions Relative to in Vitro Fertilization (IVF)

PubMed Central

Anifandis, George; Messini, Christina; Dafopoulos, Konstantinos; Sotiriou, Sotiris; Messinis, Ioannis

2014-01-01

One of the biggest prerequisites for pregnancy is the fertilization step, where a human haploid spermatozoon interacts and penetrates one haploid oocyte in order to produce the diploid zygote. Although fertilization is defined by the presence of two pronuclei and the extraction of the second polar body the process itself requires preparation of both gametes for fertilization to take place at a specific time. These preparations include a number of consecutive biochemical and molecular events with the help of specific molecules and with the consequential interaction between the two gametes. These events take place at three different levels and in a precise order, where the moving spermatozoon penetrates (a) the outer vestments of the oocyte, known as the cumulus cell layer; (b) the zona pellucida (ZP); where exocytosis of the acrosome contents take place and (c) direct interaction of the spermatozoon with the plasma membrane of the oocyte, which involves a firm adhesion of the head of the spermatozoon with the oocyte plasma membrane that culminates with the fusion of both sperm and oocyte membranes (Part I). After the above interactions, a cascade of molecular signal transductions is initiated which results in oocyte activation. Soon after the entry of the first spermatozoon into the oocyte and oocyte activation, the oocyte’s coat (the ZP) and the oocyte’s plasma membrane seem to change quickly in order to initiate a fast block to a second spermatozoon (Part II). Sometimes, two spermatozoa fuse with one oocyte, an incidence of 1%–2%, resulting in polyploid fetuses that account for up to 10%–20% of spontaneously aborted human conceptuses. The present review aims to focus on the first part of the human sperm and oocyte interactions, emphasizing the latest molecular and cellular mechanisms controlling this process. PMID:25054321

Molecular and cellular mechanisms of sperm-oocyte interactions opinions relative to in vitro fertilization (IVF).

PubMed

Anifandis, George; Messini, Christina; Dafopoulos, Konstantinos; Sotiriou, Sotiris; Messinis, Ioannis

2014-07-22

One of the biggest prerequisites for pregnancy is the fertilization step, where a human haploid spermatozoon interacts and penetrates one haploid oocyte in order to produce the diploid zygote. Although fertilization is defined by the presence of two pronuclei and the extraction of the second polar body the process itself requires preparation of both gametes for fertilization to take place at a specific time. These preparations include a number of consecutive biochemical and molecular events with the help of specific molecules and with the consequential interaction between the two gametes. These events take place at three different levels and in a precise order, where the moving spermatozoon penetrates (a) the outer vestments of the oocyte, known as the cumulus cell layer; (b) the zona pellucida (ZP); where exocytosis of the acrosome contents take place and (c) direct interaction of the spermatozoon with the plasma membrane of the oocyte, which involves a firm adhesion of the head of the spermatozoon with the oocyte plasma membrane that culminates with the fusion of both sperm and oocyte membranes (Part I). After the above interactions, a cascade of molecular signal transductions is initiated which results in oocyte activation. Soon after the entry of the first spermatozoon into the oocyte and oocyte activation, the oocyte's coat (the ZP) and the oocyte's plasma membrane seem to change quickly in order to initiate a fast block to a second spermatozoon (Part II). Sometimes, two spermatozoa fuse with one oocyte, an incidence of 1%-2%, resulting in polyploid fetuses that account for up to 10%-20% of spontaneously aborted human conceptuses. The present review aims to focus on the first part of the human sperm and oocyte interactions, emphasizing the latest molecular and cellular mechanisms controlling this process.

Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

PubMed

Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

2014-12-12

Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Concise NMR approach for molecular dynamics characterizations in organic solids.

PubMed

Aliev, Abil E; Courtier-Murias, Denis

2013-08-22

Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the α and γ polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics.

Ionophores and receptors using cation-pi interactions: collarenes.

PubMed

Choi, H S; Suh, S B; Cho, S J; Kim, K S

1998-10-13

Cation-pi interactions are important forces in molecular recognition by biological receptors, enzyme catalysis, and crystal engineering. We have harnessed these interactions in designing molecular systems with circular arrangement of benzene units that are capable of acting as ionophores and models for biological receptors. [n]Collarenes are promising candidates with high selectivity for a specific cation, depending on n, because of their structural rigidity and well-defined cavity size. The interaction energies of [n]collarenes with cations have been evaluated by using ab initio calculations. The selectivity of these [n]collarenes in aqueous solution was revealed by using statistical perturbation theory in conjunction with Monte Carlo and molecular dynamics simulations. It has been observed that in [n]collarenes the ratio of the interaction energies of a cation with it and the cation with the basic building unit (benzene) can be correlated to its ion selectivity. We find that collarenes are excellent and efficient ionophores that bind cations through cation-pi interactions. [6]Collarene is found to be a selective host for Li+ and Mg2+, [8]collarene for K+ and Sr2+, and [10]collarene for Cs+ and Ba2+. This finding indicates that [10]collarene and [8]collarene could be used for effective separation of highly radioactive isotopes, 137Cs and 90Sr, which are major constituents of nuclear wastes. More interestingly, collarenes of larger cavity size can be useful in capturing organic cations. [12]Collarene exhibits a pronounced affinity for tetramethylammonium cation and acetylcholine, which implies that it could serve as a model for acetylcholinestrase. Thus, collarenes can prove to be novel and effective ionophores/model-receptors capable of heralding a new direction in molecular recognition and host-guest chemistry.

Direct Interactions with the Integrin β1 Cytoplasmic Tail Activate the Abl2/Arg Kinase*

PubMed Central

Simpson, Mark A.; Bradley, William D.; Harburger, David; Parsons, Maddy; Calderwood, David A.; Koleske, Anthony J.

2015-01-01

Integrins are heterodimeric α/β extracellular matrix adhesion receptors that couple physically to the actin cytoskeleton and regulate kinase signaling pathways to control cytoskeletal remodeling and adhesion complex formation and disassembly. β1 integrins signal through the Abl2/Arg (Abl-related gene) nonreceptor tyrosine kinase to control fibroblast cell motility, neuronal dendrite morphogenesis and stability, and cancer cell invasiveness, but the molecular mechanisms by which integrin β1 activates Arg are unknown. We report here that the Arg kinase domain interacts directly with a lysine-rich membrane-proximal segment in the integrin β1 cytoplasmic tail, that Arg phosphorylates the membrane-proximal Tyr-783 in the β1 tail, and that the Arg Src homology domain then engages this phosphorylated region in the tail. We show that these interactions mediate direct binding between integrin β1 and Arg in vitro and in cells and activate Arg kinase activity. These findings provide a model for understanding how β1-containing integrins interact with and activate Abl family kinases. PMID:25694433

Molecular Dynamics Simulations, Challenges and Opportunities: A Biologist's Prospective.

PubMed

Kumari, Indu; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

2017-08-30

Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules. MD analysis has unravelled the various biological mechanisms (protein folding/unfolding, protein-small molecule interactions, protein-protein interactions, DNA/RNA-protein interactions, proteins embedded in membrane, lipid-lipid interactions, drug transport etc.) operating at the atomic and molecular levels. However, there are still some parameters including torsions in amino acids, carbohydrates (whose structure is extended and not well defined like that of proteins) and single stranded nucleic acids for which the force fields need further improvement, although there are several workers putting in constant efforts in these directions. The existing force fields are not efficient for studying the crowded environment inside the cells, since these interactions involve multiple factors in real time. Therefore, the improved force fields may provide the opportunities for their wider applications on the complex biosystems in diverse cellular conditions. In conclusion, the intervention of MD in the basic sciences involving interdisciplinary approaches will be helpful for understanding many fundamental biological and physiological processes at the molecular levels that may be further applied in various fields including biotechnology, fisheries, sustainable agriculture and biomedical research. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics.

PubMed

He, Yi; Liwo, Adam; Weinstein, Harel; Scheraga, Harold A

2011-01-07

A key regulator of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor traffic, PICK1 is known to interact with over 40 other proteins, including receptors, transporters and ionic channels, and to be active mostly as a homodimer. The current lack of a complete PICK1 structure determined at atomic resolution hinders the elucidation of its functional mechanisms. Here, we identify interactions between the component PDZ and BAR domains of PICK1 by calculating possible binding sites for the PDZ domain of PICK1 (PICK1-PDZ) to the homology-modeled, crescent-shaped dimer of the PICK1-BAR domain using multiplexed replica-exchange molecular dynamics (MREMD) and canonical molecular dynamics simulations with the coarse-grained UNRES force field. The MREMD results show that the preferred binding site for the single PDZ domain is the concave cavity of the BAR dimer. A second possible binding site is near the N-terminus of the BAR domain that is linked directly to the PDZ domain. Subsequent short canonical molecular dynamics simulations used to determine how the PICK1-PDZ domain moves to the preferred binding site on the BAR domain of PICK1 revealed that initial hydrophobic interactions drive the progress of the simulated binding. Thus, the concave face of the BAR dimer accommodates the PDZ domain first by weak hydrophobic interactions and then the PDZ domain slides to the center of the concave face, where more favorable hydrophobic interactions take over. Copyright © 2010 Elsevier Ltd. All rights reserved.

Discrimination of peptides by using a molecularly imprinted piezoelectric biosensor.

PubMed

Lin, Chung-Yin; Tai, Dar-Fu; Wu, Tzong-Zeng

2003-10-17

Based on the direct formation of a molecularly imprinted polymer on gold electrodes, we have developed a peptide sensor for the detection of low-molecular-weight peptides. A new cross-linking monomer, (N-Acr-L-Cys-NHBn)(2), was employed to attach the surface of the chip and to copolymerize with other monomers. Interestingly, N-benzylacrylamide participates in the polymerization and recognition is carried out in an aqueous environment. By using quartz crystal microbalance detection, short peptides can be monitored by their interaction with plastic antibodies specific for the target peptides. The selectivity of molecularly imprinted polymers and the sensitivity of such artificial biosensors have been combined to differentiate between traces of oxytocin and vasopressin to the ng mL(-1) scale.

Predicting the Highly Nonlinear Mechanical Properties of Polymeric Materials

NASA Astrophysics Data System (ADS)

Porter, David

2009-06-01

Over the past few years, we have developed models that calculate the highly nonlinear mechanical properties of polymers as a function of temperature, strain and strain rate from their molecular and morphological structure. A review of these models is presented here, with emphasis on combining the fundamental aspects of molecular physics that dictate these properties and the pragmatic need to make realistic predictions for our customers; the designer of new materials and the engineers who use these materials. The models calculate the highly nonlinear mechanical properties of polymers as a function of temperature, strain and strain rate from their molecular structure. The model is based upon the premise that mechanical properties are a direct consequence of energy stored and energy dissipated during deformation of a material. This premise is transformed into a consistent set of structure-property relations for the equation of state, EoS, and the engineering constitutive relations in a polymer by quantifying energy storage and loss at the molecular level of interactions between characteristic groups of atoms in a polymer. These relations are derived from a simple volumetric mean field Lennard-Jones potential function for the potential energy of intermolecular interactions in a polymer. First, properties such as temperature-volume relations and glass transition temperature are calculated directly from the potential function. Then, the `shock' EoS is derived simply by differentiating the potential function with respect to volume, assuming that the molecules cannot relax in the time scales of the deformation. The energy components are then used to predict the dynamic mechanical spectrum of a polymer in terms of temperature and rate. This can be transformed directly into the highly nonlinear stress-strain relations through yield. The constitutive relations are formulated as a set of analytical equations that predict properties directly in terms of a small set of structural parameters that can be calculated directly and independently from the chemical composition and morphology of a polymer. A number of examples are given to illustrate the model and also to show that the method can be applied, with appropriate modifications, to other materials.

Structural DNA Nanotechnology: State of the Art and Future Perspective

PubMed Central

2015-01-01

Over the past three decades DNA has emerged as an exceptional molecular building block for nanoconstruction due to its predictable conformation and programmable intra- and intermolecular Watson–Crick base-pairing interactions. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures of increasing complexity. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in many directions, such as directed material assembly, structural biology, biocatalysis, DNA computing, nanorobotics, disease diagnosis, and drug delivery. This Perspective discusses the state of the art in the field of structural DNA nanotechnology and presents some of the challenges and opportunities that exist in DNA-based molecular design and programming. PMID:25029570

Study of collective flows of protons and π^{{-}}_{} -mesons in p+C, Ta and He+Li, C collisions at momenta of 4.2, 4.5 and 10 AGeV/c

NASA Astrophysics Data System (ADS)

Chkhaidze, L.; Chlachidze, G.; Djobava, T.; Galoyan, A.; Kharkhelauri, L.; Togoo, R.; Uzhinsky, V.

2016-11-01

Collective flows of protons and π- -mesons are studied at the momenta of 4.2, 4.5 and 10AGeV/ c for p+C, Ta and He+Li, C interactions. The data were obtained from the streamer chamber (SKM-200-GIBS) and from the Propane Bubble Chamber (PBC-500) systems utilized at JINR. A method of Danielewicz and Odyniec has been employed in determining a directed transverse flow of particles. The values of the transverse flow parameter and the strength of the anisotropic emission were defined for each interacting nuclear pair. It is found that the directed flows of protons and pions decrease with increasing the energy and the mass numbers of colliding nucleus pairs. The π^{{-}}_{} -meson and proton flows exhibit opposite directions in all studied interactions, and the flows of protons are directed in the reaction plane. The Ultra-relativistic Quantum Molecular Dynamical Model (UrQMD) coupled with the Statistical Multi-fragmentation Model (SMM), satisfactorily describes the obtained experimental results.

Coarse grained modeling of directed assembly to form functional nanoporous films

NASA Astrophysics Data System (ADS)

Al Khatib, Amir

A coarse-grained (CG) simulation of polyethylene glycol (PEG) and Polymethylsilsesquixane nanoparticle (PMSSQ) referred to as (NP) at different sizes and concentrations were done using the Martini coarse-grained (CG) force field. The interactions between CG PEG and CG NP were parameterized from the chemical compound of each molecule and based on Martini force field. NP particles migrates to the surface of the substrate in an agreement with the experimental output at high temperature of 800K. This demonstration of nanoparticles-polymer film to direct it to self-assemble a systematically spatial pattern using the substrate surface energy as the key gating parameter. Validation of the model comparing molecular dynamics simulations with experimental data collected from previous study. NP interaction with the substrate at low interactions energy using Lennard-Johns potential were able to direct the NP to self-assemble in a hexagonal shape up to 4 layers above the substrate. This thesis established that substrate surface energy is a key gating parameter to direct the collective behavior of functional nanoparticles to form thin nanoporous films with spatially predetermined optical/dielectric constants.

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

PubMed Central

Chen, Alan A.; García, Angel E.

2013-01-01

We report the de novo folding of three hyperstable RNA tetraloops to 1–3 Å rmsd from their experimentally determined structures using molecular dynamics simulations initialized in the unfolded state. RNA tetraloops with loop sequences UUCG, GCAA, or CUUG are hyperstable because of the formation of noncanonical loop-stabilizing interactions, and they are all faithfully reproduced to angstrom-level accuracy in replica exchange molecular dynamics simulations, including explicit solvent and ion molecules. This accuracy is accomplished using unique RNA parameters, in which biases that favor rigid, highly stacked conformations are corrected to accurately capture the inherent flexibility of ssRNA loops, accurate base stacking energetics, and purine syn-anti interconversions. In a departure from traditional quantum chemistrycentric approaches to force field optimization, our parameters are calibrated directly from thermodynamic and kinetic measurements of intra- and internucleotide structural transitions. The ability to recapitulate the signature noncanonical interactions of the three most abundant hyperstable stem loop motifs represents a significant milestone to the accurate prediction of RNA tertiary structure using unbiased all-atom molecular dynamics simulations. PMID:24043821

Direct atomic force microscopic evidence of hydrogen bonding interaction in phosphatidic acid Langmuir-Blodgett bilayer

NASA Astrophysics Data System (ADS)

Chunbo, Yuan; Ying, Wu; Yueming, Sun; Zuhong, Lu; Juzheng, Liu

1997-12-01

Molecularly resolved atomic force microscopic images of phosphatidic acid Langmuir-Blodgett bilayers show that phosphate groups in polar region of the films are packing in a distorted hexagonal organization with long-range orientational and positional order. Intermolecular hydrogen bonding interactions, which should be responsible for the ordering and stability of bilayers, are visualized directly between adjacent phosphate groups in the polar region of the bilayer. Some adjacent phosphatidic acid molecules link each other through the formation of intermolecular hydrogen bonds between phosphate groups in polar region to form local supramolecules, which provide the bilayer's potential as a functionized film in the investigation on the lateral conductions of protons in the biological bilayers.

Tracking the ultrafast motion of a single molecule by femtosecond orbital imaging

NASA Astrophysics Data System (ADS)

Cocker, Tyler L.; Peller, Dominik; Yu, Ping; Repp, Jascha; Huber, Rupert

2016-11-01

Watching a single molecule move on its intrinsic timescale has been one of the central goals of modern nanoscience, and calls for measurements that combine ultrafast temporal resolution with atomic spatial resolution. Steady-state experiments access the requisite spatial scales, as illustrated by direct imaging of individual molecular orbitals using scanning tunnelling microscopy or the acquisition of tip-enhanced Raman and luminescence spectra with sub-molecular resolution. But tracking the intrinsic dynamics of a single molecule directly in the time domain faces the challenge that interactions with the molecule must be confined to a femtosecond time window. For individual nanoparticles, such ultrafast temporal confinement has been demonstrated by combining scanning tunnelling microscopy with so-called lightwave electronics, which uses the oscillating carrier wave of tailored light pulses to directly manipulate electronic motion on timescales faster even than a single cycle of light. Here we build on ultrafast terahertz scanning tunnelling microscopy to access a state-selective tunnelling regime, where the peak of a terahertz electric-field waveform transiently opens an otherwise forbidden tunnelling channel through a single molecular state. It thereby removes a single electron from an individual pentacene molecule’s highest occupied molecular orbital within a time window shorter than one oscillation cycle of the terahertz wave. We exploit this effect to record approximately 100-femtosecond snapshot images of the orbital structure with sub-ångström spatial resolution, and to reveal, through pump/probe measurements, coherent molecular vibrations at terahertz frequencies directly in the time domain. We anticipate that the combination of lightwave electronics and the atomic resolution of our approach will open the door to visualizing ultrafast photochemistry and the operation of molecular electronics on the single-orbital scale.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

PubMed

Mondal, Abhisek; Datta, Saumen

2017-06-01

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Covalent intermolecular interaction of the nitric oxide dimer (NO)2

NASA Astrophysics Data System (ADS)

Zhang, Hui; Zheng, Gui-Li; Lv, Gang; Geng, Yi-Zhao; Ji, Qing

2015-09-01

Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer, (NO)2, in its most stable conformation, a cis conformation. The natural bond orbital (NBO) analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the π bonds with bond order 0.5 of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics (MM) calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics (QM). The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary. Project supported by the National Natural Science Foundation of China (Grant Nos. 90403007 and 10975044), the Key Subject Construction Project of Hebei Provincial Universities, China, the Research Project of Hebei Education Department, China (Grant Nos. Z2012067 and Z2011133), the National Natural Science Foundation of China (Grant No. 11147103), and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5KF211CJ1).

A plasmonic nanorod that walks on DNA origami

PubMed Central

Zhou, Chao; Duan, Xiaoyang; Liu, Na

2015-01-01

In nano-optics, a formidable challenge remains in precise transport of a single optical nano-object along a programmed and routed path toward a predefined destination. Molecular motors in living cells that can walk directionally along microtubules have been the inspiration for realizing artificial molecular walkers. Here we demonstrate an active plasmonic system, in which a plasmonic nanorod can execute directional, progressive and reverse nanoscale walking on two or three-dimensional DNA origami. Such a walker comprises an anisotropic gold nanorod as its ‘body' and discrete DNA strands as its ‘feet'. Specifically, our walker carries optical information and can in situ optically report its own walking directions and consecutive steps at nanometer accuracy, through dynamic coupling to a plasmonic stator immobilized along its walking track. Our concept will enable a variety of smart nanophotonic platforms for studying dynamic light–matter interaction, which requires controlled motion at the nanoscale well below the optical diffraction limit. PMID:26303016

Protein-Binding RNA Aptamers Affect Molecular Interactions Distantly from Their Binding Sites

PubMed Central

Dupont, Daniel M.; Thuesen, Cathrine K.; Bøtkjær, Kenneth A.; Behrens, Manja A.; Dam, Karen; Sørensen, Hans P.; Pedersen, Jan S.; Ploug, Michael; Jensen, Jan K.; Andreasen, Peter A.

2015-01-01

Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126) with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site. PMID:25793507

Organic molecules on metal and oxide semiconductor substrates: Adsorption behavior and electronic energy level alignment

NASA Astrophysics Data System (ADS)

Ruggieri, Charles M.

Modern devices such as organic light emitting diodes use organic/oxide and organic/metal interfaces for crucial processes such as charge injection and charge transfer. Understanding fundamental physical processes occurring at these interfaces is essential to improving device performance. The ultimate goal of studying such interfaces is to form a predictive model of interfacial interactions, which has not yet been established. To this end, this thesis focuses on obtaining a better understanding of fundamental physical interactions governing molecular self-assembly and electronic energy level alignment at organic/metal and organic/oxide interfaces. This is accomplished by investigating both the molecular adsorption geometry using scanning tunneling microscopy, as well as the electronic structure at the interface using direct and inverse photoemission spectroscopy, and analyzing the results in the context of first principles electronic structure calculations. First, we study the adsorption geometry of zinc tetraphenylporphyrin (ZnTPP) molecules on three noble metal surfaces: Au(111), Ag(111), and Ag(100). These surfaces were chosen to systematically compare the molecular self-assembly and adsorption behavior on two metals of the same surface symmetry and two surface symmetries of one metal. From this investigation, we improve the understanding of self-assembly at organic/metal interfaces and the relative strengths of competing intermolecular and molecule-substrate interactions that influence molecular adsorption geometry. We then investigate the electronic structure of the ZnTPP/Au(111), Ag(111), and Ag(100) interfaces as examples of weakly-interacting systems. We compare these cases to ZnTPP on TiO2(110), a wide-bandgap oxide semiconductor, and explain the intermolecular and molecule-substrate interactions that determine the electronic energy level alignment at the interface. Finally we study tetracyanoquinodimethane (TCNQ), a strong electron acceptor, on TiO2(110), which exhibits chemical hybridization accompanied by molecular distortion, as well as extreme charge transfer resulting in the development of a space charge layer in the oxide. Thus, we present a broad experimental and theoretical perspective on the study of organic/metal and organic/oxide interfaces, elucidating fundamental physical interactions that govern molecular organization and energy level alignment.

Molecular dynamics study of strain-induced diffusivity of nitrogen in pure iron nanocrystalline

NASA Astrophysics Data System (ADS)

Mohammadzadeh, Roghayeh; Razmara, Naiyer; Razmara, Fereshteh

2016-12-01

In the present study, the self-diffusion process of nitrogen in pure iron nanocrystalline under strain conditions has been investigated by Molecular Dynamics (MD). The interactions between particles are modeled using Modified Embedded Atom Method (MEAM). Mean Square Displacement (MSD) of nitrogen in iron structure under strain is calculated. Strain is applied along [ 11 2 ¯ 0 ] and [ 0001 ] directions in both tensile and compression conditions. The activation energy and pre-exponential diffusion factor for nitrogen diffusion is comparatively high along [ 0001 ] direction of compressed structure of iron. The strain-induced diffusion coefficient at 973 K under the compression rate of 0.001 Å/ps along [ 0001 ] direction is about 6.72E-14 m2/s. The estimated activation energy of nitrogen under compression along [ 0001 ] direction is equal to 12.39 kcal/mol. The higher activation energy might be due to the fact that the system transforms into a more dense state when compressive stress is applied.

Progranulin Directly Binds to the CRD 2 and CRD3 of TNFR Extracellular Domains

PubMed Central

Jian, Jinlong; Zhao, Shuai; Tian, Qingyun; Gonzalez-Gugel, Elena; Mundra, Jyoti Joshi; Uddin, Sardar MZ; Liu, Ben; Richbourgh, Brendon; Brunetti, Ryan; Liu, Chuan-ju

2013-01-01

We previously reported that PGRN directly bound to TNF receptors (TNFR) in vitro and in chondrocytes (Tang, et al, Science, 2011). Here we report that PGRN also associated with TNFR in splenocytes, and inhibited the binding of TNFα to immune cells. Proper folding of PGRN is essential for its binding to TNFR, as DTT treatment abolished its binding to TNFR. In contrast, the binding of PGRN to Sortilin was enhanced by DTT. Protein interaction assays with mutants of the TNFR extracellular domain demonstrated that CRD2 and CRD3 of TNFR are important for the interaction with PGRN, similar to the binding to TNFα. Taken together, these findings provide the molecular basis underlying PGRN/TNFR interaction and PGRN-mediated anti-inflammatory activity in various autoimmune diseases and conditions. PMID:24070898

"Trampoline" ejection of organic molecules from graphene and graphite via keV cluster ions impacts.

PubMed

Verkhoturov, Stanislav V; Gołuński, Mikołaj; Verkhoturov, Dmitriy S; Geng, Sheng; Postawa, Zbigniew; Schweikert, Emile A

2018-04-14

We present the data on ejection of molecules and emission of molecular ions caused by single impacts of 50 keV C 60 2+ on a molecular layer of deuterated phenylalanine (D8Phe) deposited on free standing, 2-layer graphene. The projectile impacts on the graphene side stimulate the abundant ejection of intact molecules and the emission of molecular ions in the transmission direction. To gain insight into the mechanism of ejection, Molecular Dynamic simulations were performed. It was found that the projectile penetrates the thin layer of graphene, partially depositing the projectile's kinetic energy, and molecules are ejected from the hot area around the hole that is made by the projectile. The yield, Y, of negative ions of deprotonated phenylalanine, (D8Phe-H) - , emitted in the transmission direction is 0.1 ions per projectile impact. To characterize the ejection and ionization of molecules, we have performed the experiments on emission of (D8Phe-H) - from the surface of bulk D8Phe (Y = 0.13) and from the single molecular layer of D8Phe deposited on bulk pyrolytic graphite (Y = 0.15). We show that, despite the similar yields of molecular ions, the scenario of the energy deposition and ejection of molecules is different for the case of graphene due to the confined volume of projectile-analyte interaction. The projectile impact on the graphene-D8Phe sample stimulates the collective radial movement of analyte atoms, which compresses the D8Phe layer radially from the hole. At the same time, this compression bends and stretches the graphene membrane around the hole thus accumulating potential energy. The accumulated potential energy is transformed into the kinetic energy of correlated movement upward for membrane atoms, thus the membrane acts as a trampoline for the molecules. The ejected molecules are effectively ionized; the ionization probability is ∼30× higher compared to that obtained for the bulk D8Phe target. The proposed mechanism of ionization involves tunneling of electrons from the vibrationally excited area around the hole to the molecules. Another proposed mechanism is a direct proton transfer exchange, which is suitable for a bulk target: ions of molecular fragments (i.e., CN - ) generated in the impact area interact with intact molecules from the rim of this area. There is a direct proton exchange process for the system D8Phe molecule + CN - .

"Trampoline" ejection of organic molecules from graphene and graphite via keV cluster ions impacts

NASA Astrophysics Data System (ADS)

Verkhoturov, Stanislav V.; Gołuński, Mikołaj; Verkhoturov, Dmitriy S.; Geng, Sheng; Postawa, Zbigniew; Schweikert, Emile A.

2018-04-01

We present the data on ejection of molecules and emission of molecular ions caused by single impacts of 50 keV C602+ on a molecular layer of deuterated phenylalanine (D8Phe) deposited on free standing, 2-layer graphene. The projectile impacts on the graphene side stimulate the abundant ejection of intact molecules and the emission of molecular ions in the transmission direction. To gain insight into the mechanism of ejection, Molecular Dynamic simulations were performed. It was found that the projectile penetrates the thin layer of graphene, partially depositing the projectile's kinetic energy, and molecules are ejected from the hot area around the hole that is made by the projectile. The yield, Y, of negative ions of deprotonated phenylalanine, (D8Phe-H)-, emitted in the transmission direction is 0.1 ions per projectile impact. To characterize the ejection and ionization of molecules, we have performed the experiments on emission of (D8Phe-H)- from the surface of bulk D8Phe (Y = 0.13) and from the single molecular layer of D8Phe deposited on bulk pyrolytic graphite (Y = 0.15). We show that, despite the similar yields of molecular ions, the scenario of the energy deposition and ejection of molecules is different for the case of graphene due to the confined volume of projectile-analyte interaction. The projectile impact on the graphene-D8Phe sample stimulates the collective radial movement of analyte atoms, which compresses the D8Phe layer radially from the hole. At the same time, this compression bends and stretches the graphene membrane around the hole thus accumulating potential energy. The accumulated potential energy is transformed into the kinetic energy of correlated movement upward for membrane atoms, thus the membrane acts as a trampoline for the molecules. The ejected molecules are effectively ionized; the ionization probability is ˜30× higher compared to that obtained for the bulk D8Phe target. The proposed mechanism of ionization involves tunneling of electrons from the vibrationally excited area around the hole to the molecules. Another proposed mechanism is a direct proton transfer exchange, which is suitable for a bulk target: ions of molecular fragments (i.e., CN-) generated in the impact area interact with intact molecules from the rim of this area. There is a direct proton exchange process for the system D8Phe molecule + CN-.

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

PubMed

Duan, Lili; Liu, Xiao; Zhang, John Z H

2016-05-04

Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

Molecular Rotation Signals: Molecule Chemistry and Particle Physics

NASA Astrophysics Data System (ADS)

Grabow, Jens-Uwe

2015-06-01

Molecules - large or small - are attractive academic resources, with numerous questions on their chemical behaviour as well as problems in fundamental physics now (or still) waiting to be answered: Targeted by high-resolution spectroscopy, a rotating molecular top can turn into a laboratory for molecule chemistry or a laboratory for particle physics. Once successfully entrained (many species - depending on size and chemical composition - have insufficient vapour pressures or are of transient nature, such that specifically designed pulsed-jet sources are required for their transfer into the gas phase or in-situ generation) into the collision-free environment of a supersonic-jet expansion, each molecular top comes with its own set of challenges, theoretically and experimentally: Multiple internal interactions are causing complicated energy level schemes and the resulting spectra will be rather difficult to predict theoretically. Experimentally, these spectra are difficult to assess and assign. With today's broad-banded chirp microwave techniques, finding and identifying such spectral features have lost their major drawback of being very time consuming for many molecules. For other molecules, the unrivalled resolution and sensitivity of the narrow-banded impulse microwave techniques provide a window to tackle - at the highest precision available to date - fundamental questions in physics, even particle physics - potentially beyond the standard model. Molecular charge distribution, properties of the chemical bond, details on internal dynamics and intermolecular interaction, the (stereo-chemical) molecular structure (including the possibility of their spatial separation) as well as potential evidence for tiny yet significant interactions encode their signature in pure molecular rotation subjected to time-domain microwave spectroscopic techniques. Ongoing exciting technical developments promise rapid progress. We present recent examples from Hannover, new directions, and an outlook at the future of molecular rotation spectroscopy.

Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

NASA Astrophysics Data System (ADS)

Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

2017-10-01

Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.

Direct interaction of Plin2 with lipids on the surface of lipid droplets: a live cell FRET analysis

PubMed Central

McIntosh, Avery L.; Senthivinayagam, Subramanian; Moon, Kenneth C.; Gupta, Shipra; Lwande, Joel S.; Murphy, Cameron C.; Storey, Stephen M.

2012-01-01

Despite increasing awareness of the health risks associated with excess lipid storage in cells and tissues, knowledge of events governing lipid exchange at the surface of lipid droplets remains unclear. To address this issue, fluorescence resonance energy transfer (FRET) was performed to examine live cell interactions of Plin2 with lipids involved in maintaining lipid droplet structure and function. FRET efficiencies (E) between CFP-labeled Plin2 and fluorescently labeled phosphatidylcholine, sphingomyelin, stearic acid, and cholesterol were quantitated on a pixel-by-pixel basis to generate FRET image maps that specified areas with high E (>60%) in lipid droplets. The mean E and the distance R between the probes indicated a high yield of energy transfer and demonstrated molecular distances on the order of 44–57 Å, in keeping with direct molecular contact. In contrast, FRET between CFP-Plin2 and Nile red was not detected, indicating that the CFP-Plin2/Nile red interaction was beyond FRET proximity (>100 Å). An examination of the effect of Plin2 on cellular metabolism revealed that triacylglycerol, fatty acid, and cholesteryl ester content increased while diacylglycerol remained constant in CFP-Plin2-overexpressing cells. Total phospholipids also increased, reflecting increased phosphatidylcholine and sphingomyelin. Consistent with these results, expression levels of enzymes involved in triacylglycerol, cholesteryl ester, and phospholipid synthesis were significantly upregulated in CFP-Plin2-expressing cells while those associated with lipolysis either decreased or were unaffected. Taken together, these data show for the first time that Plin2 interacts directly with lipids on the surface of lipid droplets and influences levels of key enzymes and lipids involved in maintaining lipid droplet structure and function. PMID:22744009

Milestone in the NTB phase investigation and beyond: direct insight into molecular self-assembly.

PubMed

Ivšić, Trpimir; Vinković, Marijana; Baumeister, Ute; Mikleušević, Ana; Lesac, Andreja

2014-12-14

Although liquid-crystalline materials are most widely exploited for flat-panel displays, their ability to self-organize into periodically ordered nanostructures gives rise to a broad variety of additional applications. The recently discovered low-temperature nematic phase (N(TB)) with unusual characteristics generated considerable attention within the scientific community: despite the fact that the molecules from which the phase is composed are not chiral, the helicoidal structure of the phase is strongly implicated. Here we report on combined experimental, computational and spectroscopic studies of the structural aspects influencing formation of the N(TB) phase as well as on the molecular organization within the phase. In an extensive DFT study, the structure-property prerequisite was traced to a "bent-propeller" shape of the molecule. We also demonstrate the first utilization of liquid state NMR for direct analysis of intermolecular interactions within thermotropic liquid-crystalline phases, providing new insight into molecular packing that can lead towards design of novel chiral functional materials. The synergy of experimental, computational and NMR studies suggests a syn-parallel helical molecular organization within the N(TB) phase.

PIP2-dependent coupling is prominent in Kv7.1 due to weakened interactions between S4-S5 and S6

NASA Astrophysics Data System (ADS)

Kasimova, Marina A.; Zaydman, Mark A.; Cui, Jianmin; Tarek, Mounir

2015-01-01

Among critical aspects of voltage-gated potassium (Kv) channels' functioning is the effective communication between their two composing domains, the voltage sensor (VSD) and the pore. This communication, called coupling, might be transmitted directly through interactions between these domains and, as recently proposed, indirectly through interactions with phosphatidylinositol-4,5-bisphosphate (PIP2), a minor lipid of the inner plasma membrane leaflet. Here, we show how the two components of coupling, mediated by protein-protein or protein-lipid interactions, both contribute in the Kv7.1 functioning. On the one hand, using molecular dynamics simulations, we identified a Kv7.1 PIP2 binding site that involves residues playing a key role in PIP2-dependent coupling. On the other hand, combined theoretical and experimental approaches have shown that the direct interaction between the segments of the VSD (S4-S5) and the pore (S6) is weakened by electrostatic repulsion. Finally, we conclude that due to weakened protein-protein interactions, the PIP2-dependent coupling is especially prominent in Kv7.1.

Transgenic Mice Expressing an Inhibitory Truncated Form of p300 Exhibit Long-Term Memory Deficits

ERIC Educational Resources Information Center

Oliveira, Ana M. M.; Wood, Marcelo A.; McDonough, Conor B.; Abel, Ted

2007-01-01

The formation of many forms of long-term memory requires several molecular mechanisms including regulation of gene expression. The mechanisms directing transcription require not only activation of individual transcription factors but also recruitment of transcriptional coactivators. CBP and p300 are transcriptional coactivators that interact with…

Molecular dynamic simulations reveal the structural determinants of fatty acid binding to oxy-myoglobin

USDA-ARS?s Scientific Manuscript database

The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolite...

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

PubMed Central

Orchard, Sandra; Ammari, Mais; Aranda, Bruno; Breuza, Lionel; Briganti, Leonardo; Broackes-Carter, Fiona; Campbell, Nancy H.; Chavali, Gayatri; Chen, Carol; del-Toro, Noemi; Duesbury, Margaret; Dumousseau, Marine; Galeota, Eugenia; Hinz, Ursula; Iannuccelli, Marta; Jagannathan, Sruthi; Jimenez, Rafael; Khadake, Jyoti; Lagreid, Astrid; Licata, Luana; Lovering, Ruth C.; Meldal, Birgit; Melidoni, Anna N.; Milagros, Mila; Peluso, Daniele; Perfetto, Livia; Porras, Pablo; Raghunath, Arathi; Ricard-Blum, Sylvie; Roechert, Bernd; Stutz, Andre; Tognolli, Michael; van Roey, Kim; Cesareni, Gianni; Hermjakob, Henning

2014-01-01

IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org). PMID:24234451

Estimation of π-π Electronic Couplings from Current Measurements.

PubMed

Trasobares, J; Rech, J; Jonckheere, T; Martin, T; Aleveque, O; Levillain, E; Diez-Cabanes, V; Olivier, Y; Cornil, J; Nys, J P; Sivakumarasamy, R; Smaali, K; Leclere, P; Fujiwara, A; Théron, D; Vuillaume, D; Clément, N

2017-05-10

The π-π interactions between organic molecules are among the most important parameters for optimizing the transport and optical properties of organic transistors, light-emitting diodes, and (bio-) molecular devices. Despite substantial theoretical progress, direct experimental measurement of the π-π electronic coupling energy parameter t has remained an old challenge due to molecular structural variability and the large number of parameters that affect the charge transport. Here, we propose a study of π-π interactions from electrochemical and current measurements on a large array of ferrocene-thiolated gold nanocrystals. We confirm the theoretical prediction that t can be assessed from a statistical analysis of current histograms. The extracted value of t ≈35 meV is in the expected range based on our density functional theory analysis. Furthermore, the t distribution is not necessarily Gaussian and could be used as an ultrasensitive technique to assess intermolecular distance fluctuation at the subangström level. The present work establishes a direct bridge between quantum chemistry, electrochemistry, organic electronics, and mesoscopic physics, all of which were used to discuss results and perspectives in a quantitative manner.

New approach in direct-simulation of gas mixtures

NASA Technical Reports Server (NTRS)

Chung, Chan-Hong; De Witt, Kenneth J.; Jeng, Duen-Ren

1991-01-01

Results are reported for an investigation of a new direct-simulation Monte Carlo method by which energy transfer and chemical reactions are calculated. The new method, which reduces to the variable cross-section hard sphere model as a special case, allows different viscosity-temperature exponents for each species in a gas mixture when combined with a modified Larsen-Borgnakke phenomenological model. This removes the most serious limitation of the usefulness of the model for engineering simulations. The necessary kinetic theory for the application of the new method to mixtures of monatomic or polyatomic gases is presented, including gas mixtures involving chemical reactions. Calculations are made for the relaxation of a diatomic gas mixture, a plane shock wave in a gas mixture, and a chemically reacting gas flow along the stagnation streamline in front of a hypersonic vehicle. Calculated results show that the introduction of different molecular interactions for each species in a gas mixture produces significant differences in comparison with a common molecular interaction for all species in the mixture. This effect should not be neglected for accurate DSMC simulations in an engineering context.

Peptide-based biosensors: From self-assembled interfaces to molecular probes in electrochemical assays.

PubMed

Puiu, Mihaela; Bala, Camelia

2018-04-01

Redox-tagged peptides have emerged as functional materials with multiple applications in the area of sensing and biosensing applications due to their high stability, excellent redox properties and versatility of biomolecular interactions. They allow direct observation of molecular interactions in a wide range of affinity and enzymatic assays and act as electron mediators. Short helical peptides possess the ability to self-assemble in specific configurations with the possibility to develop in highly-ordered, stable 1D, 2D and 3D architectures in a hierarchical controlled manner. We provide here a brief overview of the electrochemical techniques available to study the electron transfer in peptide films with particular interest in developing biosensors with immobilized peptide motifs, for biological and clinical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Sequence-dependent catalytic regulation of the SpoIIIE motor activity ensures directionality of DNA translocation.

PubMed

Chara, Osvaldo; Borges, Augusto; Milhiet, Pierre-Emmanuel; Nöllmann, Marcelo; Cattoni, Diego I

2018-03-27

Transport of cellular cargo by molecular motors requires directionality to ensure proper biological functioning. During sporulation in Bacillus subtilis, directionality of chromosome transport is mediated by the interaction between the membrane-bound DNA translocase SpoIIIE and specific octameric sequences (SRS). Whether SRS regulate directionality by recruiting and orienting SpoIIIE or by simply catalyzing its translocation activity is still unclear. By using atomic force microscopy and single-round fast kinetics translocation assays we determined the localization and dynamics of diffusing and translocating SpoIIIE complexes on DNA with or without SRS. Our findings combined with mathematical modelling revealed that SpoIIIE directionality is not regulated by protein recruitment to SRS but rather by a fine-tuned balance among the rates governing SpoIIIE-DNA interactions and the probability of starting translocation modulated by SRS. Additionally, we found that SpoIIIE can start translocation from non-specific DNA, providing an alternative active search mechanism for SRS located beyond the exploratory length defined by 1D diffusion. These findings are relevant in vivo in the context of chromosome transport through an open channel, where SpoIIIE can rapidly explore DNA while directionality is modulated by the probability of translocation initiation upon interaction with SRS versus non-specific DNA.

Development of concepts on the interaction of drugs with opioid receptors

NASA Astrophysics Data System (ADS)

Kuzmina, N. E.; Kuzmin, V. S.

2011-02-01

The development of concepts on the molecular mechanisms of the action of medicinal drugs on the opioid receptors is briefly surveyed. The modern point of view on the mechanism of activation of opioid receptors is given based on the data from chimeric and site-directed mutagenesis of the cloned opioid receptors and the computer-aided simulations of the reception zone and ligand-receptor complexes. Three-dimensional models of the opioid pharmacophore derived by both conventional methods and a comparative analysis of molecular fields are described in detail.

Cross-regulatory protein-protein interactions between Hox and Pax transcription factors.

PubMed

Plaza, Serge; Prince, Frederic; Adachi, Yoshitsugu; Punzo, Claudio; Cribbs, David L; Gehring, Walter J

2008-09-09

Homeotic Hox selector genes encode highly conserved transcriptional regulators involved in the differentiation of multicellular organisms. Ectopic expression of the Antennapedia (ANTP) homeodomain protein in Drosophila imaginal discs induces distinct phenotypes, including an antenna-to-leg transformation and eye reduction. We have proposed that the eye loss phenotype is a consequence of a negative posttranslational control mechanism because of direct protein-protein interactions between ANTP and Eyeless (EY). In the present work, we analyzed the effect of various ANTP homeodomain mutations for their interaction with EY and for head development. Contrasting with the eye loss phenotype, we provide evidence that the antenna-to-leg transformation involves ANTP DNA-binding activity. In a complementary genetic screen performed in yeast, we isolated mutations located in the N terminus of the ANTP homeodomain that inhibit direct interactions with EY without abolishing DNA binding in vitro and in vivo. In a bimolecular fluorescence complementation assay, we detected the ANTP-EY interaction in vivo, these interactions occurring through the paired domain and/or the homeodomain of EY. These results demonstrate that the homeodomain supports multiple molecular regulatory functions in addition to protein-DNA and protein-RNA interactions; it is also involved in protein-protein interactions.

Cross-regulatory protein–protein interactions between Hox and Pax transcription factors

PubMed Central

Plaza, Serge; Prince, Frederic; Adachi, Yoshitsugu; Punzo, Claudio; Cribbs, David L.; Gehring, Walter J.

2008-01-01

Homeotic Hox selector genes encode highly conserved transcriptional regulators involved in the differentiation of multicellular organisms. Ectopic expression of the Antennapedia (ANTP) homeodomain protein in Drosophila imaginal discs induces distinct phenotypes, including an antenna-to-leg transformation and eye reduction. We have proposed that the eye loss phenotype is a consequence of a negative posttranslational control mechanism because of direct protein–protein interactions between ANTP and Eyeless (EY). In the present work, we analyzed the effect of various ANTP homeodomain mutations for their interaction with EY and for head development. Contrasting with the eye loss phenotype, we provide evidence that the antenna-to-leg transformation involves ANTP DNA-binding activity. In a complementary genetic screen performed in yeast, we isolated mutations located in the N terminus of the ANTP homeodomain that inhibit direct interactions with EY without abolishing DNA binding in vitro and in vivo. In a bimolecular fluorescence complementation assay, we detected the ANTP–EY interaction in vivo, these interactions occurring through the paired domain and/or the homeodomain of EY. These results demonstrate that the homeodomain supports multiple molecular regulatory functions in addition to protein–DNA and protein–RNA interactions; it is also involved in protein–protein interactions. PMID:18755899

Effect of headgroup size, charge, and solvent structure on polymer-micelle interactions, studied by molecular dynamics simulations.

PubMed

Shang, Barry Z; Wang, Zuowei; Larson, Ronald G

2009-11-19

We performed atomistic molecular dynamics simulations of anionic and cationic micelles in the presence of poly(ethylene oxide) (PEO) to understand why nonionic water-soluble polymers such as PEO interact strongly with anionic micelles but only weakly with cationic micelles. Our micelles include sodium n-dodecyl sulfate (SDS), n-dodecyl trimethylammonium chloride (DTAC), n-dodecyl ammonium chloride (DAC), and micelles in which we artificially reverse the sign of partial charges in SDS and DTAC. We observe that the polymer interacts hydrophobically with anionic SDS but only weakly with cationic DTAC and DAC, in agreement with experiment. However, the polymer also interacts with the artificial anionic DTAC but fails to interact hydrophobically with the artificial cationic SDS, illustrating that large headgroup size does not explain the weak polymer interaction with cationic micelles. In addition, we observe through simulation that this preference for interaction with anionic micelles still exists in a dipolar "dumbbell" solvent, indicating that water structure and hydrogen bonding alone cannot explain this preferential interaction. Our simulations suggest that direct electrostatic interactions between the micelle and polymer explain the preference for interaction with anionic micelles, even though the polymer overall carries no net charge. This is possible given the asymmetric distribution of negative charges on smaller atoms and positive charges on larger units in the polymer chain.

Parameter space exploration within dynamic simulations of signaling networks.

PubMed

De Ambrosi, Cristina; Barla, Annalisa; Tortolina, Lorenzo; Castagnino, Nicoletta; Pesenti, Raffaele; Verri, Alessandro; Ballestrero, Alberto; Patrone, Franco; Parodi, Silvio

2013-02-01

We started offering an introduction to very basic aspects of molecular biology, for the reader coming from computer sciences, information technology, mathematics. Similarly we offered a minimum of information about pathways and networks in graph theory, for a reader coming from the bio-medical sector. At the crossover about the two different types of expertise, we offered some definition about Systems Biology. The core of the article deals with a Molecular Interaction Map (MIM), a network of biochemical interactions involved in a small signaling-network sub-region relevant in breast cancer. We explored robustness/sensitivity to random perturbations. It turns out that our MIM is a non-isomorphic directed graph. For non physiological directions of propagation of the signal the network is quite resistant to perturbations. The opposite happens for biologically significant directions of signal propagation. In these cases we can have no signal attenuation, and even signal amplification. Signal propagation along a given pathway is highly unidirectional, with the exception of signal-feedbacks, that again have a specific biological role and significance. In conclusion, even a relatively small network like our present MIM reveals the preponderance of specific biological functions over unspecific isomorphic behaviors. This is perhaps the consequence of hundreds of millions of years of biological evolution.

On crystal versus fiber formation in dipeptide hydrogelator systems.

PubMed

Houton, Kelly A; Morris, Kyle L; Chen, Lin; Schmidtmann, Marc; Jones, James T A; Serpell, Louise C; Lloyd, Gareth O; Adams, Dave J

2012-06-26

Naphthalene dipeptides have been shown to be useful low-molecular-weight gelators. Here we have used a library to explore the relationship between the dipeptide sequence and the hydrogelation efficiency. A number of the naphthalene dipeptides are crystallizable from water, enabling us to investigate the comparison between the gel/fiber phase and the crystal phase. We succeeded in crystallizing one example directly from the gel phase. Using X-ray crystallography, molecular modeling, and X-ray fiber diffraction, we show that the molecular packing of this crystal structure differs from the structure of the gel/fiber phase. Although the crystal structures may provide important insights into stabilizing interactions, our analysis indicates a rearrangement of structural packing within the fibers. These observations are consistent with the fibrillar interactions and interatomic separations promoting 1D assembly whereas in the crystals the peptides are aligned along multiple axes, allowing 3D growth. This observation has an impact on the use of crystal structures to determine supramolecular synthons for gelators.

Molecular dynamics simulation of a needle-sphere binary mixture

NASA Astrophysics Data System (ADS)

Raghavan, Karthik

This paper investigates the dynamic behaviour of a hard needle-sphere binary system using a novel numerical technique called the Newton homotopy continuation (NHC) method. This mixture is representative of a polymer melt where both long chain molecules and monomers coexist. Since the intermolecular forces are generated from hard body interactions, the consequence of missed collisions or incorrect collision sequences have a significant bearing on the dynamic properties of the fluid. To overcome this problem, in earlier work NHC was chosen over traditional Newton-Raphson methods to solve the hard body dynamics of a needle fluid in random media composed of overlapping spheres. Furthermore, the simplicity of interactions and dynamics allows us to focus our research directly on the effects of particle shape and density on the transport behaviour of the mixture. These studies are also compared with earlier works that examined molecular chains in porous media primarily to understand the differences in molecular transport in the bulk versus porous systems.

vmdICE: a plug-in for rapid evaluation of molecular dynamics simulations using VMD.

PubMed

Knapp, Bernhard; Lederer, Nadja; Omasits, Ulrich; Schreiner, Wolfgang

2010-12-01

Molecular dynamics (MD) is a powerful in silico method to investigate the interactions between biomolecules. It solves Newton's equations of motion for atoms over a specified period of time and yields a trajectory file, containing the different spatial arrangements of atoms during the simulation. The movements and energies of each single atom are recorded. For evaluating of these simulation trajectories with regard to biomedical implications, several methods are available. Three well-known ones are the root mean square deviation (RMSD), the root mean square fluctuation (RMSF) and solvent accessible surface area (SASA). Herein, we present a novel plug-in for the software "visual molecular dynamics" (VMD) that allows an interactive 3D representation of RMSD, RMSF, and SASA, directly on the molecule. On the one hand, our plug-in is easy to handle for inexperienced users, and on the other hand, it provides a fast and flexible graphical impression of the spatial dynamics of a system for experts in the field. © 2010 Wiley Periodicals, Inc.

Ion optical design of a collinear laser-negative ion beam apparatus.

PubMed

Diehl, C; Wendt, K; Lindahl, A O; Andersson, P; Hanstorp, D

2011-05-01

An apparatus for photodetachment studies on atomic and molecular negative ions of medium up to heavy mass (M ≃ 500) has been designed and constructed. Laser and ion beams are merged in the apparatus in a collinear geometry and atoms, neutral molecules and negative ions are detected in the forward direction. The ion optical design and the components used to optimize the mass resolution and the transmission through the extended field-free interaction region are described. A 90° sector field magnet with 50 cm bending radius in combination with two slits is used for mass dispersion providing a resolution of M∕ΔM≅800 for molecular ions and M∕ΔM≅400 for atomic ions. The difference in mass resolution for atomic and molecular ions is attributed to different energy distributions of the sputtered ions. With 1 mm slits, transmission from the source through the interaction region to the final ion detector was determined to be about 0.14%.

Internal Energy Distribution in Sympathetically Cooled Molecular Ions

NASA Astrophysics Data System (ADS)

Thompson, Robert I.; Fisher, Amy; Harmon, Thomas; Winslade, Clayton; Ahmadi, Nasser

2002-05-01

Over the past year a research program at the University of Calgary has begun looking at the distribution of energy in the internal degrees of freedom (vibrational and rotational) of trapped and sympathetically cooled molecular ions. Ion traps are capable of holding mixed samples of charged atoms and molecules simultaneously. Atomic ions in the trapped cloud can be laser cooled by traditional techniques. The molecular ions are not directly laser cooled, but all of the trapped particles are charged so they interact strongly through Coulomb forces. It has been experimentally demonstrated that the external or translational degrees of freedom of the non-laser-cooled species are significantly lowered through this interaction (e.g. [1]). However, there is little known about the energy distribution in the in the internal degrees of freedom. This poster will outline the results of our theoretical work, as well as the technical design, construction, and initial work in the laboratory. [1] T. Baba and I. Waki, Jpn. J. Appl. Phys. 35, L1134 (1996).

Genetically Encoded Chemical Probes In Cells Reveal the Binding Path of Urocortin-I to CRF Class B GPCR

PubMed Central

Coin, Irene; Katritch, Vsevolod; Sun, Tingting; Xiang, Zheng; Siu, Fai Yiu; Beyermann, Michael; Stevens, Raymond C.; Wang, Lei

2014-01-01

SUMMARY Molecular determinants regulating the activation of class B G-protein coupled receptors (GPCRs) by native peptide agonists are largely unknown. We have investigated here the interaction between the corticotropin releasing factor receptor type 1 (CRF1R) and its native 40-mer peptide ligand Urocortin-I directly in mammalian cells. By incorporating unnatural amino acid photo-chemical and new click-chemical probes into the receptor, 44 inter-molecular spatial constraints have been derived for the ligand-receptor interaction. The data were analyzed in the context of the recently resolved crystal structure of CRF1R transmembrane domain and existing extracellular domain structures, yielding a complete conformational model for the peptide-receptor complex. Structural features of the receptor-ligand complex yield molecular insights on the mechanism of receptor activation. The experimental strategy provides unique information on full-length post-translationally modified GPCRs in the native membrane of the live cell, complementing in vitro biophysical reductionist approaches. PMID:24290358

Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis.

PubMed

Euro, Liliya; Haapanen, Outi; Róg, Tomasz; Vattulainen, Ilpo; Suomalainen, Anu; Sharma, Vivek

2017-03-07

DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform in the "intrinsic processivity" subdomain of the enzyme. Our data indicate that noncatalytic mutations may disrupt replisomal interactions, thereby causing Pol γ-associated neurodegenerative disorders.

Vitamin D and Colorectal Cancer: Molecular, Epidemiological, and Clinical Evidence

PubMed Central

Dou, Ruoxu; Ng, Kimmie; Giovannucci, Edward L.; Manson, JoAnn E.; Qian, Zhi Rong; Ogino, Shuji

2016-01-01

In many cells throughout the body, vitamin D is converted into its active form calcitriol, and binds to vitamin D receptor (VDR), which functions as a transcription factor to regulate various biological processes including cellular differentiation and immune response. Vitamin D metabolizing enzymes (including CYP24A1 and CYP27B1) and VDR play major roles in exerting and regulating effects of vitamin D. Preclinical and epidemiological studies provide evidence for anticancer effects of vitamin D (in particular, against colorectal cancer), though clinical trials have yet to prove its benefit. Additionally, molecular pathological epidemiology research can provide insights into the interaction of vitamin D with tumour molecular and immunity status. Other future research directions include genome-wide research on VDR transcriptional targets, gene-environment interaction analyses, and clinical trials on vitamin D efficacy in colorectal cancer patients. Here we review the literature on vitamin D and colorectal cancer from both mechanistic and population studies, and discuss the links and controversies within and between the two parts of evidence. PMID:27245104

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.

PubMed

Antipov, Sergey V; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2017-11-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H 2 , local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

PubMed Central

Antipov, Sergey V.; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2018-01-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research “Molecular Ultrafast Science and Technology,” are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase. PMID:29376107

PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3

PubMed Central

Chung, Ho-Ryun; Xu, Chao; Fuchs, Alisa; Mund, Andreas; Lange, Martin; Staege, Hannah; Schubert, Tobias; Bian, Chuanbing; Dunkel, Ilona; Eberharter, Anton; Regnard, Catherine; Klinker, Henrike; Meierhofer, David; Cozzuto, Luca; Winterpacht, Andreas; Di Croce, Luciano; Min, Jinrong; Will, Hans; Kinkley, Sarah

2016-01-01

PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes. DOI: http://dx.doi.org/10.7554/eLife.10607.001 PMID:27223324

Binding of copper to lysozyme: Spectroscopic, isothermal titration calorimetry and molecular docking studies

NASA Astrophysics Data System (ADS)

Jing, Mingyang; Song, Wei; Liu, Rutao

2016-07-01

Although copper is essential to all living organisms, its potential toxicity to human health have aroused wide concerns. Previous studies have reported copper could alter physical properties of lysozyme. The direct binding of copper with lysozyme might induce the conformational and functional changes of lysozyme and then influence the body's resistance to bacterial attack. To better understand the potential toxicity and toxic mechanisms of copper, the interaction of copper with lysozyme was investigated by biophysical methods including multi-spectroscopic measurements, isothermal titration calorimetry (ITC), molecular docking study and enzyme activity assay. Multi-spectroscopic measurements proved that copper quenched the intrinsic fluorescence of lysozyme in a static process accompanied by complex formation and conformational changes. The ITC results indicated that the binding interaction was a spontaneous process with approximately three thermodynamical binding sites at 298 K and the hydrophobic force is the predominant driven force. The enzyme activity was obviously inhibited by the addition of copper with catalytic residues Glu 35 and Asp 52 locating at the binding sites. This study helps to elucidate the molecular mechanism of the interaction between copper and lysozyme and provides reference for toxicological studies of copper.

Lipopolysaccharides in diazotrophic bacteria

PubMed Central

Serrato, Rodrigo V.

2014-01-01

Biological nitrogen fixation (BNF) is a process in which the atmospheric nitrogen (N2) is transformed into ammonia (NH3) by a select group of nitrogen-fixing organisms, or diazotrophic bacteria. In order to furnish the biologically useful nitrogen to plants, these bacteria must be in constant molecular communication with their host plants. Some of these molecular plant-microbe interactions are very specific, resulting in a symbiotic relationship between the diazotroph and the host. Others are found between associative diazotrophs and plants, resulting in plant infection and colonization of internal tissues. Independent of the type of ecological interaction, glycans, and glycoconjugates produced by these bacteria play an important role in the molecular communication prior and during colonization. Even though exopolysaccharides (EPS) and lipochitooligosaccharides (LCO) produced by diazotrophic bacteria and released onto the environment have their importance in the microbe-plant interaction, it is the lipopolysaccharides (LPS), anchored on the external membrane of these bacteria, that mediates the direct contact of the diazotroph with the host cells. These molecules are extremely variable among the several species of nitrogen fixing-bacteria, and there are evidences of the mechanisms of infection being closely related to their structure. PMID:25232535

Computer-aided design of polymers and composites

NASA Technical Reports Server (NTRS)

Kaelble, D. H.

1985-01-01

This book on computer-aided design of polymers and composites introduces and discusses the subject from the viewpoint of atomic and molecular models. Thus, the origins of stiffness, strength, extensibility, and fracture toughness in composite materials can be analyzed directly in terms of chemical composition and molecular structure. Aspects of polymer composite reliability are considered along with characterization techniques for composite reliability, relations between atomic and molecular properties, computer aided design and manufacture, polymer CAD/CAM models, and composite CAD/CAM models. Attention is given to multiphase structural adhesives, fibrous composite reliability, metal joint reliability, polymer physical states and transitions, chemical quality assurance, processability testing, cure monitoring and management, nondestructive evaluation (NDE), surface NDE, elementary properties, ionic-covalent bonding, molecular analysis, acid-base interactions, the manufacturing science, and peel mechanics.

Advanced Mass Spectrometry Technologies for the Study of Microbial Pathogenesis

PubMed Central

Moore, Jessica L.; Caprioli, Richard M.; Skaar, Eric P.

2014-01-01

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has been successfully applied to the field of microbial pathogenesis with promising results, principally in diagnostic microbiology to rapidly identify bacteria based on the molecular profiles of small cell populations. Direct profiling of molecules from serum and tissue samples by MALDI MS providesa means to study the pathogen-host interaction and to discover potential markers of infection. Systematic molecular profiling across tissue sections represents a new imaging modality, enabling regiospecific molecular measurements to be made in situ, in both two- and three-dimensional analyses. Herein, we briefly summarize work that employs MALDI MS to study the pathogenesis of microbial infection. PMID:24997399

Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions.

PubMed

Arcon, Juan Pablo; Defelipe, Lucas A; Modenutti, Carlos P; López, Elias D; Alvarez-Garcia, Daniel; Barril, Xavier; Turjanski, Adrián G; Martí, Marcelo A

2017-04-24

One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Because of its low cost relative to its experimental sibling, molecular dynamics (MD) simulations in the presence of different solvent probes mimicking specific types of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots. However, a systematic comparison of different probes and their real predictive power from a quantitative and thermodynamic point of view is still missing. In the present work, we have performed MD simulations of 18 different proteins in pure water as well as water mixtures of ethanol, acetamide, acetonitrile and methylammonium acetate, leading to a total of 5.4 μs simulation time. For each system, we determined the corresponding solvent sites, defined as space regions adjacent to the protein surface where the probability of finding a probe atom is higher than that in the bulk solvent. Finally, we compared the identified solvent sites with 121 different protein-ligand complexes and used them to perform molecular docking and ligand binding free energy estimates. Our results show that combining solely water and ethanol sites allows sampling over 70% of all possible protein-ligand interactions, especially those that coincide with ligand-based pharmacophoric points. Most important, we also show how the solvent sites can be used to significantly improve ligand docking in terms of both accuracy and precision, and that accurate predictions of ligand binding free energies, along with relative ranking of ligand affinity, can be performed.

Rational design of novel, fluorescent, tagged glutamic acid dendrimers with different terminal groups and in silico analysis of their properties

PubMed Central

Martinho, Nuno; Silva, Liana C; Florindo, Helena F; Brocchini, Steve; Zloh, Mire; Barata, Teresa S

2017-01-01

Dendrimers are hyperbranched polymers with a multifunctional architecture that can be tailored for the use in various biomedical applications. Peptide dendrimers are particularly relevant for drug delivery applications due to their versatility and safety profile. The overall lack of knowledge of their three-dimensional structure, conformational behavior and structure–activity relationship has slowed down their development. Fluorophores are often conjugated to dendrimers to study their interaction with biomolecules and provide information about their mechanism of action at the molecular level. However, these probes can change dendrimer surface properties and have a direct impact on their interactions with biomolecules and with lipid membranes. In this study, we have used computer-aided molecular design and molecular dynamics simulations to identify optimal topology of a poly(l-glutamic acid) (PG) backbone dendrimer that allows incorporation of fluorophores in the core with minimal availability for undesired interactions. Extensive all-atom molecular dynamic simulations with the CHARMM force field were carried out for different generations of PG dendrimers with the core modified with a fluorophore (nitrobenzoxadiazole and Oregon Green 488) and various surface groups (glutamic acid, lysine and tryptophan). Analysis of structural and topological features of all designed dendrimers provided information about their size, shape, internal distribution and dynamic behavior. We have found that four generations of a PG dendrimer are needed to ensure minimal exposure of a core-conjugated fluorophore to external environment and absence of undesired interactions regardless of the surface terminal groups. Our findings suggest that NBD-PG-G4 can provide a suitable scaffold to be used for biophysical studies of surface-modified dendrimers to provide a deeper understanding of their intermolecular interactions, mechanisms of action and trafficking in a biological system. PMID:29026301

Rational design of novel, fluorescent, tagged glutamic acid dendrimers with different terminal groups and in silico analysis of their properties.

PubMed

Martinho, Nuno; Silva, Liana C; Florindo, Helena F; Brocchini, Steve; Zloh, Mire; Barata, Teresa S

2017-01-01

Dendrimers are hyperbranched polymers with a multifunctional architecture that can be tailored for the use in various biomedical applications. Peptide dendrimers are particularly relevant for drug delivery applications due to their versatility and safety profile. The overall lack of knowledge of their three-dimensional structure, conformational behavior and structure-activity relationship has slowed down their development. Fluorophores are often conjugated to dendrimers to study their interaction with biomolecules and provide information about their mechanism of action at the molecular level. However, these probes can change dendrimer surface properties and have a direct impact on their interactions with biomolecules and with lipid membranes. In this study, we have used computer-aided molecular design and molecular dynamics simulations to identify optimal topology of a poly(l-glutamic acid) (PG) backbone dendrimer that allows incorporation of fluorophores in the core with minimal availability for undesired interactions. Extensive all-atom molecular dynamic simulations with the CHARMM force field were carried out for different generations of PG dendrimers with the core modified with a fluorophore (nitrobenzoxadiazole and Oregon Green 488) and various surface groups (glutamic acid, lysine and tryptophan). Analysis of structural and topological features of all designed dendrimers provided information about their size, shape, internal distribution and dynamic behavior. We have found that four generations of a PG dendrimer are needed to ensure minimal exposure of a core-conjugated fluorophore to external environment and absence of undesired interactions regardless of the surface terminal groups. Our findings suggest that NBD-PG-G4 can provide a suitable scaffold to be used for biophysical studies of surface-modified dendrimers to provide a deeper understanding of their intermolecular interactions, mechanisms of action and trafficking in a biological system.

Calsyntenin-3 molecular architecture and interaction with neurexin 1α.

PubMed

Lu, Zhuoyang; Wang, Yun; Chen, Fang; Tong, Huimin; Reddy, M V V V Sekhar; Luo, Lin; Seshadrinathan, Suchithra; Zhang, Lei; Holthauzen, Luis Marcelo F; Craig, Ann Marie; Ren, Gang; Rudenko, Gabby

2014-12-12

Calsyntenin 3 (Cstn3 or Clstn3), a recently identified synaptic organizer, promotes the development of synapses. Cstn3 localizes to the postsynaptic membrane and triggers presynaptic differentiation. Calsyntenin members play an evolutionarily conserved role in memory and learning. Cstn3 was recently shown in cell-based assays to interact with neurexin 1α (n1α), a synaptic organizer that is implicated in neuropsychiatric disease. Interaction would permit Cstn3 and n1α to form a trans-synaptic complex and promote synaptic differentiation. However, it is contentious whether Cstn3 binds n1α directly. To understand the structure and function of Cstn3, we determined its architecture by electron microscopy and delineated the interaction between Cstn3 and n1α biochemically and biophysically. We show that Cstn3 ectodomains form monomers as well as tetramers that are stabilized by disulfide bonds and Ca(2+), and both are probably flexible in solution. We show further that the extracellular domains of Cstn3 and n1α interact directly and that both Cstn3 monomers and tetramers bind n1α with nanomolar affinity. The interaction is promoted by Ca(2+) and requires minimally the LNS domain of Cstn3. Furthermore, Cstn3 uses a fundamentally different mechanism to bind n1α compared with other neurexin partners, such as the synaptic organizer neuroligin 2, because Cstn3 does not strictly require the sixth LNS domain of n1α. Our structural data suggest how Cstn3 as a synaptic organizer on the postsynaptic membrane, particularly in tetrameric form, may assemble radially symmetric trans-synaptic bridges with the presynaptic synaptic organizer n1α to recruit and spatially organize proteins into networks essential for synaptic function. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Directly calculated electrical conductivity of hot dense hydrogen from molecular dynamics simulation beyond Kubo-Greenwood formula

NASA Astrophysics Data System (ADS)

Ma, Qian; Kang, Dongdong; Zhao, Zengxiu; Dai, Jiayu

2018-01-01

Electrical conductivity of hot dense hydrogen is directly calculated by molecular dynamics simulation with a reduced electron force field method, in which the electrons are represented as Gaussian wave packets with fixed sizes. Here, the temperature is higher than electron Fermi temperature ( T > 300 eV , ρ = 40 g / cc ). The present method can avoid the Coulomb catastrophe and give the limit of electrical conductivity based on the Coulomb interaction. We investigate the effect of ion-electron coupled movements, which is lost in the static method such as density functional theory based Kubo-Greenwood framework. It is found that the ionic dynamics, which contributes to the dynamical electrical microfield and electron-ion collisions, will reduce the conductivity significantly compared with the fixed ion configuration calculations.

Differential Modulation of Functional Dynamics and Allosteric Interactions in the Hsp90-Cochaperone Complexes with p23 and Aha1: A Computational Study

PubMed Central

Blacklock, Kristin; Verkhivker, Gennady M.

2013-01-01

Allosteric interactions of the molecular chaperone Hsp90 with a large cohort of cochaperones and client proteins allow for molecular communication and event coupling in signal transduction networks. The integration of cochaperones into the Hsp90 system is driven by the regulatory mechanisms that modulate the progression of the ATPase cycle and control the recruitment of the Hsp90 clientele. In this work, we report the results of computational modeling of allosteric regulation in the Hsp90 complexes with the cochaperones p23 and Aha1. By integrating protein docking, biophysical simulations, modeling of allosteric communications, protein structure network analysis and the energy landscape theory we have investigated dynamics and stability of the Hsp90-p23 and Hsp90-Aha1 interactions in direct comparison with the extensive body of structural and functional experiments. The results have revealed that functional dynamics and allosteric interactions of Hsp90 can be selectively modulated by these cochaperones via specific targeting of the regulatory hinge regions that could restrict collective motions and stabilize specific chaperone conformations. The protein structure network parameters have quantified the effects of cochaperones on conformational stability of the Hsp90 complexes and identified dynamically stable communities of residues that can contribute to the strengthening of allosteric interactions. According to our results, p23-mediated changes in the Hsp90 interactions may provide “molecular brakes” that could slow down an efficient transmission of the inter-domain allosteric signals, consistent with the functional role of p23 in partially inhibiting the ATPase cycle. Unlike p23, Aha1-mediated acceleration of the Hsp90-ATPase cycle may be achieved via modulation of the equilibrium motions that facilitate allosteric changes favoring a closed dimerized form of Hsp90. The results of our study have shown that Aha1 and p23 can modulate the Hsp90-ATPase activity and direct the chaperone cycle by exerting the precise control over structural stability, global movements and allosteric communications in Hsp90. PMID:23977182

Thermodynamics of cellulose solvation in water and the ionic liquid 1-butyl-3-methylimidazolim chloride.

PubMed

Gross, Adam S; Bell, Alexis T; Chu, Jhih-Wei

2011-11-24

Cellulose is present in biomass as crystalline microfibrils held together by a complex network of intermolecular interactions making it difficult to initiate its hydrolysis and conversion to fuels. While cellulose is insoluble in water and most organic solvents, complete dissolution of cellulose can be achieved in certain classes of ionic liquids (ILs). The present study was undertaken to analyze the thermodynamic driving forces of this process and to understand how the anions and cations comprising an IL interact with the different moieties of glucose residues to cause dissolution. All-atom molecular dynamics (MD) simulations were performed at two extreme states of cellulose dissolution: a crystalline microfibril and a dissociated state in which all the glucan chains of the microfibril are fully separated from each other by at least four solvation shells. MD simulations of the two states were carried out in water and in the IL 1-butyl-3-methylimidazolium chloride (BmimCl) to provide a comprehensive analysis of solvent effects on cellulose dissolution. The results reveal two important molecular aspects of the mechanism of cellulose dissolution. The first is that the perturbation of solvent structures by the dissolved glucan chains can be a crucial factor in determining solubility, particularly for the insolubility of cellulose in water at 300 K. Second, both the Cl(-) and the Bmim(+) ions of BmimCl interact with the moieties of glucan residues that form intersheet contacts, the most robust component of the interaction network of crystalline cellulose. Cl(-) anions can form hydrogen bonds (HBs) with the hydroxyl groups of glucan chains from either the equatorial or the axial directions. For Bmim(+) cations, the calculated density profiles reveal that the contacts with glucan chains along the axial directions are closer than those along the equatorial directions. On the basis of the results of atomistic MD simulations, we propose that interacting with glucan chains along axial directions and disrupting the intersheet contacts of cellulose is an important ability of cellulose pretreatment solvents. © 2011 American Chemical Society

Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

PubMed Central

Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

2017-01-01

The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed. PMID:28117741

Molecular interactions between photosystem I and ferredoxin: an integrated energy frustration and experimental model

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

Cashman, Derek J.; Zhu, Tuo; Simmerman, Richard F.

2014-08-01

The stromal domain (PsaC, PsaD, and PsaE) of photosystem I (PSI) reduces transiently bound ferredoxin (Fd) or flavodoxin. Experimental structures exist for all of these protein partners individually, but no experimental structure of the PSI/Fd or PSI/flavodoxin complexes is presently available. Molecular models of Fd docked onto the stromal domain of the cyanobacterial PSI site are constructed here utilizing X-ray and NMR structures of PSI and Fd, respectively. Moreover, predictions of potential protein-protein interaction regions are based on experimental site-directed mutagenesis and cross-linking studies to guide rigid body docking calculations of Fd into PSI, complemented by energy landscape theory tomore » bring together regions of high energetic frustration on each of the interacting proteins. Results identify two regions of high localized frustration on the surface of Fd that contain negatively charged Asp and Glu residues. Our study predicts that these regions interact predominantly with regions of high localized frustration on the PsaC, PsaD, and PsaE chains of PSI, which include several residues predicted by previous experimental studies.« less

Cross-interactions between the Alzheimer Disease Amyloid-β Peptide and Other Amyloid Proteins: A Further Aspect of the Amyloid Cascade Hypothesis.

PubMed

Luo, Jinghui; Wärmländer, Sebastian K T S; Gräslund, Astrid; Abrahams, Jan Pieter

2016-08-05

Many protein folding diseases are intimately associated with accumulation of amyloid aggregates. The amyloid materials formed by different proteins/peptides share many structural similarities, despite sometimes large amino acid sequence differences. Some amyloid diseases constitute risk factors for others, and the progression of one amyloid disease may affect the progression of another. These connections are arguably related to amyloid aggregates of one protein being able to directly nucleate amyloid formation of another, different protein: the amyloid cross-interaction. Here, we discuss such cross-interactions between the Alzheimer disease amyloid-β (Aβ) peptide and other amyloid proteins in the context of what is known from in vitro and in vivo experiments, and of what might be learned from clinical studies. The aim is to clarify potential molecular associations between different amyloid diseases. We argue that the amyloid cascade hypothesis in Alzheimer disease should be expanded to include cross-interactions between Aβ and other amyloid proteins. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Protein modeling and molecular dynamics simulation of the two novel surfactant proteins SP-G and SP-H.

PubMed

Rausch, Felix; Schicht, Martin; Bräuer, Lars; Paulsen, Friedrich; Brandt, Wolfgang

2014-11-01

Surfactant proteins are well known from the human lung where they are responsible for the stability and flexibility of the pulmonary surfactant system. They are able to influence the surface tension of the gas-liquid interface specifically by directly interacting with single lipids. This work describes the generation of reliable protein structure models to support the experimental characterization of two novel putative surfactant proteins called SP-G and SP-H. The obtained protein models were complemented by predicted posttranslational modifications and placed in a lipid model system mimicking the pulmonary surface. Molecular dynamics simulations of these protein-lipid systems showed the stability of the protein models and the formation of interactions between protein surface and lipid head groups on an atomic scale. Thereby, interaction interface and strength seem to be dependent on orientation and posttranslational modification of the protein. The here presented modeling was fundamental for experimental localization studies and the simulations showed that SP-G and SP-H are theoretically able to interact with lipid systems and thus are members of the surfactant protein family.

Zwitterionic 4-bromo-6-meth-oxy-2-{[tris-(hy-droxy-meth-yl)methyl]-iminiumyl-meth-yl}phenolate: crystal structure and Hirshfeld surface analysis.

PubMed

Lee, See Mun; Lo, Kong Mun; Tan, Sang Loon; Tiekink, Edward R T

2016-08-01

In the solid state, the title compound, C12H16BrNO5 [systematic name: 4-bromo-2-((1E)-{[1,3-dihy-droxy-2-(hy-droxy-meth-yl)propan-2-yl]iminium-yl}meth-yl)-6-meth-oxy-benzen-1-olate], C12H16BrNO5, is found in the keto-amine tautomeric form, with an intra-molecular iminium-N-H⋯O(phenolate) hydrogen bond and an E conformation about the C=N bond. Both gauche (two) and anti relationships are found for the methyl-hydroxy groups. In the crystal, a supra-molecular layer in the bc plane is formed via hy-droxy-O-H⋯O(hy-droxy) and charge-assisted hy-droxy-O-H⋯O(phenolate) hydrogen-bonding inter-actions; various C-H⋯O inter-actions provide additional cohesion to the layers, which stack along the a axis with no directional inter-actions between them. A Hirshfeld surface analysis confirms the lack of specific inter-actions in the inter-layer region.

Investigation of laser-tissue interaction in medicine by means of laser spectroscopic measurements

NASA Astrophysics Data System (ADS)

Lademann, Juergen; Weigmann, Hans-Juergen

1995-01-01

Toxic and carcinogenic substances were produced during laser application in medicine for the cutting and evaporation of tissue. The laser smoke presents a danger potential for the medical staff and the patients. The laser tissue interaction process was investigated by means of laser spectroscopic measurements which give the possibility of measuring metastable molecular states directly as a prerequisite to understand and to influence fundamental laser tissue interaction processes in order to reduce the amount of harmful chemicals. Highly excited atomic and molecular states and free radicals (CN, OH, C2, CH, CH2) have been detected applying spontaneous and laser induced fluorescence methods. It was found that the formation of harmful substances in the laser plumes can be reduced significantly by optimization of the surrounding gas atmosphere. A high content of oxygen or water in the interaction zone has been found, in agreement with the results of classical and analytical methods, as a suitable way to decrease pollutant emission. The experimental methods and the principal results are applicable not only in laser medicine but in laser material treatment generally.

Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations.

PubMed

Shawon, Jakaria; Khan, Akib Mahmud; Rahman, Adhip; Hoque, Mohammad Mazharol; Khan, Mohammad Abdul Kader; Sarwar, Mohammed G; Halim, Mohammad A

2016-10-01

Molecular recognition has central role on the development of rational drug design. Binding affinity and interactions are two key components which aid to understand the molecular recognition in drug-receptor complex and crucial for structure-based drug design in medicinal chemistry. Herein, we report the binding affinity and the nonbonding interactions of azelaic acid and related compounds with the receptor DNA polymerase I (2KFN). Quantum mechanical calculation was employed to optimize the modified drugs using B3LYP/6-31G(d,p) level of theory. Charge distribution, dipole moment and thermodynamic properties such as electronic energy, enthalpy and free energy of these optimized drugs are also explored to evaluate how modifications impact the drug properties. Molecular docking calculation was performed to evaluate the binding affinity and nonbonding interactions between designed molecules and the receptor protein. We notice that all modified drugs are thermodynamically more stable and some of them are more chemically reactive than the unmodified drug. Promise in enhancing hydrogen bonds is found in case of fluorine-directed modifications as well as in the addition of trifluoroacetyl group. Fluorine participates in forming fluorine bonds and also stimulates alkyl, pi-alkyl interactions in some drugs. Designed drugs revealed increased binding affinity toward 2KFN. A1, A2 and A3 showed binding affinities of -8.7, -8.6 and -7.9 kcal/mol, respectively against 2KFN compared to the binding affinity -6.7 kcal/mol of the parent drug. Significant interactions observed between the drugs and Thr358 and Asp355 residues of 2KFN. Moreover, designed drugs demonstrated improved pharmacokinetic properties. This study disclosed that 9-octadecenoic acid and drugs containing trifluoroacetyl and trifluoromethyl groups are the best 2KFN inhibitors. Overall, these results can be useful for the design of new potential candidates against DNA polymerase I.

Direct Interactions Between Gli3, Wnt8b, and Fgfs Underlie Patterning of the Dorsal Telencephalon.

PubMed

Hasenpusch-Theil, Kerstin; Watson, Julia A; Theil, Thomas

2017-02-01

A key step in the development of the cerebral cortex is a patterning process, which subdivides the telencephalon into several molecularly distinct domains and is critical for cortical arealization. This process is dependent on a complex network of interactions between signaling molecules of the Fgf and Wnt gene families and the Gli3 transcription factor gene, but a better knowledge of the molecular basis of the interplay between these factors is required to gain a deeper understanding of the genetic circuitry underlying telencephalic patterning. Using DNA-binding and reporter gene assays, we here investigate the possibility that Gli3 and these signaling molecules interact by directly regulating each other's expression. We show that Fgf signaling is required for Wnt8b enhancer activity in the cortical hem, whereas Wnt/β-catenin signaling represses Fgf17 forebrain enhancer activity. In contrast, Fgf and Wnt/β-catenin signaling cooperate to regulate Gli3 expression. Taken together, these findings indicate that mutual interactions between Gli3, Wnt8b, and Fgf17 are crucial elements of the balance between these factors thereby conferring robustness to the patterning process. Hence, our study provides a framework for understanding the genetic circuitry underlying telencephalic patterning and how defects in this process can affect the formation of cortical areas. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Probing the energetics of organic–nanoparticle interactions of ethanol on calcite

PubMed Central

Wu, Di; Navrotsky, Alexandra

2015-01-01

Knowing the nature of interactions between small organic molecules and surfaces of nanoparticles (NP) is crucial for fundamental understanding of natural phenomena and engineering processes. Herein, we report direct adsorption enthalpy measurement of ethanol on a series of calcite nanocrystals, with the aim of mimicking organic–NP interactions in various environments. The energetics suggests a spectrum of adsorption events as a function of coverage: strongest initial chemisorption on active sites on fresh calcite surfaces, followed by major chemical binding to form an ethanol monolayer and, subsequently, very weak, near-zero energy, physisorption. These thermochemical observations directly support a structure where the ethanol monolayer is bonded to the calcite surface through its polar hydroxyl group, leaving the hydrophobic ends of the ethanol molecules to interact only weakly with the next layer of adsorbing ethanol and resulting in a spatial gap with low ethanol density between the monolayer and subsequent added ethanol molecules, as predicted by molecular dynamics and density functional calculations. Such an ordered assembly of ethanol on calcite NP is analogous to, although less strongly bonded than, a capping layer of organics intentionally introduced during NP synthesis, and suggests a continuous variation of surface structure depending on molecular chemistry, ranging from largely disordered surface layers to ordered layers that nevertheless are mobile and can rearrange or be displaced by other molecules to strongly bonded immobile organic capping layers. These differences in surface structure will affect chemical reactions, including the further nucleation and growth of nanocrystals on organic ligand-capped surfaces. PMID:25870281

Dual Role of DNA in Regulating ATP Hydrolysis by the SopA Partition Protein*

PubMed Central

Ah-Seng, Yoan; Lopez, Frederic; Pasta, Franck; Lane, David; Bouet, Jean-Yves

2009-01-01

In bacteria, mitotic stability of plasmids and many chromosomes depends on replicon-specific systems, which comprise a centromere, a centromere-binding protein and an ATPase. Dynamic self-assembly of the ATPase appears to enable active partition of replicon copies into cell-halves, but for Walker-box partition ATPases the molecular mechanism is unknown. ATPase activity appears to be essential for this process. DNA and centromere-binding proteins are known to stimulate the ATPase activity but molecular details of the stimulation mechanism have not been reported. We have investigated the interactions which stimulate ATP hydrolysis by the SopA partition ATPase of plasmid F. By using SopA and SopB proteins deficient in DNA binding, we have found that the intrinsic ability of SopA to hydrolyze ATP requires direct DNA binding by SopA but not by SopB. Our results show that two independent interactions of SopA act in synergy to stimulate its ATPase. SopA must interact with (i) DNA, through its ATP-dependent nonspecific DNA binding domain and (ii) SopB, which we show here to provide an arginine-finger motif. In addition, the latter interaction stimulates ATPase maximally when SopB is part of the partition complex. Hence, our data demonstrate that DNA acts on SopA in two ways, directly as nonspecific DNA and through SopB as centromeric DNA, to fully activate SopA ATP hydrolysis. PMID:19740757

MicroRNA319-regulated TCPs interact with FBHs and PFT1 to activate CO transcription and control flowering time in Arabidopsis.

PubMed

Liu, Jie; Cheng, Xiliu; Liu, Pan; Li, Dayong; Chen, Tao; Gu, Xiaofeng; Sun, Jiaqiang

2017-05-01

The transcription factor CONSTANS (CO) is a central component that promotes Arabidopsis flowering under long-day conditions (LDs). Here, we show that the microRNA319-regulated TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factors promote photoperiodic flowering through binding to the CO promoter and activating its transcription. Meanwhile, these TCPs directly interact with the flowering activators FLOWERING BHLH (FBHs), but not the flowering repressors CYCLING DOF FACTORs (CDFs), to additively activate CO expression. Furthermore, both the TCPs and FBHs physically interact with the flowering time regulator PHYTOCHROME AND FLOWERING TIME 1 (PFT1) to facilitate CO transcription. Our findings provide evidence that a set of transcriptional activators act directly and additively at the CO promoter to promote CO transcription, and establish a molecular mechanism underlying the regulation of photoperiodic flowering time in Arabidopsis.

MicroRNA319-regulated TCPs interact with FBHs and PFT1 to activate CO transcription and control flowering time in Arabidopsis

PubMed Central

Liu, Pan; Li, Dayong; Chen, Tao; Gu, Xiaofeng; Sun, Jiaqiang

2017-01-01

The transcription factor CONSTANS (CO) is a central component that promotes Arabidopsis flowering under long-day conditions (LDs). Here, we show that the microRNA319-regulated TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factors promote photoperiodic flowering through binding to the CO promoter and activating its transcription. Meanwhile, these TCPs directly interact with the flowering activators FLOWERING BHLH (FBHs), but not the flowering repressors CYCLING DOF FACTORs (CDFs), to additively activate CO expression. Furthermore, both the TCPs and FBHs physically interact with the flowering time regulator PHYTOCHROME AND FLOWERING TIME 1 (PFT1) to facilitate CO transcription. Our findings provide evidence that a set of transcriptional activators act directly and additively at the CO promoter to promote CO transcription, and establish a molecular mechanism underlying the regulation of photoperiodic flowering time in Arabidopsis. PMID:28558040

Budget of Turbulent Kinetic Energy in a Shock Wave Boundary-Layer Interaction

NASA Technical Reports Server (NTRS)

Vyas, Manan A.; Waindim, Mbu; Gaitonde, Datta V.

2016-01-01

Implicit large-eddy simulation (ILES) of a shock wave/boundary-layer interaction (SBLI) was performed. Quantities present in the exact equation of the turbulent kinetic energy transport were accumulated and used to calculate terms like production, dissipation, molecular diffusion, and turbulent transport. The present results for a turbulent boundary layer were validated by comparison with direct numerical simulation data. It was found that a longer development domain was necessary for the boundary layer to reach an equilibrium state and a finer mesh resolution would improve the predictions. In spite of these findings, trends of the present budget match closely with that of the direct numerical simulation. Budgets for the SBLI region are presented at key axial stations. These budgets showed interesting dynamics as the incoming boundary layer transforms and the terms of the turbulent kinetic energy budget change behavior within the interaction region.

Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy.

PubMed

Kedrov, Alexej; Janovjak, Harald; Sapra, K Tanuj; Müller, Daniel J

2007-01-01

Molecular interactions are the basic language of biological processes. They establish the forces interacting between the building blocks of proteins and other macromolecules, thus determining their functional roles. Because molecular interactions trigger virtually every biological process, approaches to decipher their language are needed. Single-molecule force spectroscopy (SMFS) has been used to detect and characterize different types of molecular interactions that occur between and within native membrane proteins. The first experiments detected and localized molecular interactions that stabilized membrane proteins, including how these interactions were established during folding of alpha-helical secondary structure elements into the native protein and how they changed with oligomerization, temperature, and mutations. SMFS also enables investigators to detect and locate molecular interactions established during ligand and inhibitor binding. These exciting applications provide opportunities for studying the molecular forces of life. Further developments will elucidate the origins of molecular interactions encoded in their lifetimes, interaction ranges, interplay, and dynamics characteristic of biological systems.

Proline 68 enhances photoisomerization yield in photoactive yellow protein.

PubMed

Rupenyan, Alisa B; Vreede, Jocelyne; van Stokkum, Ivo H M; Hospes, Marijke; Kennis, John T M; Hellingwerf, Klaas J; Groot, Marie Louise

2011-05-26

In proteins and enzymes, the local environment of an active cofactor plays an important role in controlling the outcome of a functional reaction. In photoactive yellow protein (PYP), it ensures photoisomerization of the chromophore, a prerequisite for formation of a signaling state. PYP is the prototype of a PAS domain, and the preferred model system for the studies of molecular mechanisms of biological light sensing. We investigated the effect of replacing proline-68, positioned near but not in direct contact with the chromophore, with other neutral amino acids (alanine, glycine, and valine), using ultrafast spectroscopy probing the visible and the mid-IR spectral regions, and molecular simulation to understand the interactions tuning the efficiency of light signaling. Transient absorption measurements indicate that the quantum yield of isomerization in the mutants is lower than the yield observed for the wild type. Subpicosecond mid-IR spectra and molecular dynamics simulations of the four proteins reveal that the hydrogen bond interactions around the chromophore and the access of water molecules in the active site of the protein determine the efficiency of photoisomerization. The mutants provide additional hydrogen bonds to the chromophore, directly and by allowing more water molecules access to its binding pocket. We conclude that proline-68 in the wild type protein optimizes the yield of photochemistry by maintaining a weak hydrogen bond with the chromophore, at the same time restraining the entrance of water molecules close to the alkylic part of pCa. This study provides a molecular basis for the structural optimization of biological light sensing.

Deconstructing thermodynamic parameters of a coupled system from site-specific observables.

PubMed

Chowdhury, Sandipan; Chanda, Baron

2010-11-02

Cooperative interactions mediate information transfer between structural domains of a protein molecule and are major determinants of protein function and modulation. The prevalent theories to understand the thermodynamic origins of cooperativity have been developed to reproduce the complex behavior of a global thermodynamic observable such as ligand binding or enzyme activity. However, in most cases the measurement of a single global observable cannot uniquely define all the terms that fully describe the energetics of the system. Here we establish a theoretical groundwork for analyzing protein thermodynamics using site-specific information. Our treatment involves extracting a site-specific parameter (defined as χ value) associated with a structural unit. We demonstrate that, under limiting conditions, the χ value is related to the direct interaction terms associated with the structural unit under observation and its intrinsic activation energy. We also introduce a site-specific interaction energy term (χ(diff)) that is a function of the direct interaction energy of that site with every other site in the system. When combined with site-directed mutagenesis and other molecular level perturbations, analyses of χ values of site-specific observables may provide valuable insights into protein thermodynamics and structure.

Molecular Insights into the Local Anesthetic Receptor within Voltage-Gated Sodium Channels Using Hydroxylated Analogs of Mexiletine

PubMed Central

Desaphy, Jean-François; Dipalma, Antonella; Costanza, Teresa; Carbonara, Roberta; Dinardo, Maria Maddalena; Catalano, Alessia; Carocci, Alessia; Lentini, Giovanni; Franchini, Carlo; Camerino, Diana Conte

2011-01-01

We previously showed that the β-adrenoceptor modulators, clenbuterol and propranolol, directly blocked voltage-gated sodium channels, whereas salbutamol and nadolol did not (Desaphy et al., 2003), suggesting the presence of two hydroxyl groups on the aromatic moiety of the drugs as a molecular requisite for impeding sodium channel block. To verify such an hypothesis, we synthesized five new mexiletine analogs by adding one or two hydroxyl groups to the aryloxy moiety of the sodium channel blocker and tested these compounds on hNav1.4 channels expressed in HEK293 cells. Concentration–response relationships were constructed using 25-ms-long depolarizing pulses at −30 mV applied from an holding potential of −120 mV at 0.1 Hz (tonic block) and 10 Hz (use-dependent block) stimulation frequencies. The half-maximum inhibitory concentrations (IC50) were linearly correlated to drug lipophilicity: the less lipophilic the drug, minor was the block. The same compounds were also tested on F1586C and Y1593C hNav1.4 channel mutants, to gain further information on the molecular interactions of mexiletine with its receptor within the sodium channel pore. In particular, replacement of Phe1586 and Tyr1593 by non-aromatic cysteine residues may help in the understanding of the role of π–π or π–cation interactions in mexiletine binding. Alteration of tonic block suggests that the aryloxy moiety of mexiletine may interact either directly or indirectly with Phe1586 in the closed sodium channel to produce low-affinity binding block, and that this interaction depends on the electrostatic potential of the drug aromatic tail. Alteration of use-dependent block suggests that addition of hydroxyl groups to the aryloxy moiety may modify high-affinity binding of the drug amine terminal to Phe1586 through cooperativity between the two pharmacophores, this effect being mainly related to drug lipophilicity. Mutation of Tyr1593 further impaired such cooperativity. In conclusion, these results confirm our former hypothesis by showing that the presence of hydroxyl groups to the aryloxy moiety of mexiletine greatly reduced sodium channel block, and provide molecular insights into the intimate interaction of local anesthetics with their receptor. PMID:22403541

Engineering A-kinase Anchoring Protein (AKAP)-selective Regulatory Subunits of Protein Kinase A (PKA) through Structure-based Phage Selection*

PubMed Central

Gold, Matthew G.; Fowler, Douglas M.; Means, Christopher K.; Pawson, Catherine T.; Stephany, Jason J.; Langeberg, Lorene K.; Fields, Stanley; Scott, John D.

2013-01-01

PKA is retained within distinct subcellular environments by the association of its regulatory type II (RII) subunits with A-kinase anchoring proteins (AKAPs). Conventional reagents that universally disrupt PKA anchoring are patterned after a conserved AKAP motif. We introduce a phage selection procedure that exploits high-resolution structural information to engineer RII mutants that are selective for a particular AKAP. Selective RII (RSelect) sequences were obtained for eight AKAPs following competitive selection screening. Biochemical and cell-based experiments validated the efficacy of RSelect proteins for AKAP2 and AKAP18. These engineered proteins represent a new class of reagents that can be used to dissect the contributions of different AKAP-targeted pools of PKA. Molecular modeling and high-throughput sequencing analyses revealed the molecular basis of AKAP-selective interactions and shed new light on native RII-AKAP interactions. We propose that this structure-directed evolution strategy might be generally applicable for the investigation of other protein interaction surfaces. PMID:23625929

Interactions of green coffee bean phenolics with wheat bread matrix in a model of simulated in vitro digestion.

PubMed

Świeca, Michał; Gawlik-Dziki, Urszula; Sęczyk, Łukasz; Dziki, Dariusz; Sikora, Małgorzata

2018-08-30

Interactions of phenolics from green coffee bean flour (GCS) with the matrix of wheat bread have been studied employing direct (electrophoretic and chromatographic techniques) and indirect tests (nutrient digestibility). According to the chromatograms of digests, the antiradical activity of enriched bread was exhibited by free phenolics. An increase the area of chromatograms and some additional peaks observed for enriched bread may confirm some interactions of proteins with phenolics. The electrophoretic profile of these extracts showed that the band corresponding to a protein with molecular mass of 38 kDA had much higher intensity in enriched bread. Electrophoretic analysis of pellets remaining after digestion revealed GCS dose-dependent differences in bands corresponding to proteins with molecular masses of 52 kDa and 23 kDa. The relative digestibility of both starch and proteins was slightly decreased by addition of GCS; however, these changes did not exceed 10%, which justifies the use of this functional material. Copyright © 2018 Elsevier Ltd. All rights reserved.

Spatially resolved analysis of short-range structure perturbations in a plastically bent molecular crystal

NASA Astrophysics Data System (ADS)

Panda, Manas K.; Ghosh, Soumyajit; Yasuda, Nobuhiro; Moriwaki, Taro; Mukherjee, Goutam Dev; Reddy, C. Malla; Naumov, Panče

2015-01-01

The exceptional mechanical flexibility observed with certain organic crystals defies the common perception of single crystals as brittle objects. Here, we describe the morphostructural consequences of plastic deformation in crystals of hexachlorobenzene that can be bent mechanically at multiple locations to 360° with retention of macroscopic integrity. This extraordinary plasticity proceeds by segregation of the bent section into flexible layers that slide on top of each other, thereby generating domains with slightly different lattice orientations. Microscopic, spectroscopic and diffraction analyses of the bent crystal showed that the preservation of crystal integrity when stress is applied on the (001) face requires sliding of layers by breaking and re-formation of halogen-halogen interactions. Application of stress on the (100) face, in the direction where π···π interactions dominate the packing, leads to immediate crystal disintegration. Within a broader perspective, this study highlights the yet unrecognized extraordinary malleability of molecular crystals with strongly anisotropic supramolecular interactions.

Structure-directing weak phosphoryl XH...O=P (X = C, N) hydrogen bonds in cyclic oxazaphospholidines and oxazaphosphinanes.

PubMed

van der Lee, A; Rolland, M; Marat, X; Virieux, D; Volle, J N; Pirat, J L

2008-04-01

The structures of six cyclic oxazaphospholidines and three cyclic oxazaphosphinanes have been determined and their supramolecular structures have been compared. The molecules differ with respect to the functional groups attached to the central five- or six-membered rings, but have one phosphoryl group in common. The predominant feature in the supramolecular structures is the existence of relatively weak intermolecular phosphoryl XH...O=P (X = C, N) hydrogen bonds, creating in nearly all cases linear zigzag or double molecular chains. The molecular chains are in general linked to each other via very weak CH...pi or usual hydrogen-bond interactions. A survey of the Cambridge Structural Database on similar XH...O=P interactions shows a very large flexibility of the XH...O angle, which is in agreement with the DFT calculation reported elsewhere. The strength of the XH...O=P interaction can therefore be considered as relatively weak to moderately strong, and is expected to play at least a role in the formation of secondary substructures.

Conserved conformational selection mechanism of Hsp70 chaperone-substrate interactions

PubMed Central

Velyvis, Algirdas; Zoltsman, Guy; Rosenzweig, Rina; Bouvignies, Guillaume

2018-01-01

Molecular recognition is integral to biological function and frequently involves preferred binding of a molecule to one of several exchanging ligand conformations in solution. In such a process the bound structure can be selected from the ensemble of interconverting ligands a priori (conformational selection, CS) or may form once the ligand is bound (induced fit, IF). Here we focus on the ubiquitous and conserved Hsp70 chaperone which oversees the integrity of the cellular proteome through its ATP-dependent interaction with client proteins. We directly quantify the flux along CS and IF pathways using solution NMR spectroscopy that exploits a methyl TROSY effect and selective isotope-labeling methodologies. Our measurements establish that both bacterial and human Hsp70 chaperones interact with clients by selecting the unfolded state from a pre-existing array of interconverting structures, suggesting a conserved mode of client recognition among Hsp70s and highlighting the importance of molecular dynamics in this recognition event. PMID:29460778

Supramolecular chemistry: from molecular information towards self-organization and complex matter

NASA Astrophysics Data System (ADS)

Lehn, Jean-Marie

2004-03-01

Molecular chemistry has developed a wide range of very powerful procedures for constructing ever more sophisticated molecules from atoms linked by covalent bonds. Beyond molecular chemistry lies supramolecular chemistry, which aims at developing highly complex chemical systems from components interacting via non-covalent intermolecular forces. By the appropriate manipulation of these interactions, supramolecular chemistry became progressively the chemistry of molecular information, involving the storage of information at the molecular level, in the structural features, and its retrieval, transfer, and processing at the supramolecular level, through molecular recognition processes operating via specific interactional algorithms. This has paved the way towards apprehending chemistry also as an information science. Numerous receptors capable of recognizing, i.e. selectively binding, specific substrates have been developed, based on the molecular information stored in the interacting species. Suitably functionalized receptors may perform supramolecular catalysis and selective transport processes. In combination with polymolecular organization, recognition opens ways towards the design of molecular and supramolecular devices based on functional (photoactive, electroactive, ionoactive, etc) components. A step beyond preorganization consists in the design of systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined supramolecular architectures by self-assembly from their components. Self-organization processes, directed by the molecular information stored in the components and read out at the supramolecular level through specific interactions, represent the operation of programmed chemical systems. They have been implemented for the generation of a variety of discrete functional architectures of either organic or inorganic nature. Self-organization processes also give access to advanced supramolecular materials, such as supramolecular polymers and liquid crystals, and provide an original approach to nanoscience and nanotechnology. In particular, the spontaneous but controlled generation of well-defined, functional supramolecular architectures of nanometric size through self-organization represents a means of performing programmed engineering and processing of nanomaterials. Supramolecular chemistry is intrinsically a dynamic chemistry, in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when a molecular entity contains covalent bonds that may form and break reversibly, so as to make possible a continuous change in constitution and structure by reorganization and exchange of building blocks. This behaviour defines a constitutional dynamic chemistry that allows self-organization by selection as well as by design at both the molecular and supramolecular levels. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization by selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation in a Darwinistic fashion. The merging of the features, information and programmability, dynamics and reversibility, constitution and structural diversity, points towards the emergence of adaptative and evolutionary chemistry. Together with the corresponding fields of physics and biology, it constitutes a science of informed matter, of organized, adaptative complex matter. This article was originally published in 2003 by the Israel Academy of Sciences and Humanities in the framework of its Albert Einstein Memorial Lectures series. Reprinted by permission of the Israel Academy of Sciences and Humanities.

Integrated Genomic and Network-Based Analyses of Complex Diseases and Human Disease Network.

PubMed

Al-Harazi, Olfat; Al Insaif, Sadiq; Al-Ajlan, Monirah A; Kaya, Namik; Dzimiri, Nduna; Colak, Dilek

2016-06-20

A disease phenotype generally reflects various pathobiological processes that interact in a complex network. The highly interconnected nature of the human protein interaction network (interactome) indicates that, at the molecular level, it is difficult to consider diseases as being independent of one another. Recently, genome-wide molecular measurements, data mining and bioinformatics approaches have provided the means to explore human diseases from a molecular basis. The exploration of diseases and a system of disease relationships based on the integration of genome-wide molecular data with the human interactome could offer a powerful perspective for understanding the molecular architecture of diseases. Recently, subnetwork markers have proven to be more robust and reliable than individual biomarker genes selected based on gene expression profiles alone, and achieve higher accuracy in disease classification. We have applied one of these methodologies to idiopathic dilated cardiomyopathy (IDCM) data that we have generated using a microarray and identified significant subnetworks associated with the disease. In this paper, we review the recent endeavours in this direction, and summarize the existing methodologies and computational tools for network-based analysis of complex diseases and molecular relationships among apparently different disorders and human disease network. We also discuss the future research trends and topics of this promising field. Copyright © 2015 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Metal-ligand bond directionality in the M2-NH3 complexes (M = Cu, Ag and Au)

NASA Astrophysics Data System (ADS)

Eskandari, K.; Ebadinejad, F.

2018-05-01

The metal-ligand bonds in the M2-NH3 complexes (M = Au, Ag and Cu) are directional and the M-M-N angles tend to be linear. Natural energy decomposition analysis (NEDA) and localised molecular orbital energy decomposition analysis (LMOEDA) approaches indicate that the metal-ligand bonds in these complexes are mainly electrostatic in nature, however, the electrostatic is not the cause of the linearity of M-M-N arrangements. Instead, NEDA shows that the charge transfer and core repulsion are mainly responsible for the directionality of these bonds. In the LMOEDA point of view, the repulsion term is the main reason for the linearity of these complexes. Interacting quantum atoms (IQA) analysis shows that inter-atomic and inter-fragment interactions favour the nonlinear arrangements; however, these terms are compensated by the atomic self-energies, which stabilise the linear structure.

Study of collective flows of protons and $$ \\pi^{{-}}_{}$$ π - -mesons in p+C, Ta and He+Li, C collisions at momenta of 4.2, 4.5 and 10 AGeV/c

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

Chkhaidze, L.; Chlachidze, G.; Djobava, T.

Collective flows of protons andmore » $$\\pi^{-}$$ -mesons are studied at the momenta of 4.2, 4.5 and 10AGeV/c for p+C, Ta and He+Li, C interactions. The data were obtained from the streamer chamber (SKM-200-GIBS) and from the Propane Bubble Chamber (PBC-500) systems utilized at JINR. A method of Danielewicz and Odyniec has been employed in determining a directed transverse flow of particles. The values of the transverse flow parameter and the strength of the anisotropic emission were defined for each interacting nuclear pair. It is found that the directed flows of protons and pions decrease with increasing the energy and the mass numbers of colliding nucleus pairs. The $$ \\pi^{{-}}_{}$$ -meson and proton flows exhibit opposite directions in all studied interactions, and the flows of protons are directed in the reaction plane. Lastly, the Ultra-relativistic Quantum Molecular Dynamical Model (UrQMD) coupled with the Statistical Multi-fragmentation Model (SMM), satisfactorily describes the obtained experimental results.« less

Study of collective flows of protons and $$ \\pi^{{-}}_{}$$ π - -mesons in p+C, Ta and He+Li, C collisions at momenta of 4.2, 4.5 and 10 AGeV/c

DOE PAGES

Chkhaidze, L.; Chlachidze, G.; Djobava, T.; ...

2016-11-01

Collective flows of protons andmore » $$\\pi^{-}$$ -mesons are studied at the momenta of 4.2, 4.5 and 10AGeV/c for p+C, Ta and He+Li, C interactions. The data were obtained from the streamer chamber (SKM-200-GIBS) and from the Propane Bubble Chamber (PBC-500) systems utilized at JINR. A method of Danielewicz and Odyniec has been employed in determining a directed transverse flow of particles. The values of the transverse flow parameter and the strength of the anisotropic emission were defined for each interacting nuclear pair. It is found that the directed flows of protons and pions decrease with increasing the energy and the mass numbers of colliding nucleus pairs. The $$ \\pi^{{-}}_{}$$ -meson and proton flows exhibit opposite directions in all studied interactions, and the flows of protons are directed in the reaction plane. Lastly, the Ultra-relativistic Quantum Molecular Dynamical Model (UrQMD) coupled with the Statistical Multi-fragmentation Model (SMM), satisfactorily describes the obtained experimental results.« less

Molecular dynamics simulations of the adsorption of bone morphogenetic protein-2 on surfaces with medical relevance.

PubMed

Utesch, Tillmann; Daminelli, Grazia; Mroginski, Maria Andrea

2011-11-01

Bone morphogenetic protein-2 (BMP-2) plays a crucial role in osteoblast differentiation and proliferation. Its effective therapeutic use for ectopic bone and cartilage regeneration depends, among other factors, on the interaction with the carrier at the implant site. In this study, we used classical molecular dynamics (MD) and a hybrid approach of steered molecular dynamics (SMD) combined with MD simulations to investigate the initial stages of the adsorption of BMP-2 when approaching two implant surfaces, hydrophobic graphite and hydrophilic titanium dioxide rutile. Surface adsorption was evaluated for six different orientations of the protein, two end-on and four side-on, in explicit water environment. On graphite, we observed a weak but stable adsorption. Depending on the initial orientation, hydrophobic patches as well as flexible loops of the protein were involved in the interaction with graphite. On the contrary, BMP-2 adsorbed only loosely to hydrophilic titanium dioxide. Despite a favorable interaction energy between protein and the TiO(2) surface, the rapid formation of a two-layer water structure prevented the direct interaction between protein and titanium dioxide. The first water adlayer had a strong repulsive effect on the protein, while the second attracted the protein toward the surface. For both surfaces, hydrophobic graphite and hydrophilic titanium dioxide, denaturation of BMP-2 induced by adsorption was not observed on the nanosecond time scale.

Structure of a tethered polymer under flow using molecular dynamics and hybrid molecular-continuum simulations

NASA Astrophysics Data System (ADS)

Delgado-Buscalioni, Rafael; Coveney, Peter V.

2006-03-01

We analyse the structure of a single polymer tethered to a solid surface undergoing a Couette flow. We study the problem using molecular dynamics (MD) and hybrid MD-continuum simulations, wherein the polymer and the surrounding solvent are treated via standard MD, and the solvent flow farther away from the polymer is solved by continuum fluid dynamics (CFD). The polymer represents a freely jointed chain (FJC) and is modelled by Lennard-Jones (LJ) beads interacting through the FENE potential. The solvent (modelled as a LJ fluid) and a weakly attractive wall are treated at the molecular level. At large shear rates the polymer becomes more elongated than predicted by existing theoretical scaling laws. Also, along the normal-to-wall direction the structure observed for the FJC is, surprisingly, very similar to that predicted for a semiflexible chain. Comparison with previous Brownian dynamics simulations (which exclude both solvent and wall potential) indicates that these effects are due to the polymer-solvent and polymer-wall interactions. The hybrid simulations are in perfect agreement with the MD simulations, showing no trace of finite size effects. Importantly, the extra cost required to couple the MD and CFD domains is negligible.

Monodisperse, molecularly imprinted polymers for creatinine by modified precipitation polymerization and their applications to creatinine assays for human serum and urine.

PubMed

Miura, Chitose; Funaya, Noriko; Matsunaga, Hisami; Haginaka, Jun

2013-11-01

Molecularly imprinted polymers (MIPs) for creatinine were prepared by modified precipitation polymerization using methacrylic acid as a functional monomer and divinylbenzene as a crosslinker. The prepared MIPs were monodispersed with a narrow particle size distribution. Binding experiments and Scatchard analyses revealed that two classes of binding sites, high- and low-affinity sites, were formed on the MIPs. The retention and molecular-recognition properties of the MIPs were evaluated by hydrophilic interaction chromatography using a mixture of ammonium acetate buffer and acetonitrile as a mobile phase. With an increase of acetonitrile content, the retention factor of creatinine was increased on the MIP. In addition to shape recognition, hydrophilic interactions seemed to enhance the recognition of creatinine on the MIP. The MIPs' molecular-recognition ability was specific for creatinine; the structurally related compounds such as hydantoin, 1-methylhydantoin, 2-pyrrolidone, N-hydroxysuccinimide and creatine were not recognized. Furthermore, the creatinine concentrations in human serum and urine were successfully determined by direct injection of the deproteinized serum and diluted urine samples onto the MIP. Copyright © 2013 Elsevier B.V. All rights reserved.

Chemokines and their receptors: insights from molecular modeling and crystallography.

PubMed

Kufareva, Irina

2016-10-01

Chemokines are small secreted proteins that direct cell migration in development, immunity, inflammation, and cancer. They do so by binding and activating specific G protein coupled receptors on the surface of migrating cells. Despite the importance of receptor:chemokine interactions, their structural basis remained unclear for a long time. In 2015, the first atomic resolution insights were obtained with the publication of X-ray structures for two distantly related receptors bound to chemokines. In conjunction with experiment-guided molecular modeling, the structures suggest a conserved receptor:chemokine complex architecture, while highlighting the diverse details and functional roles of individual interaction epitopes. Novel findings promote the development and detailed structural interpretation of the canonical two-site hypothesis of receptor:chemokine recognition, and suggest new avenues for pharmacological modulation of chemokine receptors. Copyright © 2016 Elsevier Ltd. All rights reserved.

World Wide Web-based system for the calculation of substituent parameters and substituent similarity searches.

PubMed

Ertl, P

1998-02-01

Easy to use, interactive, and platform-independent WWW-based tools are ideal for development of chemical applications. By using the newly emerging Web technologies such as Java applets and sophisticated scripting, it is possible to deliver powerful molecular processing capabilities directly to the desk of synthetic organic chemists. In Novartis Crop Protection in Basel, a Web-based molecular modelling system has been in use since 1995. In this article two new modules of this system are presented: a program for interactive calculation of important hydrophobic, electronic, and steric properties of organic substituents, and a module for substituent similarity searches enabling the identification of bioisosteric functional groups. Various possible applications of calculated substituent parameters are also discussed, including automatic design of molecules with the desired properties and creation of targeted virtual combinatorial libraries.

Atomistic Computer Simulations of Water Interactions and Dissolution of Inorganic Glasses

DOE PAGES

Du, Jincheng; Rimsza, Jessica

2017-09-01

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Gro2mat: a package to efficiently read gromacs output in MATLAB.

PubMed

Dien, Hung; Deane, Charlotte M; Knapp, Bernhard

2014-07-30

Molecular dynamics (MD) simulations are a state-of-the-art computational method used to investigate molecular interactions at atomic scale. Interaction processes out of experimental reach can be monitored using MD software, such as Gromacs. Here, we present the gro2mat package that allows fast and easy access to Gromacs output files from Matlab. Gro2mat enables direct parsing of the most common Gromacs output formats including the binary xtc-format. No openly available Matlab parser currently exists for this format. The xtc reader is orders of magnitudes faster than other available pdb/ascii workarounds. Gro2mat is especially useful for scientists with an interest in quick prototyping of new mathematical and statistical approaches for Gromacs trajectory analyses. © 2014 Wiley Periodicals, Inc. Copyright © 2014 Wiley Periodicals, Inc.

Molecular Docking and Prediction of Pharmacokinetic Properties of Dual Mechanism Drugs that Block MAO-B and Adenosine A2A Receptors for the Treatment of Parkinson's Disease

PubMed Central

Azam, Faizul; Madi, Arwa M.; Ali, Hamed I.

2012-01-01

Monoamine oxidase B (MAO-B) inhibitory potential of adenosine A2A receptor (AA2AR) antagonists has raised the possibility of designing dual-target–directed drugs that may provide enhanced symptomatic relief and that may also slow the progression of Parkinson's disease (PD) by protecting against further neurodegeneration. To explain the dual inhibition of MAO-B and AA2AR at the molecular level, molecular docking technique was employed. Lamarckian genetic algorithm methodology was used for flexible ligand docking studies. A good correlation (R2= 0.524 and 0.627 for MAO-B and AA2AR, respectively) was established between docking predicted and experimental Ki values, which confirms that the molecular docking approach is reliable to study the mechanism of dual interaction of caffeinyl analogs with MAO-B and AA2AR. Parameters for Lipinski's “Rule-of-Five” were also calculated to estimate the pharmacokinetic properties of dual-target–directed drugs where both MAO-B inhibition and AA2AR antagonism exhibited a positive correlation with calculated LogP having a correlation coefficient R2 of 0.535 and 0.607, respectively. These results provide some beneficial clues in structural modification for designing new inhibitors as dual-target–directed drugs with desired pharmacokinetic properties for the treatment of PD. PMID:23112538

VPAC receptors: structure, molecular pharmacology and interaction with accessory proteins.

PubMed

Couvineau, Alain; Laburthe, Marc

2012-05-01

The vasoactive intestinal peptide (VIP) is a neuropeptide with wide distribution in both central and peripheral nervous systems, where it plays important regulatory role in many physiological processes. VIP displays a large biological functions including regulation of exocrine secretions, hormone release, fetal development, immune responses, etc. VIP appears to exert beneficial effect in neuro-degenerative and inflammatory diseases. The mechanism of action of VIP implicates two subtypes of receptors (VPAC1 and VPAC2), which are members of class B receptors belonging to the super-family of GPCR. This article reviews the current knowledge regarding the structure and molecular pharmacology of VPAC receptors. The structure-function relationship of VPAC1 receptor has been extensively studied, allowing to understand the molecular basis for receptor affinity, specificity, desensitization and coupling to adenylyl cyclase. Those studies have clearly demonstrated the crucial role of the N-terminal ectodomain (N-ted) of VPAC1 receptor in VIP recognition. By using different approaches including directed mutagenesis, photoaffinity labelling, NMR, molecular modelling and molecular dynamic simulation, it has been shown that the VIP molecule interacts with the N-ted of VPAC1 receptor, which is itself structured as a 'Sushi' domain. VPAC1 receptor also interacts with a few accessory proteins that play a role in cell signalling of receptors. Recent advances in the structural characterization of VPAC receptor and more generally of class B GPCRs will lead to the design of new molecules, which could have considerable interest for the treatment of inflammatory and neuro-degenerative diseases. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

Facile and controllable one-step fabrication of molecularly imprinted polymer membrane by magnetic field directed self-assembly for electrochemical sensing of glutathione.

PubMed

Zhu, Wanying; Jiang, Guoyi; Xu, Lei; Li, Bingzhi; Cai, Qizhi; Jiang, Huijun; Zhou, Xuemin

2015-07-30

Based on magnetic field directed self-assembly (MDSA) of the ternary Fe3O4@PANI/rGO nanocomposites, a facile and controllable molecularly imprinted electrochemical sensor (MIES) was fabricated through a one-step approach for detection of glutathione (GSH). The ternary Fe3O4@PANI/rGO nanocomposites were obtained by chemical oxidative polymerization and intercalation of Fe3O4@PANI into the graphene oxide layers via π-π stacking interaction, followed by reduction of graphene oxide in the presence of hydrazine hydrate. In molecular imprinting process, the pre-polymers, including GSH as template molecule, Fe3O4@PANI/rGO nanocomposites as functional monomers and pyrrole as both cross-linker and co-monomer, was assembled through N-H hydrogen bonds and the electrostatic interaction, and then was rapidly oriented onto the surface of MGCE under the magnetic field induction. Subsequently, the electrochemical GSH sensor was formed by electropolymerization. In this work, the ternary Fe3O4@PANI/rGO nanocomposites could not only provide available functionalized sites in the matrix to form hydrogen bond and electrostatic interaction with GSH, but also afford a promoting network for electron transfer. Moreover, the biomimetic sensing membrane could be controlled more conveniently and effectively by adjusting the magnetic field strength. The as-prepared controllable sensor showed good stability and reproducibility for the determination of GSH with the detection limit reaching 3 nmol L(-1) (S/N = 3). In addition, the highly sensitive and selective biomimetic sensor has been successfully used for the clinical determination of GSH in biological samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Investigation of the ellipsoidal-statistical Bhatnagar-Gross-Krook kinetic model applied to gas-phase transport of heat and tangential momentum between parallel walls

NASA Astrophysics Data System (ADS)

Gallis, M. A.; Torczynski, J. R.

2011-03-01

The ellipsoidal-statistical Bhatnagar-Gross-Krook (ES-BGK) kinetic model is investigated for steady gas-phase transport of heat, tangential momentum, and mass between parallel walls (i.e., Fourier, Couette, and Fickian flows). This investigation extends the original study of Cercignani and Tironi, who first applied the ES-BGK model to heat transport (i.e., Fourier flow) shortly after this model was proposed by Holway. The ES-BGK model is implemented in a molecular-gas-dynamics code so that results from this model can be compared directly to results from the full Boltzmann collision term, as computed by the same code with the direct simulation Monte Carlo (DSMC) algorithm of Bird. A gas of monatomic molecules is considered. These molecules collide in a pairwise fashion according to either the Maxwell or the hard-sphere interaction and reflect from the walls according to the Cercignani-Lampis-Lord model with unity accommodation coefficients. Simulations are performed at pressures from near-free-molecular to near-continuum. Unlike the BGK model, the ES-BGK model produces heat-flux and shear-stress values that both agree closely with the DSMC values at all pressures. However, for both interactions, the ES-BGK model produces molecular-velocity-distribution functions that are qualitatively similar to those determined for the Maxwell interaction from Chapman-Enskog theory for small wall temperature differences and moment-hierarchy theory for large wall temperature differences. Moreover, the ES-BGK model does not produce accurate values of the mass self-diffusion coefficient for either interaction. Nevertheless, given its reasonable accuracy for heat and tangential-momentum transport, its sound theoretical foundation (it obeys the H-theorem), and its available extension to polyatomic molecules, the ES-BGK model may be a useful method for simulating certain classes of single-species noncontinuum gas flows, as Cercignani suggested.

Type I γ Phosphatidylinositol Phosphate 5-Kinase i5 Controls the Ubiquitination and Degradation of the Tumor Suppressor Mitogen-inducible Gene 6.

PubMed

Sun, Ming; Cai, Jinyang; Anderson, Richard A; Sun, Yue

2016-10-07

Mitogen-inducible gene 6 (Mig6) is a tumor suppressor, and the disruption of Mig6 expression is associated with cancer development. Mig6 directly interacts with epidermal growth factor receptor (EGFR) to suppress the activation and downstream signaling of EGFR. Therefore, loss of Mig6 enhances EGFR-mediated signaling and promotes EGFR-dependent carcinogenesis. The molecular mechanism modulating Mig6 expression in cancer remains unclear. Here we demonstrate that type I γ phosphatidylinositol phosphate 5-kinase i5 (PIPKIγi5), an enzyme producing phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P 2 ), stabilizes Mig6 expression. Knockdown of PIPKIγi5 leads to the loss of Mig6 expression, which dramatically enhances and prolongs EGFR-mediated cell signaling. Loss of PIPKIγi5 significantly promotes Mig6 protein degradation via proteasomes, but it does not affect the Mig6 mRNA level. PIPKIγi5 directly interacts with the E3 ubiquitin ligase neuronal precursor cell-expressed developmentally down-regulated 4-1 (NEDD4-1). The C-terminal domain of PIPKIγi5 and the WW1 and WW2 domains of NEDD4-1 are required for their interaction. The C2 domain of NEDD4-1 is required for its interaction with PtdIns(4,5)P 2 By binding with NEDD4-1 and producing PtdIns(4,5)P 2 , PIPKIγi5 perturbs NEDD4-1-mediated Mig6 ubiquitination and the subsequent proteasomal degradation. Thus, loss of NEDD4-1 can rescue Mig6 expression in PIPKIγi5 knockdown cells. In this way, PIPKIγi5, NEDD4-1, and Mig6 form a novel molecular nexus that controls EGFR activation and downstream signaling. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides.

PubMed

Kalathiya, Umesh; Padariya, Monikaben; Baginski, Maciej

2017-03-01

Shelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate the molecular basis of these interactions, we employed molecular dynamics (MD) simulations of TRF1 TRFH -TIN2 TBM and TRF2 TRFH -TIN2 TBM /Apollo TBM complexes and of the isolated proteins. MD enabled a structural and dynamical comparison of protein-peptide complexes including H-bond interactions and interfacial residues that may regulate TRF protein binding to the given peptides, especially focusing on interactions described in crystallographic data. Residues with a selective function in both TRF1 TRFH and TRF2 TRFH and forming a stable hydrogen bond network with TIN2 TBM or Apollo TBM peptides were traced. Our study revealed that TIN2 TBM forms a well-defined binding mode with TRF1 TRFH as compared to TRF2 TRFH , and that the binding pocket of TIN2 TBM is deeper for TRF2 TRFH protein than Apollo TBM . The MD data provide a basis for the reinterpretation of mutational data obtained in crystallographic work for the TRF proteins. Together, the previously determined X-ray structure and our MD provide a detailed view of the TRF-peptide binding mode and the structure of TRF1/2 binding pockets. Particular TRF-peptide interactions are very specific for the formation of each protein-peptide complex, identifying TRF proteins as potential targets for the design of inhibitors/drugs modulating telomere machinery for anticancer therapy.

Recent Developments and Applications of the MMPBSA Method

PubMed Central

Wang, Changhao; Greene, D'Artagnan; Xiao, Li; Qi, Ruxi; Luo, Ray

2018-01-01

The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method. PMID:29367919

A molecular dynamics study of freezing in a confined geometry

NASA Technical Reports Server (NTRS)

Ma, Wen-Jong; Banavar, Jayanth R.; Koplik, Joel

1992-01-01

The dynamics of freezing of a Lennard-Jones liquid in narrow channels bounded by molecular walls is studied by computer simulation. The time development of ordering is quantified and a novel freezing mechanism is observed. The liquid forms layers and subsequent in-plane ordering within a layer is accompanied by a sharpening of the layer in the transverse direction. The effects of channel size, the methods of quench, the liquid-wall interaction and the roughness of walls on the freezing mechanism are elucidated. Comparison with recent experiments on freezing in confined geometries is presented.

A molecular dawn for biogeochemistry

USGS Publications Warehouse

Zak, D.R.; Blackwood, C.B.; Waldrop, M.P.

2006-01-01

Biogeochemistry is at the dawn of an era in which molecular advances enable the discovery of novel microorganisms having unforeseen metabolic capabilities, revealing new insight into the underlying processes regulating elemental cycles at local to global scales. Traditionally, biogeochemical inquiry began by studying a process of interest, and then focusing downward to uncover the microorganisms and metabolic pathways mediating that process. With the ability to sequence functional genes from the environment, molecular approaches now enable the flow of inquiry in the opposite direction. Here, we argue that a focus on functional genes, the microorganisms in which they reside, and the interaction of those organisms with the broader microbial community could transform our understanding of many globally important biogeochemical processes. ?? 2006 Elsevier Ltd. All rights reserved.

Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein

PubMed Central

Hao, Ge-Fei; Xu, Wei-Fang; Yang, Sheng-Gang; Yang, Guang-Fu

2015-01-01

Protein and peptide structure predictions are of paramount importance for understanding their functions, as well as the interactions with other molecules. However, the use of molecular simulation techniques to directly predict the peptide structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale. We developed here a new strategy, named Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) to identify the native states of a peptide and miniprotein. A cluster of near native structures could be obtained by using the MSA-MD method, which turned out to be significantly more efficient in reaching the native structure compared to continuous MD and conventional SA-MD simulation. PMID:26492886

Identification of Direct Activator of Adenosine Monophosphate-Activated Protein Kinase (AMPK) by Structure-Based Virtual Screening and Molecular Docking Approach.

PubMed

Huang, Tonghui; Sun, Jie; Zhou, Shanshan; Gao, Jian; Liu, Yi

2017-06-30

Adenosine monophosphate-activated protein kinase (AMPK) plays a critical role in the regulation of energy metabolism and has been targeted for drug development of therapeutic intervention in Type II diabetes and related diseases. Recently, there has been renewed interest in the development of direct β1-selective AMPK activators to treat patients with diabetic nephropathy. To investigate the details of AMPK domain structure, sequence alignment and structural comparison were used to identify the key amino acids involved in the interaction with activators and the structure difference between β1 and β2 subunits. Additionally, a series of potential β1-selective AMPK activators were identified by virtual screening using molecular docking. The retrieved hits were filtered on the basis of Lipinski's rule of five and drug-likeness. Finally, 12 novel compounds with diverse scaffolds were obtained as potential starting points for the design of direct β1-selective AMPK activators.

Liquid-phase characterization of molecular interactions in polyunsaturated and n-fatty acid methyl esters by (1)H low-field nuclear magnetic resonance.

PubMed

Meiri, Nitzan; Berman, Paula; Colnago, Luiz Alberto; Moraes, Tiago Bueno; Linder, Charles; Wiesman, Zeev

2015-01-01

To identify and develop the best renewable and low carbon footprint biodiesel substitutes for petroleum diesel, the properties of different biodiesel candidates should be studied and characterized with respect to molecular structures versus biodiesel liquid property relationships. In our previous paper, (1)H low-field nuclear magnetic resonance (LF-NMR) relaxometry was investigated as a tool for studying the liquid-phase molecular packing interactions and morphology of fatty acid methyl esters (FAMEs). The technological potential was demonstrated with oleic acid and methyl oleate standards having similar alkyl chains but different head groups. In the present work, molecular organization versus segmental and translational movements of FAMEs in their pure liquid phase, with different alkyl chain lengths (10-20 carbons) and degrees of unsaturation (0-3 double bonds), were studied with (1)H LF-NMR relaxometry and X-ray, (1)H LF-NMR diffusiometry, and (13)C high-field NMR. Based on density values and X-ray measurements, it was proposed that FAMEs possess a liquid crystal-like order above their melting point, consisting of random liquid crystal aggregates with void spaces between them, whose morphological properties depend on chain length and degree of unsaturation. FAMEs were also found to exhibit different degrees of rotational and translational motions, which were rationalized by chain organization within the clusters, and the degree and type of molecular interactions and temperature effects. At equivalent fixed temperature differences from melting point, saturated FAME molecules were found to have similar translational motion regardless of chain length, expressed by viscosity, self-diffusion coefficients, and spin-spin (T 2) (1)H LF-NMR. T 2 distributions suggest increased alkyl chain rigidity, and reduced temperature response of the peaks' relative contribution with increasing unsaturation is a direct result of the alkyl chain's morphological packing and molecular interactions. Both the peaks' assignments for T 2 distributions of FAMEs and the model for their liquid crystal-like morphology in the liquid phase were confirmed. The study of morphological structures within liquids and their response to temperature changes by (1)H LF-NMR has a high value in the field of biodiesel and other research and applied disciplines in numerous physicochemical- and organizational-based properties, processes, and mechanisms of alkyl chains, molecular interactions, and morphologies.

Dopamine D1A directly interacts with otoferlin synaptic pathway proteins: Ca2+ and phosphorylation underlie an NSF-to-AP2mu1 molecular switch.

PubMed

Selvakumar, Dakshnamurthy; Drescher, Marian J; Deckard, Nathan A; Ramakrishnan, Neeliyath A; Morley, Barbara J; Drescher, Dennis G

2017-01-01

Dopamine receptors regulate exocytosis via protein-protein interactions (PPIs) as well as via adenylyl cyclase transduction pathways. Evidence has been obtained for PPIs in inner ear hair cells coupling D1A to soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor (SNARE)-related proteins snapin, otoferlin, N-ethylmaleimide-sensitive factor (NSF), and adaptor-related protein complex 2, mu 1 (AP2mu1), dependent on [Ca 2+ ] and phosphorylation. Specifically, the carboxy terminus of dopamine D1A was found to directly bind t-SNARE-associated protein snapin in teleost and mammalian hair cell models by yeast two-hybrid (Y2H) and pull-down assays, and snapin directly interacts with hair cell calcium-sensor otoferlin. Surface plasmon resonance (SPR) analysis, competitive pull-downs, and co-immunoprecipitation indicated that these interactions were promoted by Ca 2+ and occur together. D1A was also found to separately interact with NSF, but with an inverse dependence on Ca 2+ Evidence was obtained, for the first time, that otoferlin domains C2A, C2B, C2D, and C2F interact with NSF and AP2mu1, whereas C2C or C2E do not bind to either protein, representing binding characteristics consistent with respective inclusion or omission in individual C2 domains of the tyrosine motif YXXΦ. In competitive pull-down assays, as predicted by K D values from SPR (+Ca 2+ ), C2F pulled down primarily NSF as opposed to AP2mu1. Phosphorylation of AP2mu1 gave rise to a reversal: an increase in binding by C2F to phosphorylated AP2mu1 was accompanied by a decrease in binding to NSF, consistent with a molecular switch for otoferlin from membrane fusion (NSF) to endocytosis (AP2mu1). An increase in phosphorylated AP2mu1 at the base of the cochlear inner hair cell was the observed response elicited by a dopamine D1A agonist, as predicted. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Hole-phonon coupling effect on the band dispersion of organic molecular semiconductors.

PubMed

Bussolotti, F; Yang, J; Yamaguchi, T; Yonezawa, K; Sato, K; Matsunami, M; Tanaka, K; Nakayama, Y; Ishii, H; Ueno, N; Kera, S

2017-08-02

The dynamic interaction between the traveling charges and the molecular vibrations is critical for the charge transport in organic semiconductors. However, a direct evidence of the expected impact of the charge-phonon coupling on the band dispersion of organic semiconductors is yet to be provided. Here, we report on the electronic properties of rubrene single crystal as investigated by angle resolved ultraviolet photoelectron spectroscopy. A gap opening and kink-like features in the rubrene electronic band dispersion are observed. In particular, the latter results in a large enhancement of the hole effective mass (> 1.4), well above the limit of the theoretical estimations. The results are consistent with the expected modifications of the band structures in organic semiconductors as introduced by hole-phonon coupling effects and represent an important experimental step toward the understanding of the charge localization phenomena in organic materials.The charge transport properties in organic semiconductors are affected by the impact of molecular vibrations, yet it has been challenging to quantify them to date. Here, Bussolotti et al. provide direct experimental evidence on the band dispersion modified by molecular vibrations in a rubrene single crystal.

Brownian dynamics simulation of a polymer chain in a solid-state nanopore attached to a molecular stop

NASA Astrophysics Data System (ADS)

Wells, Craig; Hulings, Zachery; Melnikov, Dmitriy; Gracheva, Maria

We study a nanopore inside a silicon dioxide membrane submerged in a KCl solution with a negatively charged polymer chain of varying lengths whose movement is described using Brownian dynamics. The polymer is attached to a molecule with a radius larger than that of the nanopore's which acts as a molecular stop, allowing the chain to thread the nanopore but preventing it from translocating. We found that the polymer chain's variation of movement along the nanopore decreased when increasing applied biases and chain lengths for portions of the chain closest to the molecular stop. The chain displacement within the pore is also compared to a freely translocating polymer where preliminary results show the free polymer having a greater variation in the radial direction. Overall, our preliminary results indicate that the radial direction of the polymer chain is dominated by the confinement in the narrow nanopore with restrictions imposed by the molecular stop and bias playing a lesser role. Understanding the interaction behavior of the polymer chain-stop molecule may lead to methods that decrease movement variation, facilitating an improvement on characterizing and identification of molecules. NSF DMR and CBET Grant No. 1352218.

Advances of Molecular Targeted Therapy in Gastric Cancer.

PubMed

Cetin, Bulent; Gumusay, Ozge; Cengiz, Mustafa; Ozet, Ahmet

2016-06-01

Gastric cancer is the second most common cause of cancer-related death in the world, and its prognosis remains poor with a median overall survival of 12 months for advanced disease. Advances in the understanding of molecular genetics have led to the development of directed molecular targeted therapy in gastric cancer, leading to improve patient outcomes and quality of life. In the treatment of human epidermal growth factor receptor 2 (HER2)-positive gastric cancer, the addition of trastuzumab significantly improves survival in the first-line setting of therapy. Ramucirumab, an antibody directed against vascular endothelial growth factor receptor 2, significantly improved progression-free and overall survival and has been approved for second-line treatment of gastric cancer. Anti-mesenchymal-epithelial transition (c-MET), mammalian target of rapamycin inhibitors, and polo-like kinase 1 inhibitors are under investigation as a novel therapeutic option for the treatment of gastric cancer. The novel therapies target the key immune checkpoint interaction between a T cell co-inhibitory receptor called programmed death 1 (PD-1) and one of its immunosuppressive ligands, PD-L1. This article reviews molecular targeted therapies in gastric cancer, in light of recent advances.

Laser manipulation of atomic and molecular flows

NASA Astrophysics Data System (ADS)

Lilly, Taylor C.

The continuing advance of laser technology enables a range of broadly applicable, laser-based flow manipulation techniques. The characteristics of these laser-based flow manipulations suggest that they may augment, or be superior to, such traditional electro-mechanical methods as ionic flow control, shock tubes, and small scale wind tunnels. In this study, methodology was developed for investigating laser flow manipulation techniques, and testing their feasibility for a number of aerospace, basic physics, and micro technology applications. Theories for laser-atom and laser-molecule interactions have been under development since the advent of laser technology. The theories have yet to be adequately integrated into kinetic flow solvers. Realizing this integration would greatly enhance the scaling of laser-species interactions beyond the realm of ultra-cold atomic physics. This goal was realized in the present study. A representative numerical investigation, of laser-based neutral atomic and molecular flow manipulations, was conducted using near-resonant and non-resonant laser fields. To simulate the laser interactions over a range of laser and flow conditions, the following tools were employed: a custom collisionless gas particle trajectory code and a specifically modified version of the Direct Simulation Monte Carlo statistical kinetic solver known as SMILE. In addition to the numerical investigations, a validating experiment was conducted. The experimental results showed good agreement with the numerical simulations when experimental parameters, such as finite laser line width, were taken into account. Several areas of interest were addressed: laser induced neutral flow steering, collimation, direct flow acceleration, and neutral gas heating. Near-resonant continuous wave laser, and non-resonant pulsed laser, interactions with cesium and nitrogen were simulated. These simulations showed trends and some limitations associated with these interactions, used for flow steering and collimation. The use of one of these interactions, the induced dipole force, was extended beyond a single Gaussian laser field. The interference patterns associated with counter-propagating laser fields, or "optical lattices," were shown to be capable of both direct species acceleration and gas heating. This study resulted in predictions for a continuous, resonant laser-cesium flow with accelerations of 106 m/s2. For this circumstance, a future straightforward proof of principle experiment has been identified. To demonstrate non-resonant gas heating, a series of pulsed optical lattices were simulated interacting with neutral non-polar species. An optimum time between pulses was identified as a function of the collisional relaxation time. Using the optimum time between pulses, molecular nitrogen simulations showed an increase in gas temperature from 300 K to 2470 K at 1 atm, for 50 successive optical lattice pulses. A second proof of principle experiment was identified for future investigation.

Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity.

PubMed

Petzold, Christine; Marceau, Aimee H; Miller, Katherine H; Marqusee, Susan; Keck, James L

2015-06-05

Single-stranded (ss) DNA-binding proteins (SSBs) bind and protect ssDNA intermediates formed during replication, recombination, and repair reactions. SSBs also directly interact with many different genome maintenance proteins to stimulate their enzymatic activities and/or mediate their proper cellular localization. We have identified an interaction formed between Escherichia coli SSB and ribonuclease HI (RNase HI), an enzyme that hydrolyzes RNA in RNA/DNA hybrids. The RNase HI·SSB complex forms by RNase HI binding the intrinsically disordered C terminus of SSB (SSB-Ct), a mode of interaction that is shared among all SSB interaction partners examined to date. Residues that comprise the SSB-Ct binding site are conserved among bacterial RNase HI enzymes, suggesting that RNase HI·SSB complexes are present in many bacterial species and that retaining the interaction is important for its cellular function. A steady-state kinetic analysis shows that interaction with SSB stimulates RNase HI activity by lowering the reaction Km. SSB or RNase HI protein variants that disrupt complex formation nullify this effect. Collectively our findings identify a direct RNase HI/SSB interaction that could play a role in targeting RNase HI activity to RNA/DNA hybrid substrates within the genome. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

PubMed

Caetano, Fabiana A; Dirk, Brennan S; Tam, Joshua H K; Cavanagh, P Craig; Goiko, Maria; Ferguson, Stephen S G; Pasternak, Stephen H; Dikeakos, Jimmy D; de Bruyn, John R; Heit, Bryan

2015-12-01

Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell.

``Making the Molecular Movie'': First Frames

NASA Astrophysics Data System (ADS)

Miller, R. J. Dwayne

2011-03-01

Femtosecond Electron Diffraction has enabled atomic resolution to structural changes as they occur, essentially watching atoms move in real time--directly observe transition states. This experiment has been referred to as ``making the molecular movie'' and has been previously discussed in the context of a gedanken experiment. With the recent development of femtosecond electron pulses with sufficient number density to execute single shot structure determinations, this experiment has been finally realized. A new concept in electron pulse generation was developed based on a solution to the N-body electron propagation problem involving up to 10,000 interacting electrons that has led to a new generation of extremely bright electron pulsed sources that minimizes space charge broadening effects. Previously thought intractable problems of determining t=0 and fully characterizing electron pulses on the femtosecond time scale have now been solved through the use of the laser pondermotive potential to provide a time dependent scattering source. Synchronization of electron probe and laser excitation pulses is now possible with an accuracy of 10 femtoseconds to follow even the fastest nuclear motions. The camera for the ``molecular movie'' is well in hand based on high bunch charge electron sources. Several movies depicting atomic motions during passage through structural transitions will be shown. Atomic level views of the simplest possible structural transition, melting, will be presented for a number of systems in which both thermal and purely electronically driven atomic displacements can be correlated to the degree of directional bonding. Optical manipulation of charge distributions and effects on interatomic forces/bonding can be directly observed through the ensuing atomic motions. New phenomena involving strongly correlated electron systems will be presented in which an exceptionally cooperative phase transitions has been observed. The primitive origin of molecular cooperativity has also been discovered in recent studies of molecular crystals. These new developments will be discussed in the context of developing the necessary technology to directly observe the structure-function correlation in biomolecules--the fundamental molecular basis of biological systems.

Identification of N-methyl-D-aspartic acid (NMDA) receptor subtype-specific binding sites that mediate direct interactions with scaffold protein PSD-95.

PubMed

Cousins, Sarah L; Stephenson, F Anne

2012-04-13

N-methyl-D-aspartate (NMDA) neurotransmitter receptors and the postsynaptic density-95 (PSD-95) membrane-associated guanylate kinase (MAGUK) family of scaffolding proteins are integral components of post-synaptic macromolecular signaling complexes that serve to propagate glutamate responses intracellularly. Classically, NMDA receptor NR2 subunits associate with PSD-95 MAGUKs via a conserved ES(E/D)V amino acid sequence located at their C termini. We previously challenged this dogma to demonstrate a second non-ES(E/D)V PSD-95-binding site in both NMDA receptor NR2A and NR2B subunits. Here, using a combination of co-immunoprecipitations from transfected mammalian cells, yeast two-hybrid interaction assays, and glutathione S-transferase (GST) pulldown assays, we show that NR2A subunits interact directly with PSD-95 via the C-terminal ESDV motif and additionally via an Src homology 3 domain-binding motif that associates with the Src homology 3 domain of PSD-95. Peptide inhibition of co-immunoprecipitations of NR2A and PSD-95 demonstrates that both the ESDV and non-ESDV sites are required for association in native brain tissue. Furthermore, we refine the non-ESDV site within NR2B to residues 1149-1157. These findings provide a molecular basis for the differential association of NMDA receptor subtypes with PSD-95 MAGUK scaffold proteins. These selective interactions may contribute to the organization, lateral mobility, and ultimately the function of NMDA receptor subtypes at synapses. Furthermore, they provide a more general molecular mechanism by which the scaffold, PSD-95, may discriminate between potential interacting partner proteins.

Identification of N-Methyl-d-aspartic Acid (NMDA) Receptor Subtype-specific Binding Sites That Mediate Direct Interactions with Scaffold Protein PSD-95*

PubMed Central

Cousins, Sarah L.; Stephenson, F. Anne

2012-01-01

N-methyl-d-aspartate (NMDA) neurotransmitter receptors and the postsynaptic density-95 (PSD-95) membrane-associated guanylate kinase (MAGUK) family of scaffolding proteins are integral components of post-synaptic macromolecular signaling complexes that serve to propagate glutamate responses intracellularly. Classically, NMDA receptor NR2 subunits associate with PSD-95 MAGUKs via a conserved ES(E/D)V amino acid sequence located at their C termini. We previously challenged this dogma to demonstrate a second non-ES(E/D)V PSD-95-binding site in both NMDA receptor NR2A and NR2B subunits. Here, using a combination of co-immunoprecipitations from transfected mammalian cells, yeast two-hybrid interaction assays, and glutathione S-transferase (GST) pulldown assays, we show that NR2A subunits interact directly with PSD-95 via the C-terminal ESDV motif and additionally via an Src homology 3 domain-binding motif that associates with the Src homology 3 domain of PSD-95. Peptide inhibition of co-immunoprecipitations of NR2A and PSD-95 demonstrates that both the ESDV and non-ESDV sites are required for association in native brain tissue. Furthermore, we refine the non-ESDV site within NR2B to residues 1149–1157. These findings provide a molecular basis for the differential association of NMDA receptor subtypes with PSD-95 MAGUK scaffold proteins. These selective interactions may contribute to the organization, lateral mobility, and ultimately the function of NMDA receptor subtypes at synapses. Furthermore, they provide a more general molecular mechanism by which the scaffold, PSD-95, may discriminate between potential interacting partner proteins. PMID:22375001

Molecular Interactions at Marine Interfaces

DTIC Science & Technology

1994-09-20

Microbial Attachment and Biofilm Formation 9:00 Michael Sinnott Structure of Extracellular Polysaccharides of Pseudomonas atlantica 9:30 Herb Waite...sit/ i u~ . Direct Measurements of the Intermolecular F~rccs Between Polysaccharide Exopolymers from marine Bacter"a and Solid Substrates Georges...aqueous medium of high ionic strength. Effect of Polysaccharide Surface Structurt on Microbial Attachment and Biofilm Formation David C. White and A

A trough for improved SFG spectroscopy of lipid monolayers.

PubMed

Franz, Johannes; van Zadel, Marc-Jan; Weidner, Tobias

2017-05-01

Lipid monolayers are indispensable model systems for biological membranes. The main advantage over bilayer model systems is that the surface pressure within the layer can be directly and reliably controlled. The sensitive interplay between surface pressure and temperature determines the molecular order within a model membrane and consequently determines the membrane phase behavior. The lipid phase is of crucial importance for a range of membrane functions such as protein interactions and membrane permeability. A very reliable method to probe the structure of lipid monolayers is sum frequency generation (SFG) vibrational spectroscopy. Not only is SFG extremely surface sensitive but it can also directly access critical parameters such as lipid order and orientation, and it can provide valuable information about protein interactions along with interfacial hydration. However, recent studies have shown that temperature gradients caused by high power laser beams perturb the lipid layers and potentially obscure the spectroscopic results. Here we demonstrate how the local heating problem can be effectively reduced by spatially distributing the laser pulses on the sample surface using a translating Langmuir trough for SFG experiments at lipid monolayers. The efficiency of the trough is illustrated by the detection of enhanced molecular order due to reduced heat load.

A trough for improved SFG spectroscopy of lipid monolayers

NASA Astrophysics Data System (ADS)

Franz, Johannes; van Zadel, Marc-Jan; Weidner, Tobias

2017-05-01

Lipid monolayers are indispensable model systems for biological membranes. The main advantage over bilayer model systems is that the surface pressure within the layer can be directly and reliably controlled. The sensitive interplay between surface pressure and temperature determines the molecular order within a model membrane and consequently determines the membrane phase behavior. The lipid phase is of crucial importance for a range of membrane functions such as protein interactions and membrane permeability. A very reliable method to probe the structure of lipid monolayers is sum frequency generation (SFG) vibrational spectroscopy. Not only is SFG extremely surface sensitive but it can also directly access critical parameters such as lipid order and orientation, and it can provide valuable information about protein interactions along with interfacial hydration. However, recent studies have shown that temperature gradients caused by high power laser beams perturb the lipid layers and potentially obscure the spectroscopic results. Here we demonstrate how the local heating problem can be effectively reduced by spatially distributing the laser pulses on the sample surface using a translating Langmuir trough for SFG experiments at lipid monolayers. The efficiency of the trough is illustrated by the detection of enhanced molecular order due to reduced heat load.

ZNRF3 functions in mammalian sex determination by inhibiting canonical WNT signaling.

PubMed

Harris, Abigail; Siggers, Pam; Corrochano, Silvia; Warr, Nick; Sagar, Danielle; Grimes, Daniel T; Suzuki, Makoto; Burdine, Rebecca D; Cong, Feng; Koo, Bon-Kyoung; Clevers, Hans; Stévant, Isabelle; Nef, Serge; Wells, Sara; Brauner, Raja; Ben Rhouma, Bochra; Belguith, Neïla; Eozenou, Caroline; Bignon-Topalovic, Joelle; Bashamboo, Anu; McElreavey, Ken; Greenfield, Andy

2018-05-22

Mammalian sex determination is controlled by the antagonistic interactions of two genetic pathways: The SRY-SOX9-FGF9 network promotes testis determination partly by opposing proovarian pathways, while RSPO1/WNT-β-catenin/FOXL2 signals control ovary development by inhibiting SRY-SOX9-FGF9. The molecular basis of this mutual antagonism is unclear. Here we show that ZNRF3, a WNT signaling antagonist and direct target of RSPO1-mediated inhibition, is required for sex determination in mice. XY mice lacking ZNRF3 exhibit complete or partial gonadal sex reversal, or related defects. These abnormalities are associated with ectopic WNT/β-catenin activity and reduced Sox9 expression during fetal sex determination. Using exome sequencing of individuals with 46,XY disorders of sex development, we identified three human ZNRF3 variants in very rare cases of XY female presentation. We tested two missense variants and show that these disrupt ZNRF3 activity in both human cell lines and zebrafish embryo assays. Our data identify a testis-determining function for ZNRF3 and indicate a mechanism of direct molecular interaction between two mutually antagonistic organogenetic pathways. Copyright © 2018 the Author(s). Published by PNAS.

Atomistic Modeling of the Fluid-Solid Interface in Simple Fluids

NASA Astrophysics Data System (ADS)

Hadjiconstantinou, Nicolas; Wang, Gerald

2017-11-01

Fluids can exhibit pronounced structuring effects near a solid boundary, typically manifested in a layered structure that has been extensively shown to directly affect transport across the interface. We present and discuss several results from molecular-mechanical modeling and molecular-dynamics (MD) simulations aimed at characterizing the structure of the first fluid layer directly adjacent to the solid. We identify a new dimensionless group - termed the Wall number - which characterizes the degree of fluid layering, by comparing the competing effects of wall-fluid interaction and thermal energy. We find that in the layering regime, several key features of the first layer layer - including its distance from the solid, its width, and its areal density - can be described using mean-field-energy arguments, as well as asymptotic analysis of the Nernst-Planck equation. For dense fluids, the areal density and the width of the first layer can be related to the bulk fluid density using a simple scaling relation. MD simulations show that these results are broadly applicable and robust to the presence of a second confining solid boundary, different choices of wall structure and thermalization, strengths of fluid-solid interaction, and wall geometries.

ZNRF3 functions in mammalian sex determination by inhibiting canonical WNT signaling

PubMed Central

Harris, Abigail; Siggers, Pam; Warr, Nick; Sagar, Danielle; Grimes, Daniel T.; Cong, Feng; Koo, Bon-Kyoung; Clevers, Hans; Stévant, Isabelle; Nef, Serge; Wells, Sara; Brauner, Raja; Ben Rhouma, Bochra; Belguith, Neïla; Eozenou, Caroline; Bignon-Topalovic, Joelle; Bashamboo, Anu; McElreavey, Ken

2018-01-01

Mammalian sex determination is controlled by the antagonistic interactions of two genetic pathways: The SRY-SOX9-FGF9 network promotes testis determination partly by opposing proovarian pathways, while RSPO1/WNT-β-catenin/FOXL2 signals control ovary development by inhibiting SRY-SOX9-FGF9. The molecular basis of this mutual antagonism is unclear. Here we show that ZNRF3, a WNT signaling antagonist and direct target of RSPO1-mediated inhibition, is required for sex determination in mice. XY mice lacking ZNRF3 exhibit complete or partial gonadal sex reversal, or related defects. These abnormalities are associated with ectopic WNT/β-catenin activity and reduced Sox9 expression during fetal sex determination. Using exome sequencing of individuals with 46,XY disorders of sex development, we identified three human ZNRF3 variants in very rare cases of XY female presentation. We tested two missense variants and show that these disrupt ZNRF3 activity in both human cell lines and zebrafish embryo assays. Our data identify a testis-determining function for ZNRF3 and indicate a mechanism of direct molecular interaction between two mutually antagonistic organogenetic pathways. PMID:29735715

Sulfamide-Lattice Restructuring To Form Dimensionally Controlled Molecular Arrays and Gel-Forming Systems.

PubMed

Raghava, Saripalli V; Gopinath, Pushparathinam; Srivastava, Bhartendu K; Ramkumar, Venkatachalam; Muraleedharan, Kannoth M

2017-03-13

A design approach that incorporates structural requirements for the formation of a 1D assembly, fibril stability, and fibril-fibril interactions for gelation was attempted by using amino acid-based sulfamides with the general structure Aa-NH-SO 2 -NH-Aa (Aa=amino acid). A preference for 1D assembly alone was not a sufficient condition for gelation, which became evident from studies involving sulfamide esters 1-5. Reducing the crystallization tendency without hindering unidirectional growth was executed through diacids of the sulfamide precursors with various amines that form an envelope around the sulfamide core through salt bridges. This strategy was fruitful, and gels of a wide variety of solvents could be formed by varying the acid and amine components. The use of dodecylamine or benzylamine, which could stabilize the molecular layers through alkyl-chain segregation or π-π interactions improved the gelation tendency, whereas the nature of the amino acid side chain, especially the rotational freedom and hydrophobicity, had a direct role in dictating the solvent preference. Crystallographic studies of these two-component systems gave molecular-level insight into the assembly and showed the importance of anisotropy in the distribution of secondary interactions in gelation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inhibition kinetics and molecular simulation of p-substituted cinnamic acid derivatives on tyrosinase.

PubMed

Cui, Yi; Hu, Yong-Hua; Yu, Feng; Zheng, Jing; Chen, Lin-Shan; Chen, Qing-Xi; Wang, Qin

2017-02-01

This study was to investigate the inhibition effects of para-substituted cinnamic acid derivatives (4-chlorocinnamic acid, 4-ethoxycinnamic acid and 4-nitrocinnamic acid) on tyrosinase catalyzing the substrates, with the purpose of elucidating the inhibition mechanism of the tested derivatives on tyrosinase by the UV-vis spectrum, fluorescence spectroscopy, copper interacting and molecular docking, respectively. The native-PAGE results showed that 4-chlorocinnamic acid (4-CCA), 4-ethoxycinnamic acid (4-ECA) and 4-nitrocinnamic acid (4-NCA) had inhibitory effects on tyrosinase. Spectrophotometric analysis used to determine the inhibition capabilities of these compounds on tyrosinase catalyzing L-tyrosine (L-Tyr) and L-3,4-Dihydroxyphenylalanine (L-DOPA) as well. The IC 50 values and inhibition constants were further determined. Moreover, quenching mechanisms of tested compounds to tyrosinase belonged to static type and a red shift on fluorescence emission peak occurred when 4-NCA added. Copper interacting and molecular docking demonstrated that 4-CCA could not bind directly to the copper, but it could interact with residues in the active center of tyrosinase. Meanwhile, 4-ECA and 4-NCA could chelate a copper ion of tyrosinase. Anti-tyrosinase activities of para-substituted cinnamic acid derivatives would lay scientific foundation for their utilization in designing of novel tyrosinase inhibitors. Copyright © 2016 Elsevier B.V. All rights reserved.

Hypothesis on interactions of macromolecules based on molecular vibration patterns in cells and tissues.

PubMed

Jaross, Werner

2018-01-01

The molecular vibration patterns of structure-forming macromolecules in the living cell create very specific electromagnetic frequency patterns which might be used for information on spatial position in the three-dimensional structure as well as the chemical characteristics. Chemical change of a molecule results in a change of the vibration pattern and thus in a change of the emitted electromagnetic frequency pattern. These patterns have to be received by proteins responsible for the necessary interactions and functions. Proteins can function as resonators for frequencies in the range of 1013-1015 Hz. The individual frequency pattern is defined by the amino acid sequence and the polarity of every amino acid caused by their functional groups. If the arriving electromagnetic signal pattern and the emitted pattern of the absorbing protein are matched in relevant parts and in opposite phase, photon energy in the characteristic frequencies can be transferred resulting in a conformational change of that molecule and respectively in an increase of its specific activity. The electromagnetic radiation is very weak. The possibilities to overcome intracellular distances are shown. The motor-driven directed transport of macromolecules starts in the Golgi apparatus. The relevance of molecular interactions based on this signaling for the induction and navigation in the intracellular transport is discussed.

Structural basis for alpha fetoprotein-mediated inhibition of caspase-3 activity in hepatocellular carcinoma cells.

PubMed

Lin, Bo; Zhu, Mingyue; Wang, Wenting; Li, Wei; Dong, Xu; Chen, Yi; Lu, Yan; Guo, Junli; Li, Mengsen

2017-10-01

Alpha-fetoprotein (AFP) is an early serum growth factor in the foetal liver development and hepatic carcinogenesis; However, the precise biological role of cytoplasmic AFP remains elusive. Although we recently demonstrated that cytoplasmic AFP might interact with caspase-3 and inhibit the signal transduction of apoptosis in human hepatocellular carcinoma (HCC) cells, the details of this interaction are not clear. To reveal the molecular relationship between AFP and caspase-3, we performed molecular docking, co-immunoprecipitation (Co-IP), laser confocal microscopy, site-directed mutagenesis and functional experiments to analyse the key amino acid residues in the binding site of caspase-3. The results of Co-IP, laser confocal microscopy and functional analyses were consistent with the computational model. We also used the model to explain why AFP cannot bind to caspase-8. These results provide the molecular basis for the AFP-mediated inhibition of caspase-3 activity in HCC cells. Altogether, we found that AFP interacts with caspase-3 through precise amino acids, namely loop-4 residues Glu-248, Asp-253 and His-257. The results further demonstrated that AFP plays a critical role in the inhibition of the apoptotic signal transduction that mediated by caspase-3. Thus, AFP might represent a novel biotarget for the therapy of HCC patients. © 2017 UICC.

Quantum mechanical force fields for condensed phase molecular simulations

NASA Astrophysics Data System (ADS)

Giese, Timothy J.; York, Darrin M.

2017-09-01

Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

Adaptation of Tri-molecular fluorescence complementation allows assaying of regulatory Csr RNA-protein interactions in bacteria.

PubMed

Gelderman, Grant; Sivakumar, Anusha; Lipp, Sarah; Contreras, Lydia

2015-02-01

sRNAs play a significant role in controlling and regulating cellular metabolism. One of the more interesting aspects of certain sRNAs is their ability to make global changes in the cell by interacting with regulatory proteins. In this work, we demonstrate the use of an in vivo Tri-molecular Fluorescence Complementation assay to detect and visualize the central regulatory sRNA-protein interaction of the Carbon Storage Regulatory system in E. coli. The Carbon Storage Regulator consists primarily of an RNA binding protein, CsrA, that alters the activity of mRNA targets and of an sRNA, CsrB, that modulates the activity of CsrA. We describe the construction of a fluorescence complementation system that detects the interactions between CsrB and CsrA. Additionally, we demonstrate that the intensity of the fluorescence of this system is able to detect changes in the affinity of the CsrB-CsrA interaction, as caused by mutations in the protein sequence of CsrA. While previous methods have adopted this technique to study mRNA or RNA localization, this is the first attempt to use this technique to study the sRNA-protein interaction directly in bacteria. This method presents a potentially powerful tool to study complex bacterial RNA protein interactions in vivo. © 2014 Wiley Periodicals, Inc.

Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

PubMed

Nandy, Suman Kumar; Seal, Alpana

2016-01-01

Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

Bimolecular fluorescence complementation (BiFC) analysis as a probe of protein interactions in living cells.

PubMed

Kerppola, Tom K

2008-01-01

Protein interactions are a fundamental mechanism for the generation of biological regulatory specificity. The study of protein interactions in living cells is of particular significance because the interactions that occur in a particular cell depend on the full complement of proteins present in the cell and the external stimuli that influence the cell. Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions in living cells. The BiFC assay is based on the association between two nonfluorescent fragments of a fluorescent protein when they are brought in proximity to each other by an interaction between proteins fused to the fragments. Numerous protein interactions have been visualized using the BiFC assay in many different cell types and organisms. The BiFC assay is technically straightforward and can be performed using standard molecular biology and cell culture reagents and a regular fluorescence microscope or flow cytometer.

Vitamin D and colorectal cancer: molecular, epidemiological and clinical evidence.

PubMed

Dou, Ruoxu; Ng, Kimmie; Giovannucci, Edward L; Manson, JoAnn E; Qian, Zhi Rong; Ogino, Shuji

2016-05-01

In many cells throughout the body, vitamin D is converted into its active form calcitriol and binds to the vitamin D receptor (VDR), which functions as a transcription factor to regulate various biological processes including cellular differentiation and immune response. Vitamin D-metabolising enzymes (including CYP24A1 and CYP27B1) and VDR play major roles in exerting and regulating the effects of vitamin D. Preclinical and epidemiological studies have provided evidence for anti-cancer effects of vitamin D (particularly against colorectal cancer), although clinical trials have yet to prove its benefit. In addition, molecular pathological epidemiology research can provide insights into the interaction of vitamin D with tumour molecular and immunity status. Other future research directions include genome-wide research on VDR transcriptional targets, gene-environment interaction analyses and clinical trials on vitamin D efficacy in colorectal cancer patients. In this study, we review the literature on vitamin D and colorectal cancer from both mechanistic and population studies and discuss the links and controversies within and between the two parts of evidence.

The Tbr2 Molecular Network Controls Cortical Neuronal Differentiation Through Complementary Genetic and Epigenetic Pathways.

PubMed

Sessa, Alessandro; Ciabatti, Ernesto; Drechsel, Daniela; Massimino, Luca; Colasante, Gaia; Giannelli, Serena; Satoh, Takashi; Akira, Shizuo; Guillemot, Francois; Broccoli, Vania

2017-06-01

The T-box containing Tbr2 gene encodes for a transcription factor essential for the specification of the intermediate neural progenitors (INPs) originating the excitatory neurons of the cerebral cortex. However, its overall mechanism of action, direct target genes and cofactors remain unknown. Herein, we carried out global gene expression profiling combined with genome-wide binding site identification to determine the molecular pathways regulated by TBR2 in INPs. This analysis led to the identification of novel protein-protein interactions that control multiple features of INPs including cell-type identity, morphology, proliferation and migration dynamics. In particular, NEUROG2 and JMJD3 were found to associate with TBR2 revealing unexplored TBR2-dependent mechanisms. These interactions can explain, at least in part, the role of this transcription factor in the implementation of the molecular program controlling developmental milestones during corticogenesis. These data identify TBR2 as a major determinant of the INP-specific traits by regulating both genetic and epigenetic pathways. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Soft matter interactions at the molecular scale: interaction forces and energies between single hydrophobic model peptides.

PubMed

Stock, Philipp; Utzig, Thomas; Valtiner, Markus

2017-02-08

In all realms of soft matter research a fundamental understanding of the structure/property relationships based on molecular interactions is crucial for developing a framework for the targeted design of soft materials. However, a molecular picture is often difficult to ascertain and yet essential for understanding the many different competing interactions at play, including entropies and cooperativities, hydration effects, and the enormous design space of soft matter. Here, we characterized for the first time the interaction between single hydrophobic molecules quantitatively using atomic force microscopy, and demonstrated that single molecular hydrophobic interaction free energies are dominated by the area of the smallest interacting hydrophobe. The interaction free energy amounts to 3-4 kT per hydrophobic unit. Also, we find that the transition state of the hydrophobic interactions is located at 3 Å with respect to the ground state, based on Bell-Evans theory. Our results provide a new path for understanding the nature of hydrophobic interactions at the single molecular scale. Our approach enables us to systematically vary hydrophobic and any other interaction type by utilizing peptide chemistry providing a strategic advancement to unravel molecular surface and soft matter interactions at the single molecular scale.

Molecular-dynamics Simulation-based Cohesive Zone Representation of Intergranular Fracture Processes in Aluminum

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin I.; Saether, Erik; Phillips, Dawn R.; Glaessgen, Edward H.

2006-01-01

A traction-displacement relationship that may be embedded into a cohesive zone model for microscale problems of intergranular fracture is extracted from atomistic molecular-dynamics simulations. A molecular-dynamics model for crack propagation under steady-state conditions is developed to analyze intergranular fracture along a flat 99 [1 1 0] symmetric tilt grain boundary in aluminum. Under hydrostatic tensile load, the simulation reveals asymmetric crack propagation in the two opposite directions along the grain boundary. In one direction, the crack propagates in a brittle manner by cleavage with very little or no dislocation emission, and in the other direction, the propagation is ductile through the mechanism of deformation twinning. This behavior is consistent with the Rice criterion for cleavage vs. dislocation blunting transition at the crack tip. The preference for twinning to dislocation slip is in agreement with the predictions of the Tadmor and Hai criterion. A comparison with finite element calculations shows that while the stress field around the brittle crack tip follows the expected elastic solution for the given boundary conditions of the model, the stress field around the twinning crack tip has a strong plastic contribution. Through the definition of a Cohesive-Zone-Volume-Element an atomistic analog to a continuum cohesive zone model element - the results from the molecular-dynamics simulation are recast to obtain an average continuum traction-displacement relationship to represent cohesive zone interaction along a characteristic length of the grain boundary interface for the cases of ductile and brittle decohesion. Keywords: Crack-tip plasticity; Cohesive zone model; Grain boundary decohesion; Intergranular fracture; Molecular-dynamics simulation

Probing the energetics of organic–nanoparticle interactions of ethanol on calcite

DOE PAGES

Wu, Di; Navrotsky, Alexandra

2015-04-13

Knowing the nature of interactions between small organic molecules and surfaces of nanoparticles (NP) is crucial for fundamental understanding of natural phenomena and engineering processes. In this paper, we report direct adsorption enthalpy measurement of ethanol on a series of calcite nanocrystals, with the aim of mimicking organic–NP interactions in various environments. The energetics suggests a spectrum of adsorption events as a function of coverage: strongest initial chemisorption on active sites on fresh calcite surfaces, followed by major chemical binding to form an ethanol monolayer and, subsequently, very weak, near-zero energy, physisorption. Furthermore, these thermochemical observations directly support a structuremore » where the ethanol monolayer is bonded to the calcite surface through its polar hydroxyl group, leaving the hydrophobic ends of the ethanol molecules to interact only weakly with the next layer of adsorbing ethanol and resulting in a spatial gap with low ethanol density between the monolayer and subsequent added ethanol molecules, as predicted by molecular dynamics and density functional calculations. Such an ordered assembly of ethanol on calcite NP is analogous to, although less strongly bonded than, a capping layer of organics intentionally introduced during NP synthesis, and suggests a continuous variation of surface structure depending on molecular chemistry, ranging from largely disordered surface layers to ordered layers that nevertheless are mobile and can rearrange or be displaced by other molecules to strongly bonded immobile organic capping layers. Finally, these differences in surface structure will affect chemical reactions, including the further nucleation and growth of nanocrystals on organic ligand-capped surfaces.« less

p62/Sequestosome-1, Autophagy-related Gene 8, and Autophagy in Drosophila Are Regulated by Nuclear Factor Erythroid 2-related Factor 2 (NRF2), Independent of Transcription Factor TFEB.

PubMed

Jain, Ashish; Rusten, Tor Erik; Katheder, Nadja; Elvenes, Julianne; Bruun, Jack-Ansgar; Sjøttem, Eva; Lamark, Trond; Johansen, Terje

2015-06-12

The selective autophagy receptor p62/sequestosome 1 (SQSTM1) interacts directly with LC3 and is involved in oxidative stress signaling in two ways in mammals. First, p62 is transcriptionally induced upon oxidative stress by the NF-E2-related factor 2 (NRF2) by direct binding to an antioxidant response element in the p62 promoter. Second, p62 accumulation, occurring when autophagy is impaired, leads to increased p62 binding to the NRF2 inhibitor KEAP1, resulting in reduced proteasomal turnover of NRF2. This gives chronic oxidative stress signaling through a feed forward loop. Here, we show that the Drosophila p62/SQSTM1 orthologue, Ref(2)P, interacts directly with DmAtg8a via an LC3-interacting region motif, supporting a role for Ref(2)P in selective autophagy. The ref(2)P promoter also contains a functional antioxidant response element that is directly bound by the NRF2 orthologue, CncC, which can induce ref(2)P expression along with the oxidative stress-associated gene gstD1. However, distinct from the situation in mammals, Ref(2)P does not interact directly with DmKeap1 via a KEAP1-interacting region motif; nor does ectopically expressed Ref(2)P or autophagy deficiency activate the oxidative stress response. Instead, DmAtg8a interacts directly with DmKeap1, and DmKeap1 is removed upon programmed autophagy in Drosophila gut cells. Strikingly, CncC induced increased Atg8a levels and autophagy independent of TFEB/MitF in fat body and larval gut tissues. Thus, these results extend the intimate relationship between oxidative stress-sensing NRF2/CncC transcription factors and autophagy and suggest that NRF2/CncC may regulate autophagic activity in other organisms too. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Rational Design of Charge-Transfer Interactions in Halogen-Bonded Co-crystals toward Versatile Solid-State Optoelectronics.

PubMed

Zhu, Weigang; Zheng, Renhui; Zhen, Yonggang; Yu, Zhenyi; Dong, Huanli; Fu, Hongbing; Shi, Qiang; Hu, Wenping

2015-09-02

Charge-transfer (CT) interactions between donor (D) and acceptor (A) groups, as well as CT exciton dynamics, play important roles in optoelectronic devices, such as organic solar cells, photodetectors, and light-emitting sources, which are not yet well understood. In this contribution, the self-assembly behavior, molecular stacking structure, CT interactions, density functional theory (DFT) calculations, and corresponding physicochemical properties of two similar halogen-bonded co-crystals are comprehensively investigated and compared, to construct an "assembly-structure-CT-property" relationship. Bpe-IFB wire-like crystals (where Bpe = 1,2-bis(4-pyridyl)ethylene and IFB = 1,3,5-trifluoro-2,4,6-triiodobenzene), packed in a segregated stacking form with CT ground and excited states, are measured to be quasi-one-dimensional (1D) semiconductors and show strong violet-blue photoluminescence (PL) from the lowest CT1 excitons (ΦPL = 26.1%), which can be confined and propagate oppositely along the 1D axial direction. In comparison, Bpe-F4DIB block-like crystals (F4DIB = 1,4-diiodotetrafluorobenzene), packed in a mixed stacking form without CT interactions, are determined to be insulators and exhibit unique white light emission and two-dimensional optical waveguide property. Surprisingly, it seems that the intrinsic spectroscopic states of Bpe and F4DIB do not change after co-crystallization, which is also confirmed by theoretical calculations, thus offering a new design principle for white light emitting materials. More importantly, we show that the CT interactions in co-crystals are related to their molecular packing and can be triggered or suppressed by crystal engineering, which eventually leads to distinct optoelectronic properties. These results help us to rationally control the CT interactions in organic D-A systems by tuning the molecular stacking, toward the development of a fantastic "optoelectronic world".

Exploring the molecular mechanisms of electron shuttling across the microbe/metal space

PubMed Central

Paquete, Catarina M.; Fonseca, Bruno M.; Cruz, Davide R.; Pereira, Tiago M.; Pacheco, Isabel; Soares, Cláudio M.; Louro, Ricardo O.

2014-01-01

Dissimilatory metal reducing organisms play key roles in the biogeochemical cycle of metals as well as in the durability of submerged and buried metallic structures. The molecular mechanisms that support electron transfer across the microbe-metal interface in these organisms remain poorly explored. It is known that outer membrane proteins, in particular multiheme cytochromes, are essential for this type of metabolism, being responsible for direct and indirect, via electron shuttles, interaction with the insoluble electron acceptors. Soluble electron shuttles such as flavins, phenazines, and humic acids are known to enhance extracellular electron transfer. In this work, this phenomenon was explored. All known outer membrane decaheme cytochromes from Shewanella oneidensis MR-1 with known metal terminal reductase activity and a undecaheme cytochrome from Shewanella sp. HRCR-6 were expressed and purified. Their interactions with soluble electron shuttles were studied using stopped-flow kinetics, NMR spectroscopy, and molecular simulations. The results show that despite the structural similarities, expected from the available structural data and sequence homology, the detailed characteristics of their interactions with soluble electron shuttles are different. MtrC and OmcA appear to interact with a variety of different electron shuttles in the close vicinity of some of their hemes, and with affinities that are biologically relevant for the concentrations typical found in the medium for this type of compounds. All data support a view of a distant interaction between the hemes of MtrF and the electron shuttles. For UndA a clear structural characterization was achieved for the interaction with AQDS a humic acid analog. These results provide guidance for future work of the manipulation of these proteins toward modulation of their role in metal attachment and reduction. PMID:25018753

An activation switch in the rhodopsin family of G protein-coupled receptors: the thyrotropin receptor.

PubMed

Urizar, Eneko; Claeysen, Sylvie; Deupí, Xavier; Govaerts, Cedric; Costagliola, Sabine; Vassart, Gilbert; Pardo, Leonardo

2005-04-29

We aimed at understanding molecular events involved in the activation of a member of the G protein-coupled receptor family, the thyrotropin receptor. We have focused on the transmembrane region and in particular on a network of polar interactions between highly conserved residues. Using molecular dynamics simulations and site-directed mutagenesis techniques we have identified residue Asn-7.49, of the NPxxY motif of TM 7, as a molecular switch in the mechanism of thyrotropin receptor (TSHr) activation. Asn-7.49 appears to adopt two different conformations in the inactive and active states. These two states are characterized by specific interactions between this Asn and polar residues in the transmembrane domain. The inactive gauche+ conformation is maintained by interactions with residues Thr-6.43 and Asp-6.44. Mutation of these residues into Ala increases the constitutive activity of the receptor by factors of approximately 14 and approximately 10 relative to wild type TSHr, respectively. Upon receptor activation Asn-7.49 adopts the trans conformation to interact with Asp-2.50 and a putatively charged residue that remains to be identified. In addition, the conserved Leu-2.46 of the (N/S)LxxxD motif also plays a significant role in restraining the receptor in the inactive state because the L2.46A mutation increases constitutive activity by a factor of approximately 13 relative to wild type TSHr. As residues Leu-2.46, Asp-2.50, and Asn-7.49 are strongly conserved, this molecular mechanism of TSHr activation can be extended to other members of the rhodopsin-like family of G protein-coupled receptors.

Force transduction and lipid binding in MscL: A continuum-molecular approach

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

Vanegas, Juan M.; Arroyo, Marino; Fotiadis, Dimitrios

2014-12-01

The bacterial mechanosensitive channel MscL, a small protein mainly activated by membrane tension, is a central model system to study the transduction of mechanical stimuli into chemical signals. Mutagenic studies suggest that MscL gating strongly depends on both intra-protein and interfacial lipid-protein interactions. However, there is a gap between this detailed chemical information and current mechanical models of MscL gating. Here, we investigate the MscL bilayer-protein interface through molecular dynamics simulations, and take a combined continuum-molecular approach to connect chemistry and mechanics. We quantify the effect of membrane tension on the forces acting on the surface of the channel, andmore » identify interactions that may be critical in the force transduction between the membrane and MscL. We find that the local stress distribution on the protein surface is largely asymmetric, particularly under tension, with the cytoplasmic side showing significantly larger and more localized forces, which pull the protein radially outward. The molecular interactions that mediate this behavior arise from hydrogen bonds between the electronegative oxygens in the lipid headgroup and a cluster of positively charged lysine residues on the amphipathic S1 domain and the C-terminal end of the second trans-membrane helix. We take advantage of this strong interaction (estimated to be 10–13 kT per lipid) to actuate the channel (by applying forces on protein-bound lipids) and explore its sensitivity to the pulling magnitude and direction. We conclude by highlighting the simple motif that confers MscL with strong anchoring to the bilayer, and its presence in various integral membrane proteins including the human mechanosensitive channel K2P1 and bovine rhodopsin.« less

Coordination-Driven Syntheses of Compact Supramolecular Metallacycles toward Extended Metallo-organic Stacked Supramolecular Assemblies.

PubMed

Lescop, Christophe

2017-04-18

One important concept associated with supramolecular chemistry is supramolecular self-assembly, which deals with the way discrete individual components interact via intermolecular interactions in order to build, upon their spontaneous association, high order functional assemblies. The accumulation of these very simple and localized noncovalent interactions (such as H-bonding, dipole-dipole, hydrophobic/hydrophilic, van der Waals, π-π, π-CH, etc.) is ubiquitous in the complexity of natural systems (such as DNA, proteins, membranes, micelles, etc.). It can also be transposed to the directed synthesis of intricate artificial scaffolds, which have anticipated geometries and properties. Among the synthetic strategies based on this concept, coordination-driven supramolecular chemistry uses the robust, reversible, and directional metal-to-ligand coordinative bond to build discrete metallo-supramolecular architectures. Within the last two decades, coordination-driven supramolecular chemistry has proved to be one of the most powerful contemporary synthetic approaches and has provided a significant number of increasingly complex supramolecular assemblies, which have predetermined sizes and geometries. While much focus has been devoted to architectures bearing internal cavities for host-guest chemistry or to generate specific reactivity, particular attention can also be paid to compact supramolecular assemblies given that their specific structures are characterized by peculiar synthetic guiding rules as well as by alternative long-range self-assembling properties. This Account describes how a preassembled Cu I bimetallic clip bearing short intermetallic distances can be used as a U-shaped molecular clip to give general and versatile access to a large variety of original compact supramolecular metallacycles. When this Cu I precursor is reacted with various cyano-capped ditopic linkers that have increasing lengths and complexities, specific effects guiding the selective and straightforward syntheses of such compact supramolecular objects are highlighted. Whereas a subtle compromise between the length of the ditopic linkers and the steric bulk of the molecular clip appears to be a purely stereogeometric preliminary parameter to master, lateral interlinker interactions (π-π stacking interactions or aurophilic interactions depending on the nature of the internal cores of the linkers) can circumvent these constraints regardless of the length of the linkers and allow the selective formation of new compact supramolecular structures. Generally, such derivatives presented a strong tendency to self-assemble in the solid state due to inter-supramolecule interactions. This approach thus opens a new door toward molecular materials having an attractive solid state structure for potential applications related to charge carrier mobility and luminescence properties. These compact supramolecular assemblies can therefore be considered as original secondary binding units directing the predictive preparation of such extended networks. The on-purpose design of original building blocks bearing specific cores allowed the formation of new compact supramolecular metallacycles such as "U-shaped" π-stacked assemblies or "pseudodouble paracyclophanes". Similarly, the control of the secondary structure of one-dimensional coordination polymers alternating π-stacked compact supramolecular metallacycles was also conducted. The results that are discussed in this Account illustrate how the rational design of both preassembled polymetallic precursors bearing short intermetallic distances and ditopic linkers able to induce cumulative lateral weak interactions can implement the general synthetic guiding rules of coordination driven supramolecular chemistry. This opens perspectives to use such compact supramolecular assemblies as secondary building blocks for the design of long-range organized functional molecular materials that have predictable architectures and targeted properties.

Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

PubMed

Anwar, Jamshed; Zahn, Dirk

2011-02-25

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clues for biomimetics from natural composite materials

PubMed Central

Lapidot, Shaul; Meirovitch, Sigal; Sharon, Sigal; Heyman, Arnon; Kaplan, David L; Shoseyov, Oded

2013-01-01

Bio-inspired material systems are derived from different living organisms such as plants, arthropods, mammals and marine organisms. These biomaterial systems from nature are always present in the form of composites, with molecular-scale interactions optimized to direct functional features. With interest in replacing synthetic materials with natural materials due to biocompatibility, sustainability and green chemistry issues, it is important to understand the molecular structure and chemistry of the raw component materials to also learn from their natural engineering, interfaces and interactions leading to durable and highly functional material architectures. This review will focus on applications of biomaterials in single material forms, as well as biomimetic composites inspired by natural organizational features. Examples of different natural composite systems will be described, followed by implementation of the principles underlying their composite organization into artificial bio-inspired systems for materials with new functional features for future medicine. PMID:22994958

Clues for biomimetics from natural composite materials.

PubMed

Lapidot, Shaul; Meirovitch, Sigal; Sharon, Sigal; Heyman, Arnon; Kaplan, David L; Shoseyov, Oded

2012-09-01

Bio-inspired material systems are derived from different living organisms such as plants, arthropods, mammals and marine organisms. These biomaterial systems from nature are always present in the form of composites, with molecular-scale interactions optimized to direct functional features. With interest in replacing synthetic materials with natural materials due to biocompatibility, sustainability and green chemistry issues, it is important to understand the molecular structure and chemistry of the raw component materials to also learn from their natural engineering, interfaces and interactions leading to durable and highly functional material architectures. This review will focus on applications of biomaterials in single material forms, as well as biomimetic composites inspired by natural organizational features. Examples of different natural composite systems will be described, followed by implementation of the principles underlying their composite organization into artificial bio-inspired systems for materials with new functional features for future medicine.

Nonlinear two-dimensional terahertz photon echo and rotational spectroscopy in the gas phase.

PubMed

Lu, Jian; Zhang, Yaqing; Hwang, Harold Y; Ofori-Okai, Benjamin K; Fleischer, Sharly; Nelson, Keith A

2016-10-18

Ultrafast 2D spectroscopy uses correlated multiple light-matter interactions for retrieving dynamic features that may otherwise be hidden under the linear spectrum; its extension to the terahertz regime of the electromagnetic spectrum, where a rich variety of material degrees of freedom reside, remains an experimental challenge. We report a demonstration of ultrafast 2D terahertz spectroscopy of gas-phase molecular rotors at room temperature. Using time-delayed terahertz pulse pairs, we observe photon echoes and other nonlinear signals resulting from molecular dipole orientation induced by multiple terahertz field-dipole interactions. The nonlinear time domain orientation signals are mapped into the frequency domain in 2D rotational spectra that reveal J-state-resolved nonlinear rotational dynamics. The approach enables direct observation of correlated rotational transitions and may reveal rotational coupling and relaxation pathways in the ground electronic and vibrational state.

Structural Analysis of Chemokine Receptor–Ligand Interactions

PubMed Central

2017-01-01

This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors. PMID:28165741

Vitamin E: A Role in Signal Transduction.

PubMed

Zingg, Jean-Marc

2015-01-01

Vitamin E modulates the activity of several signal transduction enzymes with consequent alterations of gene expression. At the molecular level, vitamin E may directly bind to these enzymes and compete with their substrates, or it may change their activity by redox regulation. The translocation of several of these enzymes to the plasma membrane is regulated by vitamin E, suggesting the modulation of protein-membrane interactions as a common mechanism for vitamin E action. Enzyme-membrane interactions can be affected by vitamin E by interference with binding to specific membrane lipids or by altering cellular structures such as membrane microdomains (lipid rafts). Moreover, competition by vitamin E for common binding sites within lipid transport proteins may alter the traffic of lipid mediators and thus affect their signaling and enzymatic conversion. In this review, the main effects of vitamin E on enzymes involved in signal transduction are summarized and possible molecular mechanisms leading to enzyme modulation are evaluated.

Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions.

PubMed

Wong, Hon Lun; Ahmed-Cox, Aria; Burns, Brendan Paul

2016-01-05

Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S'Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems.

Emerging applications of label-free optical biosensors

NASA Astrophysics Data System (ADS)

Zanchetta, Giuliano; Lanfranco, Roberta; Giavazzi, Fabio; Bellini, Tommaso; Buscaglia, Marco

2017-01-01

Innovative technical solutions to realize optical biosensors with improved performance are continuously proposed. Progress in material fabrication enables developing novel substrates with enhanced optical responses. At the same time, the increased spectrum of available biomolecular tools, ranging from highly specific receptors to engineered bioconjugated polymers, facilitates the preparation of sensing surfaces with controlled functionality. What remains often unclear is to which extent this continuous innovation provides effective breakthroughs for specific applications. In this review, we address this challenging question for the class of label-free optical biosensors, which can provide a direct signal upon molecular binding without using secondary probes. Label-free biosensors have become a consolidated approach for the characterization and screening of molecular interactions in research laboratories. However, in the last decade, several examples of other applications with high potential impact have been proposed. We review the recent advances in label-free optical biosensing technology by focusing on the potential competitive advantage provided in selected emerging applications, grouped on the basis of the target type. In particular, direct and real-time detection allows the development of simpler, compact, and rapid analytical methods for different kinds of targets, from proteins to DNA and viruses. The lack of secondary interactions facilitates the binding of small-molecule targets and minimizes the perturbation in single-molecule detection. Moreover, the intrinsic versatility of label-free sensing makes it an ideal platform to be integrated with biomolecular machinery with innovative functionality, as in case of the molecular tools provided by DNA nanotechnology.

Direct interaction of Ski with either Smad3 or Smad4 is necessary and sufficient for Ski-mediated repression of transforming growth factor-beta signaling.

PubMed

Ueki, Nobuhide; Hayman, Michael J

2003-08-29

The oncoprotein Ski represses transforming growth factor (TGF)-beta signaling in an N-CoR-independent manner. However, the molecular mechanism(s) underlying this event has not been elucidated. Here, we identify an additional domain in Ski that mediates interaction with Smad3 which is important for this repression. This domain is distinct from the previously reported N-terminal Smad3 binding domain in Ski. Individual alanine substitution of several residues in the domain significantly affected Ski-Smad3 interaction. Furthermore, combined mutations within this domain, together with those in the previously identified Smad3 binding domain, can completely abolish the interaction of Ski with Smad3, while mutation in each domain alone retained partial interaction. By introducing those mutations that abolish direct interaction with Smad3 or Smad4 individually, or in combination, we show that interaction of Ski with either Smad3 or Smad4 is sufficient for Ski-mediated repression of TGF-beta signaling. Furthermore our results clearly demonstrate that Ski does not disrupt Smad3-Smad4 heteromer formation, and recruitment of Ski to the Smad3/4 complex through binding to either Smad3 or Smad4 is both necessary and sufficient for repression.

Molecular Level Characterization of the Structure and Interactions in Peptide-Functionalized Metal-Organic Frameworks.

PubMed

Todorova, Tanya K; Rozanska, Xavier; Gervais, Christel; Legrand, Alexandre; Ho, Linh N; Berruyer, Pierrick; Lesage, Anne; Emsley, Lyndon; Farrusseng, David; Canivet, Jérôme; Mellot-Draznieks, Caroline

2016-11-07

We use density functional theory, newly parameterized molecular dynamics simulations, and last generation 15 N dynamic nuclear polarization surface enhanced solid-state NMR spectroscopy (DNP SENS) to understand graft-host interactions and effects imposed by the metal-organic framework (MOF) host on peptide conformations in a peptide-functionalized MOF. Focusing on two grafts typified by MIL-68-proline (-Pro) and MIL-68-glycine-proline (-Gly-Pro), we identified the most likely peptide conformations adopted in the functionalized hybrid frameworks. We found that hydrogen bond interactions between the graft and the surface hydroxyl groups of the MOF are essential in determining the peptides conformation(s). DNP SENS methodology shows unprecedented signal enhancements when applied to these peptide-functionalized MOFs. The calculated chemical shifts of selected MIL-68-NH-Pro and MIL-68-NH-Gly-Pro conformations are in a good agreement with the experimentally obtained 15 N NMR signals. The study shows that the conformations of peptides when grafted in a MOF host are unlikely to be freely distributed, and conformational selection is directed by strong host-guest interactions. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database

PubMed Central

Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E.

2017-01-01

The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed. PMID:27915230

A sensory complex consisting of an ATP-binding cassette transporter and a two-component regulatory system controls bacitracin resistance in Bacillus subtilis.

PubMed

Dintner, Sebastian; Heermann, Ralf; Fang, Chong; Jung, Kirsten; Gebhard, Susanne

2014-10-03

Resistance against antimicrobial peptides in many Firmicutes bacteria is mediated by detoxification systems that are composed of a two-component regulatory system (TCS) and an ATP-binding cassette (ABC) transporter. The histidine kinases of these systems depend entirely on the transporter for sensing of antimicrobial peptides, suggesting a novel mode of signal transduction where the transporter constitutes the actual sensor. The aim of this study was to investigate the molecular mechanisms of this unusual signaling pathway in more detail, using the bacitracin resistance system BceRS-BceAB of Bacillus subtilis as an example. To analyze the proposed communication between TCS and the ABC transporter, we characterized their interactions by bacterial two-hybrid analyses and could show that the permease BceB and the histidine kinase BceS interact directly. In vitro pulldown assays confirmed this interaction, which was found to be independent of bacitracin. Because it was unknown whether BceAB-type transporters could detect their substrate peptides directly or instead recognized the peptide-target complex in the cell envelope, we next analyzed substrate binding by the transport permease, BceB. Direct and specific binding of bacitracin by BceB was demonstrated by surface plasmon resonance spectroscopy. Finally, in vitro signal transduction assays indicated that complex formation with the transporter influenced the autophosphorylation activity of the histidine kinase. Taken together, our findings clearly show the existence of a sensory complex composed of TCS and ABC transporters and provide the first functional insights into the mechanisms of stimulus perception, signal transduction, and antimicrobial resistance employed by Bce-like detoxification systems. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Hydrogen bonding interactions and supramolecular assemblies in 2-amino guanidinium 4-methyl benzene sulphonate crystal structure: Hirshfeld surfaces and computational calculations

NASA Astrophysics Data System (ADS)

Muthuraja, P.; Joselin Beaula, T.; Balachandar, S.; Bena Jothy, V.; Dhandapani, M.

2017-10-01

2-aminoguanidinium 4-methyl benzene sulphonate (AGMS), an organic compound with big assembly of hydrogen bonding interactions was crystallized at room temperature. The structure of the compound was confirmed by FT-IR, NMR and single crystal X-ray diffraction analysis. Numerous hydrogen bonded interactions were found to form supramolecular assemblies in the molecular structure. Fingerprint plots of Hirshfeld surface analysis spells out the interactions in various directions. The molecular structure of AGMS was optimised by HF, MP2 and DFT (B3LYP and CAM-B3LYP) methods at 6-311G (d,p) basis set and the geometrical parameters were compared. Electrostatic potential calculations of the reactants and product confirm the transfer of proton. Optical properties of AGMS were ascertained by UV-Vis absorbance and reflectance spectra. The band gap of AGMS is found to be 2.689 eV. Due to numerous hydrogen bonds, the crystal is thermally stable up to 200 °C. Hyperconjugative interactions which are responsible for the second hyperpolarizabilities were accounted by NBO analysis. Static and frequency dependent optical properties were calculated at HF and DFT methods. The hyperpolarizabilities of AGMS increase rapidly at frequencies 0.0428 and 0.08 a.u. compared to static one. The compound exhibits violet and blue emission.

Membrane proteins from the cyanobacterium Synechocystis sp. PCC 6803 interacting with thioredoxin.

PubMed

Mata-Cabana, Alejandro; Florencio, Francisco J; Lindahl, Marika

2007-11-01

Cysteine dithiol/disulphide exchange forms the molecular basis for regulation of a wide variety of enzymatic activities and for transduction of cellular signals. Thus, the search for proteins with reactive, accessible cysteines is expected to contribute to the unravelling of new molecular mechanisms for enzyme regulation and signal transduction. Several methods have been designed for this purpose taking advantage of the interactions between thioredoxins and their protein substrates. Thioredoxins comprise a family of redox-active enzymes, which catalyse reduction of protein disulphides and sulphenic acids. Due to the inherent practical difficulties associated with studies of membrane proteins these have been largely overlooked in the many proteomic studies of thioredoxin-interacting proteins. In the present work, we have developed a procedure to isolate membrane proteins interacting with thioredoxin by binding in situ to a monocysteinic His-tagged thioredoxin added directly to the intact membranes. Following fractionation and solubilisation of the membranes, thioredoxin target proteins were isolated by Ni-affinity chromatography and 2-DE SDS-PAGE under nonreducing/reducing conditions. Applying this method to total membranes, including thylakoid and plasma membranes, from the cyanobacterium Synechocystis sp. PCC 6803 we have identified 50 thioredoxin-interacting proteins. Among the 38 newly identified thioredoxin targets are the ATP-binding subunits of several transporters and members of the AAA-family of ATPases.

Hybrid molecular-colloidal liquid crystals.

PubMed

Mundoor, Haridas; Park, Sungoh; Senyuk, Bohdan; Wensink, Henricus H; Smalyukh, Ivan I

2018-05-18

Order and fluidity often coexist, with examples ranging from biological membranes to liquid crystals, but the symmetry of these soft-matter systems is typically higher than that of the constituent building blocks. We dispersed micrometer-long inorganic colloidal rods in a nematic liquid crystalline fluid of molecular rods. Both types of uniaxial building blocks, while freely diffusing, interact to form an orthorhombic nematic fluid, in which like-sized rods are roughly parallel to each other and the molecular ordering direction is orthogonal to that of colloidal rods. A coarse-grained model explains the experimental temperature-concentration phase diagram with one biaxial and two uniaxial nematic phases, as well as the orientational distributions of rods. Displaying properties of biaxial optical crystals, these hybrid molecular-colloidal fluids can be switched by electric and magnetic fields. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

In vivo nanoparticle-mediated radiopharmaceutical-excited fluorescence molecular imaging

PubMed Central

Hu, Zhenhua; Qu, Yawei; Wang, Kun; Zhang, Xiaojun; Zha, Jiali; Song, Tianming; Bao, Chengpeng; Liu, Haixiao; Wang, Zhongliang; Wang, Jing; Liu, Zhongyu; Liu, Haifeng; Tian, Jie

2015-01-01

Cerenkov luminescence imaging utilizes visible photons emitted from radiopharmaceuticals to achieve in vivo optical molecular-derived signals. Since Cerenkov radiation is weak, non-optimum for tissue penetration and continuous regardless of biological interactions, it is challenging to detect this signal with a diagnostic dose. Therefore, it is challenging to achieve useful activated optical imaging for the acquisition of direct molecular information. Here we introduce a novel imaging strategy, which converts γ and Cerenkov radiation from radioisotopes into fluorescence through europium oxide nanoparticles. After a series of imaging studies, we demonstrate that this approach provides strong optical signals with high signal-to-background ratios, an ideal tissue penetration spectrum and activatable imaging ability. In comparison with present imaging techniques, it detects tumour lesions with low radioactive tracer uptake or small tumour lesions more effectively. We believe it will facilitate the development of nuclear and optical molecular imaging for new, highly sensitive imaging applications. PMID:26123615

Insights into the interfacial strengthening mechanisms of calcium-silicate-hydrate/polymer nanocomposites.

PubMed

Zhou, Yang; Hou, Dongshuai; Geng, Guoqing; Feng, Pan; Yu, Jiao; Jiang, Jinyang

2018-03-28

The mechanical properties of organic/inorganic composites can be highly dependent on the interfacial interactions. In this work, with organic polymers intercalated into the interlayer of inorganic calcium silicate hydrate (C-S-H), the primary binding phase of Portland cement, great ductility improvement is obtained for the nanocomposites. Employing reactive molecular dynamics, the simulation results indicate that strong interfacial interactions between the polymers and the substrate contribute greatly to strengthening the materials, when C-S-H/poly ethylene glycol (PEG), C-S-H/poly acrylic acid (PAA), and C-S-H/poly vinyl alcohol (PVA) were subject to uniaxial tension along different lattice directions. In the x and z direction tensile processes, the Si-OCa bonds of the C-S-H gel, which were elongated and broken to form Si-OH and Ca-OH, play a critical role in loading resistance, while the incorporation of polymers bridged the neighboring silicate sheets, and activated more the hydrolytic reactions at the interfaces to avoid strain localization, thus increasing the tensile strength and postponing the fracture. On the other hand, Si-O-Si bonds of C-S-H mainly take the load when tension was applied along the y direction. During the post-yield stage, rearrangements of silicate tetrahedra occurred to prevent rapid damage. The polymer intercalation further elongates this post-yield period by forming interfacial Si-O-C bonds, which promote rearrangements and improve the connectivity of the defective silicate morphology, significantly improving the ductility. Among the polymers, PEG exhibits the strongest interaction with C-S-H, and thus C-S-H/PEG possesses the highest ductility. We expect that the molecular-scale mechanisms interpreted here will shed new light on the stress-activated chemical interactions at the organic/inorganic interfaces, and help eliminate the brittleness of cement-based materials on a genetic level.

Crystal structures of (2E)-1-(3-bromo-thio-phen-2-yl)-3-(2-meth-oxy-phen-yl)prop-2-en-1-one and (2E)-1-(3-bromo-thio-phen-2-yl)-3-(3,4-di-meth-oxy-phen-yl)prop-2-en-1-one.

PubMed

Naik, Vasant S; Shettigar, Venkataraya; Berglin, Tyler S; Coburn, Jillian S; Jasinski, Jerry P; Yathirajan, Hemmige S

2015-08-01

In the mol-ecules of the title compounds, (2E)-1-(3-bromo-thio-phen-2-yl)-3-(2-meth-oxy-phen-yl)prop-2-en-1-one, C14H11BrO2S, (I), which crystallizes in the space group P-1 with four independent mol-ecules in the asymmetric unit (Z' = 8), and (2E)-1-(3-bromo-thio-phen-2-yl)-3-(3,4-di-meth-oxy-phen-yl)prop-2-en-1-one, C15H13BrO3S, (II), which crystallizes with Z' = 8 in the space group I2/a, the non-H atoms are nearly coplanar. The mol-ecules of (I) pack with inversion symmetry stacked diagonally along the a-axis direction. Weak C-H⋯Br intra-molecular inter-actions in each of the four mol-ecules in the asymmetric unit are observed. In (II), weak C-H⋯O, bifurcated three-center inter-molecular inter-actions forming dimers along with weak C-H⋯π and π-π stacking inter-actions are observed, linking the mol-ecules into sheets along [001]. A weak C-H⋯Br intra-molecular inter-action is also present. There are no classical hydrogen bonds present in either structure.

Binding site exploration of CCR5 using in silico methodologies: a 3D-QSAR approach.

PubMed

Gadhe, Changdev G; Kothandan, Gugan; Cho, Seung Joo

2013-01-01

Chemokine receptor 5 (CCR5) is an important receptor used by human immunodeficiency virus type 1 (HIV-1) to gain viral entry into host cell. In this study, we used a combined approach of comparative modeling, molecular docking, and three dimensional quantitative structure activity relationship (3D-QSAR) analyses to elucidate detailed interaction of CCR5 with their inhibitors. Docking study of the most potent inhibitor from a series of compounds was done to derive the bioactive conformation. Parameters such as random selection, rational selection, different charges and grid spacing were utilized in the model development to check their performance on the model predictivity. Final comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were chosen based on the rational selection method, Gasteiger-Hückel charges and a grid spacing of 0.5 Å. Rational model for CoMFA (q(2) = 0.722, r(2) = 0.884, Q(2) = 0.669) and CoMSIA (q(2) = 0.712, r(2) = 0.825, Q(2) = 0.522) was obtained with good statistics. Mapping of contour maps onto CCR5 interface led us to better understand of the ligand-protein interaction. Docking analysis revealed that the Glu283 is crucial for interaction. Two new amino acid residues, Tyr89 and Thr167 were identified as important in ligand-protein interaction. No site directed mutagenesis studies on these residues have been reported.

Modeling of molecular diffusion and thermal conduction with multi-particle interaction in compressible turbulence

NASA Astrophysics Data System (ADS)

Tai, Y.; Watanabe, T.; Nagata, K.

2018-03-01

A mixing volume model (MVM) originally proposed for molecular diffusion in incompressible flows is extended as a model for molecular diffusion and thermal conduction in compressible turbulence. The model, established for implementation in Lagrangian simulations, is based on the interactions among spatially distributed notional particles within a finite volume. The MVM is tested with the direct numerical simulation of compressible planar jets with the jet Mach number ranging from 0.6 to 2.6. The MVM well predicts molecular diffusion and thermal conduction for a wide range of the size of mixing volume and the number of mixing particles. In the transitional region of the jet, where the scalar field exhibits a sharp jump at the edge of the shear layer, a smaller mixing volume is required for an accurate prediction of mean effects of molecular diffusion. The mixing time scale in the model is defined as the time scale of diffusive effects at a length scale of the mixing volume. The mixing time scale is well correlated for passive scalar and temperature. Probability density functions of the mixing time scale are similar for molecular diffusion and thermal conduction when the mixing volume is larger than a dissipative scale because the mixing time scale at small scales is easily affected by different distributions of intermittent small-scale structures between passive scalar and temperature. The MVM with an assumption of equal mixing time scales for molecular diffusion and thermal conduction is useful in the modeling of the thermal conduction when the modeling of the dissipation rate of temperature fluctuations is difficult.

Cell biochemistry studied by single-molecule imaging.

PubMed

Mashanov, G I; Nenasheva, T A; Peckham, M; Molloy, J E

2006-11-01

Over the last decade, there have been remarkable developments in live-cell imaging. We can now readily observe individual protein molecules within living cells and this should contribute to a systems level understanding of biological pathways. Direct observation of single fluorophores enables several types of molecular information to be gathered. Temporal and spatial trajectories enable diffusion constants and binding kinetics to be deduced, while analyses of fluorescence lifetime, intensity, polarization or spectra give chemical and conformational information about molecules in their cellular context. By recording the spatial trajectories of pairs of interacting molecules, formation of larger molecular complexes can be studied. In the future, multicolour and multiparameter imaging of single molecules in live cells will be a powerful analytical tool for systems biology. Here, we discuss measurements of single-molecule mobility and residency at the plasma membrane of live cells. Analysis of diffusional paths at the plasma membrane gives information about its physical properties and measurement of temporal trajectories enables rates of binding and dissociation to be derived. Meanwhile, close scrutiny of individual fluorophore trajectories enables ideas about molecular dimerization and oligomerization related to function to be tested directly.

Direct Interaction between the WD40 Repeat Protein WDR-23 and SKN-1/Nrf Inhibits Binding to Target DNA

PubMed Central

Leung, Chi K.; Hasegawa, Koichi; Wang, Ying; Deonarine, Andrew; Tang, Lanlan; Miwa, Johji

2014-01-01

SKN-1/Nrf transcription factors activate cytoprotective genes in response to reactive small molecules and strongly influence stress resistance, longevity, and development. The molecular mechanisms of SKN-1/Nrf regulation are poorly defined. We previously identified the WD40 repeat protein WDR-23 as a repressor of Caenorhabditis elegans SKN-1 that functions with a ubiquitin ligase to presumably target the factor for degradation. However, SKN-1 activity and nuclear accumulation are not always correlated, suggesting that there could be additional regulatory mechanisms. Here, we integrate forward genetics and biochemistry to gain insights into how WDR-23 interacts with and regulates SKN-1. We provide evidence that WDR-23 preferentially regulates one of three SKN-1 variants through a direct interaction that is required for normal stress resistance and development. Homology modeling predicts that WDR-23 folds into a β-propeller, and we identify the top of this structure and four motifs at the termini of SKN-1c as essential for the interaction. Two of these SKN-1 motifs are highly conserved in human Nrf1 and Nrf2 and two directly interact with target DNA. Lastly, we demonstrate that WDR-23 can block the ability of SKN-1c to interact with DNA sequences of target promoters identifying a new mechanism of regulation that is independent of the ubiquitin proteasome system, which can become occupied with damaged proteins during stress. PMID:24912676

Molecular Modeling, Docking, Dynamics and simulation of Gefitinib and its derivatives with EGFR in Non-Small Cell Lung Cancer.

PubMed

Reddy, Pulakuntla Swetha; Lokhande, Kiran Bharat; Nagar, Shuchi; Reddy, Vaddi Damodara; Murthy, P Sushma; Swamy, K Venkateswara

2018-02-27

Gefitinib (lressa) is the most prescribed drug, highly effective to treat of non-small cell lung cancer; primarily it was considered targeted therapy is a kinase inhibitor. The non-small cell lung cancer caused by the mutation in the Epithelial Growth Factor Receptor (EGFR) gene, Iressa works by blocking the EGFR protein that helps the cancer cell growth. EGFR protein has lead to the development of anticancer therapeutics directed against EGFR inhibitor including Gefitinib for non-small cell lung cancer. To explore research on Gefitinib and its derivatives interaction with crystal structure EGFR to understand the better molecular insights interaction strategies. Molecular modeling of ligands (Gefitinib and its derivatives) was carried out by Avogadro software till atomic angle stable confirmation obtained. The partial charges for the ligands were assigned as per standard protocol for molecular docking. All docking simulations were performed with AutoDockVina. Virtual screening carried out based on binding energy and hydrogen bonding affinity. Molecular dynamics (MD) and Simulation EGFR was done using GROMACS 5.1.1 software to explore the interaction stability in a cell. The stable conformation for EGFR protein trajectories were captured at various time intervals 0-20ns. Few compounds screen based on high affinity as the inhibitor for EGFR may inhibit the cell cycle signalling in non-small cell lung cancer. These result suggested that a computer aided screening approach of a Gefitinib derivatives compounds with regard to their binding to EGFR for identifying novel drugs for the treatment of non-small cell lung cancer. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Molecular Modeling of Thermodynamic and Transport Properties for CO 2 and Aqueous Brines

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

Jiang, Hao; Economou, Ioannis G.; Panagiotopoulos, Athanassios Z.

Molecular simulation techniques using classical force-fields occupy the space between ab initio quantum mechanical methods and phenomenological correlations. In particular, Monte Carlo and molecular dynamics algorithms can be used to provide quantitative predictions of thermodynamic and transport properties of fluids relevant for geologic carbon sequestration at conditions for which experimental data are uncertain or not available. These methods can cover time and length scales far exceeding those of quantum chemical methods, while maintaining transferability and predictive power lacking from phenomenological correlations. The accuracy of predictions depends sensitively on the quality of the molecular models used. Many existing fixed-point-charge models formore » water and aqueous mixtures fail to represent accurately these fluid properties, especially when descriptions covering broad ranges of thermodynamic conditions are needed. Recent work on development of accurate models for water, CO 2, and dissolved salts, as well as their mixtures, is summarized in this Account. Polarizable models that can respond to the different dielectric environments in aqueous versus nonaqueous phases are necessary for predictions of properties over extended ranges of temperatures and pressures. Phase compositions and densities, activity coefficients of the dissolved salts, interfacial tensions, viscosities and diffusivities can be obtained in near-quantitative agreement to available experimental data, using relatively modest computational resources. In some cases, for example, for the composition of the CO 2-rich phase in coexistence with an aqueous phase, recent results from molecular simulations have helped discriminate among conflicting experimental data sets. The sensitivity of properties on the quality of the intermolecular interaction model varies significantly. Properties such as the phase compositions or electrolyte activity coefficients are much more sensitive than phase densities, viscosities, or component diffusivities. Strong confinement effects on physical properties in nanoscale media can also be directly obtained from molecular simulations. Future work on molecular modeling for CO 2 and aqueous brines is likely to be focused on more systematic generation of interaction models by utilizing quantum chemical as well as direct experimental measurements. New ion models need to be developed for use with the current generation of polarizable water models, including ion–ion interactions that will allow for accurate description of dense, mixed brines. Methods will need to be devised that go beyond the use of effective potentials for incorporation of quantum effects known to be important for water, and reactive force fields developed that can handle bond creation and breaking in systems with carbonate and silicate minerals. Lastly, another area of potential future work is the integration of molecular simulation methods in multiscale models for the chemical reactions leading to mineral dissolution and flow within the porous media in underground formations.« less

Molecular Modeling of Thermodynamic and Transport Properties for CO2 and Aqueous Brines.

PubMed

Jiang, Hao; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

2017-04-18

Molecular simulation techniques using classical force-fields occupy the space between ab initio quantum mechanical methods and phenomenological correlations. In particular, Monte Carlo and molecular dynamics algorithms can be used to provide quantitative predictions of thermodynamic and transport properties of fluids relevant for geologic carbon sequestration at conditions for which experimental data are uncertain or not available. These methods can cover time and length scales far exceeding those of quantum chemical methods, while maintaining transferability and predictive power lacking from phenomenological correlations. The accuracy of predictions depends sensitively on the quality of the molecular models used. Many existing fixed-point-charge models for water and aqueous mixtures fail to represent accurately these fluid properties, especially when descriptions covering broad ranges of thermodynamic conditions are needed. Recent work on development of accurate models for water, CO 2 , and dissolved salts, as well as their mixtures, is summarized in this Account. Polarizable models that can respond to the different dielectric environments in aqueous versus nonaqueous phases are necessary for predictions of properties over extended ranges of temperatures and pressures. Phase compositions and densities, activity coefficients of the dissolved salts, interfacial tensions, viscosities and diffusivities can be obtained in near-quantitative agreement to available experimental data, using relatively modest computational resources. In some cases, for example, for the composition of the CO 2 -rich phase in coexistence with an aqueous phase, recent results from molecular simulations have helped discriminate among conflicting experimental data sets. The sensitivity of properties on the quality of the intermolecular interaction model varies significantly. Properties such as the phase compositions or electrolyte activity coefficients are much more sensitive than phase densities, viscosities, or component diffusivities. Strong confinement effects on physical properties in nanoscale media can also be directly obtained from molecular simulations. Future work on molecular modeling for CO 2 and aqueous brines is likely to be focused on more systematic generation of interaction models by utilizing quantum chemical as well as direct experimental measurements. New ion models need to be developed for use with the current generation of polarizable water models, including ion-ion interactions that will allow for accurate description of dense, mixed brines. Methods will need to be devised that go beyond the use of effective potentials for incorporation of quantum effects known to be important for water, and reactive force fields developed that can handle bond creation and breaking in systems with carbonate and silicate minerals. Another area of potential future work is the integration of molecular simulation methods in multiscale models for the chemical reactions leading to mineral dissolution and flow within the porous media in underground formations.

Molecular Modeling of Thermodynamic and Transport Properties for CO 2 and Aqueous Brines

DOE PAGES

Jiang, Hao; Economou, Ioannis G.; Panagiotopoulos, Athanassios Z.

2017-02-24

Molecular simulation techniques using classical force-fields occupy the space between ab initio quantum mechanical methods and phenomenological correlations. In particular, Monte Carlo and molecular dynamics algorithms can be used to provide quantitative predictions of thermodynamic and transport properties of fluids relevant for geologic carbon sequestration at conditions for which experimental data are uncertain or not available. These methods can cover time and length scales far exceeding those of quantum chemical methods, while maintaining transferability and predictive power lacking from phenomenological correlations. The accuracy of predictions depends sensitively on the quality of the molecular models used. Many existing fixed-point-charge models formore » water and aqueous mixtures fail to represent accurately these fluid properties, especially when descriptions covering broad ranges of thermodynamic conditions are needed. Recent work on development of accurate models for water, CO 2, and dissolved salts, as well as their mixtures, is summarized in this Account. Polarizable models that can respond to the different dielectric environments in aqueous versus nonaqueous phases are necessary for predictions of properties over extended ranges of temperatures and pressures. Phase compositions and densities, activity coefficients of the dissolved salts, interfacial tensions, viscosities and diffusivities can be obtained in near-quantitative agreement to available experimental data, using relatively modest computational resources. In some cases, for example, for the composition of the CO 2-rich phase in coexistence with an aqueous phase, recent results from molecular simulations have helped discriminate among conflicting experimental data sets. The sensitivity of properties on the quality of the intermolecular interaction model varies significantly. Properties such as the phase compositions or electrolyte activity coefficients are much more sensitive than phase densities, viscosities, or component diffusivities. Strong confinement effects on physical properties in nanoscale media can also be directly obtained from molecular simulations. Future work on molecular modeling for CO 2 and aqueous brines is likely to be focused on more systematic generation of interaction models by utilizing quantum chemical as well as direct experimental measurements. New ion models need to be developed for use with the current generation of polarizable water models, including ion–ion interactions that will allow for accurate description of dense, mixed brines. Methods will need to be devised that go beyond the use of effective potentials for incorporation of quantum effects known to be important for water, and reactive force fields developed that can handle bond creation and breaking in systems with carbonate and silicate minerals. Lastly, another area of potential future work is the integration of molecular simulation methods in multiscale models for the chemical reactions leading to mineral dissolution and flow within the porous media in underground formations.« less

Three Dimensional Projection Environment for Molecular Design and Surgical Simulation

DTIC Science & Technology

2011-08-01

bypasses the cumbersome meshing process . The deformation model is only comprised of mass nodes, which are generated by sampling the object volume before...force should minimize the penetration volume, the haptic feedback force is derived directly. Additionally, a post- processing technique is developed to...render distinct physi-cal tissue properties across different interaction areas. The proposed approach does not require any pre- processing and is

Development of the Nuclear-Electronic Orbital Approach and Applications to Ionic Liquids and Tunneling Processes

DTIC Science & Technology

2010-02-24

electronic Schrodinger equation . In previous grant cycles, we implemented the NEO approach at the Hartree-Fock (NEO-HF),13 configuration interaction...electronic and nuclear molecular orbitals. The resulting electronic and nuclear Hartree-Fock-Roothaan equations are solved iteratively until self...directly into the standard Hartree- Fock-Roothaan equations , which are solved iteratively to self-consistency. The density matrix representation

Norovirus translation requires an interaction between the C Terminus of the genome-linked viral protein VPg and eukaryotic translation initiation factor 4G.

PubMed

Chung, Liliane; Bailey, Dalan; Leen, Eoin N; Emmott, Edward P; Chaudhry, Yasmin; Roberts, Lisa O; Curry, Stephen; Locker, Nicolas; Goodfellow, Ian G

2014-08-01

Viruses have evolved a variety of mechanisms to usurp the host cell translation machinery to enable translation of the viral genome in the presence of high levels of cellular mRNAs. Noroviruses, a major cause of gastroenteritis in man, have evolved a mechanism that relies on the interaction of translation initiation factors with the virus-encoded VPg protein covalently linked to the 5' end of the viral RNA. To further characterize this novel mechanism of translation initiation, we have used proteomics to identify the components of the norovirus translation initiation factor complex. This approach revealed that VPg binds directly to the eIF4F complex, with a high affinity interaction occurring between VPg and eIF4G. Mutational analyses indicated that the C-terminal region of VPg is important for the VPg-eIF4G interaction; viruses with mutations that alter or disrupt this interaction are debilitated or non-viable. Our results shed new light on the unusual mechanisms of protein-directed translation initiation. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Advances in direct T-cell alloreactivity: function, avidity, biophysics and structure.

PubMed

Smith, C; Miles, J J; Khanna, R

2012-01-01

Although T-cell-based adaptive immunity plays a crucial role in protection against infectious pathogens and uncontrolled outgrowth of malignant cells, a large portion of these T cells are also capable of responding to allogeneic HLA molecules, violating the paradigm of self-major histocompatibility complex (MHC) restriction. Recent studies have provided insights into the mechanisms by which these T cells recognize allogeneic targets. The role of antiviral T cells in direct alloreactivity through peptide-dependent molecular mimicry and alternate peptide-MHC docking modes has emerged as major models for the human alloresponse. Here, we review in depth recent advances in this field and discuss how molecular interactions between T cells and HLA molecules drive the activation of these effector cells and its potential implications for alloreactivity in human transplantation. ©Copyright 2011 American Society of Transplantation and the American Society of Transplant Surgeons.

A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock.

PubMed

Pruneda-Paz, Jose L; Breton, Ghislain; Para, Alessia; Kay, Steve A

2009-03-13

Transcriptional feedback loops constitute the molecular circuitry of the plant circadian clock. In Arabidopsis, a core loop is established between CCA1 and TOC1. Although CCA1 directly represses TOC1, the TOC1 protein has no DNA binding domains, which suggests that it cannot directly regulate CCA1. We established a functional genomic strategy that led to the identification of CHE, a TCP transcription factor that binds specifically to the CCA1 promoter. CHE is a clock component partially redundant with LHY in the repression of CCA1. The expression of CHE is regulated by CCA1, thus adding a CCA1/CHE feedback loop to the Arabidopsis circadian network. Because CHE and TOC1 interact, and CHE binds to the CCA1 promoter, a molecular linkage between TOC1 and CCA1 gene regulation is established.

β-Sheet Containment by Flanking Prolines: Molecular Dynamic Simulations of the Inhibition of β-Sheet Elongation by Proline Residues in Human Prion Protein

PubMed Central

Shamsir, Mohd S.; Dalby, Andrew R.

2007-01-01

Previous molecular dynamic simulations have reported elongation of the existing β-sheet in prion proteins. Detailed examination has shown that these elongations do not extend beyond the proline residues flanking these β-sheets. In addition, proline has also been suggested to possess a possible structural role in preserving protein interaction sites by preventing invasion of neighboring secondary structures. In this work, we have studied the possible structural role of the flanking proline residues by simulating mutant structures with alternate substitution of the proline residues with valine. Simulations showed a directional inhibition of elongation, with the elongation progressing in the direction of valine including evident inhibition of elongation by existing proline residues. This suggests that the flanking proline residues in prion proteins may have a containment role and would confine the β-sheet within a specific length. PMID:17172295

Nanomedicine: de novo design of nanodrugs

NASA Astrophysics Data System (ADS)

Yang, Zaixing; Kang, Seung-Gu; Zhou, Ruhong

2013-12-01

Phenomenal advances in nanotechnology and nanoscience have been accompanied by exciting progress in de novo design of nanomedicines. Nanoparticles with their large space of structural amenability and excellent mechanical and electrical properties have become ideal candidates for high efficacy nanomedicines in both diagnostics and therapeutics. The therapeutic nanomedicines can be further categorized into nanocarriers for conventional drugs and nanodrugs with direct curing of target diseases. Here we review some of the recent advances in de novo design of nanodrugs, with an emphasis on the molecular level understanding of their interactions with biological systems including key proteins and cell membranes. We also include some of the latest advances in the development of nanocarriers with both passive and active targeting for completeness. These studies may shed light on a better understanding of the molecular mechanisms behind these nanodrugs, and also provide new insights and direction for the future design of nanomedicines.

A direct ab initio molecular dynamics (MD) study on the benzophenone-water 1 : 1 complex.

PubMed

Tachikawa, Hiroto; Iyama, Tetsuji; Kato, Kohichi

2009-07-28

Direct ab initio molecular dynamics (MD) method has been applied to a benzophenone-water 1 : 1 complex Bp(H(2)O) and free benzophenone (Bp) to elucidate the effects of zero-point energy (ZPE) vibration and temperature on the absorption spectra of Bp(H(2)O). The n-pi transition of free-Bp (S(1) state) was blue-shifted by the interaction with a water molecule, whereas three pi-pi transitions (S(2), S(3) and S(4)) were red-shifted. The effects of the ZPE vibration and temperature of Bp(H(2)O) increased the intensity of the n-pi transition of Bp(H(2)O) and caused broadening of the pi-pi transitions. In case of the temperature effect, the intensity of n-pi transition increases with increasing temperature. The electronic states of Bp(H(2)O) were discussed on the basis of the theoretical results.

The Arrow of Time and the Action of the Mind at the Molecular Level

NASA Astrophysics Data System (ADS)

Burns, Jean E.

2006-10-01

A new event is defined as an intervention in the time reversible dynamical trajectories of particles in a system. New events are then assumed to be quantum fluctuations in the spatial and momentum coordinates, and mental action is assumed to work by ordering such fluctuations. It is shown that when the cumulative values of such fluctuations in a mean free path of a molecule are magnified by molecular interaction at the end of that path, the momentum of a molecule can be changed from its original direction to any other direction. In this way mental action can produce effects through the ordering of thermal motions. Examples are given which show that the ordering of 104-105 molecules is sufficient to (a) produce detectible PK results and (b) open sufficient ion channels in the brain to initiate a physical action. The relationship of the above model to the arrow of time is discussed.

Nanomedicine: de novo design of nanodrugs.

PubMed

Yang, Zaixing; Kang, Seung-gu; Zhou, Ruhong

2014-01-21

Phenomenal advances in nanotechnology and nanoscience have been accompanied by exciting progress in de novo design of nanomedicines. Nanoparticles with their large space of structural amenability and excellent mechanical and electrical properties have become ideal candidates for high efficacy nanomedicines in both diagnostics and therapeutics. The therapeutic nanomedicines can be further categorized into nanocarriers for conventional drugs and nanodrugs with direct curing of target diseases. Here we review some of the recent advances in de novo design of nanodrugs, with an emphasis on the molecular level understanding of their interactions with biological systems including key proteins and cell membranes. We also include some of the latest advances in the development of nanocarriers with both passive and active targeting for completeness. These studies may shed light on a better understanding of the molecular mechanisms behind these nanodrugs, and also provide new insights and direction for the future design of nanomedicines.

Conformation-based signal transfer and processing at the single-molecule level

NASA Astrophysics Data System (ADS)

Li, Chao; Wang, Zhongping; Lu, Yan; Liu, Xiaoqing; Wang, Li

2017-11-01

Building electronic components made of individual molecules is a promising strategy for the miniaturization and integration of electronic devices. However, the practical realization of molecular devices and circuits for signal transmission and processing at room temperature has proven challenging. Here, we present room-temperature intermolecular signal transfer and processing using SnCl2Pc molecules on a Cu(100) surface. The in-plane orientations of the molecules are effectively coupled via intermolecular interaction and serve as the information carrier. In the coupled molecular arrays, the signal can be transferred from one molecule to another in the in-plane direction along predesigned routes and processed to realize logical operations. These phenomena enable the use of molecules displaying intrinsic bistable states as complex molecular devices and circuits with novel functions.

Non-interacting surface solvation and dynamics in protein-protein interactions.

PubMed

Visscher, Koen M; Kastritis, Panagiotis L; Bonvin, Alexandre M J J

2015-03-01

Protein-protein interactions control a plethora of cellular processes, including cell proliferation, differentiation, apoptosis, and signal transduction. Understanding how and why proteins interact will inevitably lead to novel structure-based drug design methods, as well as design of de novo binders with preferred interaction properties. At a structural and molecular level, interface and rim regions are not enough to fully account for the energetics of protein-protein binding, even for simple lock-and-key rigid binders. As we have recently shown, properties of the global surface might also play a role in protein-protein interactions. Here, we report on molecular dynamics simulations performed to understand solvent effects on protein-protein surfaces. We compare properties of the interface, rim, and non-interacting surface regions for five different complexes and their free components. Interface and rim residues become, as expected, less mobile upon complexation. However, non-interacting surface appears more flexible in the complex. Fluctuations of polar residues are always lower compared with charged ones, independent of the protein state. Further, stable water molecules are often observed around polar residues, in contrast to charged ones. Our analysis reveals that (a) upon complexation, the non-interacting surface can have a direct entropic compensation for the lower interface and rim entropy and (b) the mobility of the first hydration layer, which is linked to the stability of the protein-protein complex, is influenced by the local chemical properties of the surface. These findings corroborate previous hypotheses on the role of the hydration layer in shielding protein-protein complexes from unintended protein-protein interactions. © 2014 Wiley Periodicals, Inc.

ZikaBase: An integrated ZIKV- Human Interactome Map database.

PubMed

Gurumayum, Sanathoi; Brahma, Rahul; Naorem, Leimarembi Devi; Muthaiyan, Mathavan; Gopal, Jeyakodi; Venkatesan, Amouda

2018-01-15

Re-emergence of ZIKV has caused infections in more than 1.5 million people. The molecular mechanism and pathogenesis of ZIKV is not well explored due to unavailability of adequate model and lack of publically accessible resources to provide information of ZIKV-Human protein interactome map till today. This study made an attempt to curate the ZIKV-Human interaction proteins from published literatures and RNA-Seq data. 11 direct interaction, 12 associated genes are retrieved from literatures and 3742 Differentially Expressed Genes (DEGs) are obtained from RNA-Seq analysis. The genes have been analyzed to construct the ZIKV-Human Interactome Map. The importance of the study has been illustrated by the enrichment analysis and observed that direct interaction and associated genes are enriched in viral entry into host cell. Also, ZIKV infection modulates 32% signal and 27% immune system pathways. The integrated database, ZikaBase has been developed to help the virology research community and accessible at https://test5.bicpu.edu.in. Copyright © 2017 Elsevier Inc. All rights reserved.

Nonconvective mixing of miscible ionic liquids.

PubMed

Frost, Denzil S; Machas, Michael; Perea, Brian; Dai, Lenore L

2013-08-13

Ionic liquids (ILs) are ionic compounds that are liquid at room temperature. We studied the spontaneous mixing behavior between two ILs, ethylammonium nitrate (EAN) and 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]), and observed notable phenomena. Experimental studies showed that the interface between the two ILs was unusually long-lived, despite the ILs being miscible with one another. Molecular dynamics (MD) simulations supported these findings and provided insight into the micromixing behavior of the ILs. We found that not only did the ions experience slow diffusion as they mix but also exhibited significant ordering into distinct regions. We suspect that this ordering disrupted concentration gradients in the direction normal to the interface, thus hindering diffusion in this direction and allowing the macroscopic interface to remain for long periods of time. Intermolecular interactions responsible for this behavior included the O-NH interaction between the EAN ions and the carbon chain-carbon chain interactions between the [BMIM](+) cations, which associate more strongly in the mixed state than in the pure IL state.

Direct simulation of amphiphilic nanoparticle mediated membrane interactions

NASA Astrophysics Data System (ADS)

Tahir, Mukarram; Alexander-Katz, Alfredo

Membrane fusion is a critical step in the transport of biological cargo through membrane-bound compartments like vesicles. Membrane proteins that alleviate energy barriers for initial stalk formation and eventual rupture of the hemifusion intermediate during fusion generally assist this process. Gold nanoparticles functionalized with a combination of hydrophobic and hydrophilic alkanethiol ligands have recently been shown to induce membrane re-arrangements that are similar to those associated with these fusion proteins. In this work, we utilize molecular dynamics simulation to systematically design nanoparticles that exhibit targeted interactions with membranes. We introduce a method for rapidly parameterizing nanoparticle topology for the MARTINI biomolecular force field to permit long timescale simulation of their interactions with lipid bilayers. We leverage this model to investigate how ligand chemistry governs the nanoparticle's insertion efficacy and the perturbations it generates in the membrane environment. We further demonstrate through unbiased simulations that these nanoparticles can direct the fusion of lipid assemblies such as micelles and vesicles in a manner that mimics the function of biological fusion peptides and SNARE proteins.

Block copolymer templated self-assembly of disk-shaped molecules

NASA Astrophysics Data System (ADS)

Aragones, J. L.; Alexander-Katz, A.

2017-08-01

Stacking of disk-shaped organic molecules is a promising strategy to develop electronic and photovoltaic devices. Here, we investigate the capability of a soft block copolymer matrix that microphase separates into a cylindrical phase to direct the self-assembly of disk-shaped molecules by means of molecular simulations. We show that two disk molecules confined in the cylinder domain experience a depletion force, induced by the polymer chains, which results in the formation of stacks of disks. This entropic interaction and the soft confinement provided by the matrix are both responsible for the structures that can be self-assembled, which include slanted or columnar stacks. In addition, we evidence the transmission of stresses between the different minority domains of the microphase, which results in the establishment of a long-ranged interaction between disk molecules embedded in different domains; this interaction is of the order of the microphase periodicity and may be exploited to direct assembly of disks at larger scales.

[Hyperfine structure analysis in magnetic resonance spectroscopy: from astrophysical measurements towards endogenous biosensors in human tissue].

PubMed

Schröder, Leif

2007-01-01

The hyperfine interaction of two spins is a well studied effect in atomic systems. Magnetic resonance experiments demonstrate that the detectable dipole transitions are determined by the magnetic moments of the constituents and the external magnetic field. Transferring the corresponding quantum mechanics to molecular bound nuclear spins allows for precise prediction of NMR spectra obtained from metabolites in human tissue. This molecular hyperfine structure has been neglected so far in in vivo NMR spectroscopy but contains useful information, especially when studying molecular dynamics. This contribution represents a review of the concept of applying the Breit-Rabi formalism to coupled nuclear spins and discusses the immobilization of different metabolites in anisotropic tissue revealed by 1H NMR spectra of carnosine, phosphocreatine and taurine. Comparison of atomic and molecular spin systems allows for statements on the biological constraints for direct spin-spin interactions. Moreover, the relevance of hyperfine effects on the line shapes of multiplets of indirectly-coupled spin systems with more than two constituents can be predicted by analyzing quantum mechanical parameters. As an example, the superposition of eigenstates of the A MX system of adenosine 5'-triphosphate and its application for better quantification of 31P-NMR spectra will be discussed.

Molecular dynamics simulations of structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces.

PubMed

He, Guangzhi; Zhang, Meiyi; Zhou, Qin; Pan, Gang

2015-09-01

Concentration and salinity conditions are the dominant environmental factors affecting the behavior of perfluorinated compounds (PFCs) on the surfaces of a variety of solid matrices (suspended particles, sediments, and natural minerals). However, the mechanism has not yet been examined at molecular scales. Here, the structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces induced by changes of the concentration level of PFOS and salt condition was investigated using molecular dynamics (MD) simulations. At low and intermediate concentrations all PFOS molecules directly interacted with the rutile (110) surface mainly by the sulfonate headgroups through electrostatic attraction, yielding a typical monolayer structure. As the concentration of PFOS increased, the molecules aggregated in a complex multi-layered structure, where an irregular assembling configuration was adsorbed on the monolayer structure by the van der Waals interactions between the perfluoroalkyl chains. When adding CaCl2 to the system, the multi-layered structure changed to a monolayer again, indicating that the addition of CaCl2 enhanced the critical concentration value to yield PFOS multilayer assemblies. The divalent Ca(2+) substituted for monovalent K(+) as the bridging counterion in PFOS adsorption. MD simulation may trigger wide applications in study of perfluorinated compounds (PFCs) from atomic/molecular scale. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular interactions between general anesthetics and the 5HT2B receptor.

PubMed

Matsunaga, Felipe; Gao, Lu; Huang, Xi-Ping; Saven, Jeffery G; Roth, Bryan L; Liu, Renyu

2015-01-01

Serotonin modulates many processes through a family of seven serotonin receptors. However, no studies have screened for interactions between general anesthetics currently in clinical use and serotonergic G-protein-coupled receptors (GPCRs). Given that both intravenous and inhalational anesthetics have been shown to target other classes of GPCRs, we hypothesized that general anesthetics might interact directly with some serotonin receptors and thus modify their function. Radioligand binding assays were performed to screen serotonin receptors for interactions with propofol and isoflurane as well as for affinity determinations. Docking calculations using the crystal structure of 5-HT2B were performed to computationally confirm the binding assay results and locate anesthetic binding sites. The 5-HT2B class of receptors interacted significantly with both propofol and isoflurane in the primary screen. The affinities for isoflurane and propofol were determined to be 7.78 and .95 μM, respectively, which were at or below the clinical concentrations for both anesthetics. The estimated free energy derived from docking calculations for propofol (-6.70 kcal/mol) and isoflurane (-5.10 kcal/mol) correlated with affinities from the binding assay. The anesthetics were predicted to dock at a pharmacologically relevant binding site of 5HT2B. The molecular interactions between propofol and isoflurane with the 5-HT2B class of receptors were discovered and characterized. This finding implicates the serotonergic GPCRs as potential anesthetic targets.

In-situ molecular-level elucidation of organofluorine binding sites in a whole peat soil.

PubMed

Longstaffe, James G; Courtier-Murias, Denis; Soong, Ronald; Simpson, Myrna J; Maas, Werner E; Fey, Michael; Hutchins, Howard; Krishnamurthy, Sridevi; Struppe, Jochem; Alaee, Mehran; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Simpson, André J

2012-10-02

The chemical nature of xenobiotic binding sites in soils is of vital importance to environmental biogeochemistry. Interactions between xenobiotics and the naturally occurring organic constituents of soils are strongly correlated to environmental persistence, bioaccessibility, and ecotoxicity. Nevertheless, because of the complex structural and chemical heterogeneity of soils, studies of these interactions are most commonly performed indirectly, using correlative methods, fractionation, or chemical modification. Here we identify the organic components of an unmodified peat soil where some organofluorine xenobiotic compounds interact using direct molecular-level methods. Using (19)F→(1)H cross-polarization magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR) spectroscopy, the (19)F nuclei of organofluorine compounds are used to induce observable transverse magnetization in the (1)H nuclei of organic components of the soil with which they interact after sorption. The observed (19)F→(1)H CP-MAS spectra and dynamics are compared to those produced using model soil organic compounds, lignin and albumin. It is found that lignin-like components can account for the interactions observed in this soil for heptafluoronaphthol (HFNap) while protein structures can account for the interactions observed for perfluorooctanoic acid (PFOA). This study employs novel comprehensive multi-phase (CMP) NMR technology that permits the application of solution-, gel-, and solid-state NMR experiments on intact soil samples in their swollen state.

Structural basis of clade-specific HIV-1 neutralization by humanized anti-V3 monoclonal antibody KD-247.

PubMed

Kirby, Karen A; Ong, Yee Tsuey; Hachiya, Atsuko; Laughlin, Thomas G; Chiang, Leslie A; Pan, Yun; Moran, Jennifer L; Marchand, Bruno; Singh, Kamalendra; Gallazzi, Fabio; Quinn, Thomas P; Yoshimura, Kazuhisa; Murakami, Toshio; Matsushita, Shuzo; Sarafianos, Stefan G

2015-01-01

Humanized monoclonal antibody KD-247 targets the Gly(312)-Pro(313)-Gly(314)-Arg(315) arch of the third hypervariable (V3) loop of the HIV-1 surface glycoprotein. It potently neutralizes many HIV-1 clade B isolates, but not of other clades. To understand the molecular basis of this specificity, we solved a high-resolution (1.55 Å) crystal structure of the KD-247 antigen binding fragment and examined the potential interactions with various V3 loop targets. Unlike most antibodies, KD-247 appears to interact with its target primarily through light chain residues. Several of these interactions involve Arg(315) of the V3 loop. To evaluate the role of light chain residues in the recognition of the V3 loop, we generated 20 variants of KD-247 single-chain variable fragments with mutations in the antigen-binding site. Purified proteins were assessed for V3 loop binding using AlphaScreen technology and for HIV-1 neutralization. Our data revealed that recognition of the clade-specificity defining residue Arg(315) of the V3 loop is based on a network of interactions that involve Tyr(L32), Tyr(L92), and Asn(L27d) that directly interact with Arg(315), thus elucidating the molecular interactions of KD-247 with its V3 loop target. © FASEB.

Biochemical and Molecular Mechanisms of Plant-Microbe-Metal Interactions: Relevance for Phytoremediation

PubMed Central

Ma, Ying; Oliveira, Rui S.; Freitas, Helena; Zhang, Chang

2016-01-01

Plants and microbes coexist or compete for survival and their cohesive interactions play a vital role in adapting to metalliferous environments, and can thus be explored to improve microbe-assisted phytoremediation. Plant root exudates are useful nutrient and energy sources for soil microorganisms, with whom they establish intricate communication systems. Some beneficial bacteria and fungi, acting as plant growth promoting microorganisms (PGPMs), may alleviate metal phytotoxicity and stimulate plant growth indirectly via the induction of defense mechanisms against phytopathogens, and/or directly through the solubilization of mineral nutrients (nitrogen, phosphate, potassium, iron, etc.), production of plant growth promoting substances (e.g., phytohormones), and secretion of specific enzymes (e.g., 1-aminocyclopropane-1-carboxylate deaminase). PGPM can also change metal bioavailability in soil through various mechanisms such as acidification, precipitation, chelation, complexation, and redox reactions. This review presents the recent advances and applications made hitherto in understanding the biochemical and molecular mechanisms of plant–microbe interactions and their role in the major processes involved in phytoremediation, such as heavy metal detoxification, mobilization, immobilization, transformation, transport, and distribution. PMID:27446148

Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions

PubMed Central

Scholes, Natalie S.; Weinzierl, Robert O. J.

2016-01-01

Transcriptional activation domains (ADs) are generally thought to be intrinsically unstructured, but capable of adopting limited secondary structure upon interaction with a coactivator surface. The indeterminate nature of this interface made it hitherto difficult to study structure/function relationships of such contacts. Here we used atomistic accelerated molecular dynamics (aMD) simulations to study the conformational changes of the GCN4 AD and variants thereof, either free in solution, or bound to the GAL11 coactivator surface. We show that the AD-coactivator interactions are highly dynamic while obeying distinct rules. The data provide insights into the constant and variable aspects of orientation of ADs relative to the coactivator, changes in secondary structure and energetic contributions stabilizing the various conformers at different time points. We also demonstrate that a prediction of α-helical propensity correlates directly with the experimentally measured transactivation potential of a large set of mutagenized ADs. The link between α-helical propensity and the stimulatory activity of ADs has fundamental practical and theoretical implications concerning the recruitment of ADs to coactivators. PMID:27175900

Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis.

PubMed

Bai, Fang; Morcos, Faruck; Cheng, Ryan R; Jiang, Hualiang; Onuchic, José N

2016-12-13

Protein-protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein-protein interfaces. (i) This method explores the binding of fragment-sized molecular probes on the protein surface using a molecular docking-based screen. (ii) The energetically favorable binding sites of the probes, called hot spots, are spatially clustered to map out candidate binding sites on the protein surface. (iii) A coevolution-based interface interaction score is used to discriminate between different candidate binding sites, yielding potential interfacial targets for therapeutic drug design. This approach is validated for important, well-studied disease-related proteins with known pharmaceutical targets, and also identifies targets that have yet to be studied. Moreover, therapeutic agents are proposed by chemically connecting the fragments that are strongly bound to the hot spots.

Modeling Nanoparticle Wrapping or Translocation in Bilayer Membranes

PubMed Central

Curtis, Emily M.; Bahrami, Amir H.; Weikl, Thomas R.; Hall, Carol K.

2015-01-01

The spontaneous wrapping of nanoparticles by membranes is of increasing interest as nanoparticles become more prevalent in consumer products and hence more likely to enter the human body. We introduce a simulations-based tool that can be used to visualize the molecular level interaction between nanoparticles and bilayer membranes. By combining LIME, an intermediate resolution, implicit solvent model for phospholipids, with discontinuous molecular dynamics (DMD), we are able to simulate the wrapping or embedding of nanoparticles by 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer membranes. Simulations of hydrophilic nanoparticles with diameters from 10Å to 250Å show that hydrophilic nanoparticles with diameters greater than 20Å become wrapped while the nanoparticle with a diameter of 10Å does not . Instead this smaller particle became embedded in the bilayer surface where it could interact with the hydrophilic head groups of the lipid molecules. We also investigate the interaction between a DPPC bilayer and hydrophobic nanoparticles with diameters 10Å to 40Å. These nanoparticles do not undergo the wrapping process; instead they directly penetrate the membrane and embed themselves within the inner hydrophobic core of the bilayers. PMID:26260123

Inhibition of cathelicidin activity by bacterial exopolysaccharides.

PubMed

Foschiatti, Michela; Cescutti, Paola; Tossi, Alessandro; Rizzo, Roberto

2009-06-01

The interaction of bacterial exopolysaccharides, produced by opportunistic lung pathogens, with antimicrobial peptides of the innate primate immune system was investigated. The exopolysaccharides were produced by Pseudomonas aeruginosa, Inquilinus limosus and clinical isolates of the Burkholderia cepacia complex, bacteria that are all involved in lung infections of cystic fibrosis patients. The effects of the biological activities of three orthologous cathelicidins from Homo sapiens sapiens, Pongo pygmaeus (orangutan) and Presbitys obscurus (dusky leaf monkey) were examined. Inhibition of the antimicrobial activity of peptides was assessed using minimum inhibitory concentration assays on a reference Escherichia coli strain in the presence and absence of exopolysaccharides, whereas complex formation between peptides and exopolysaccharides was investigated by means of circular dichroism, fluorescence spectroscopy and atomic force microscopy. Biological assays revealed that the higher the negative charge of exopolysaccharides the stronger was their inhibiting effect. Spectroscopic studies indicated the formation of molecular complexes of varying stability between peptides and exopolysaccharides, explaining the inhibition. Atomic force microscopy provided a direct visualization of the molecular complexes. A model is proposed where peptides with an alpha-helical conformation interact with exopolysaccharides through electrostatic and other non-covalent interactions.

Probing molecular interactions of poly(styrene-co-maleic acid) with lipid matrix models to interpret the therapeutic potential of the co-polymer.

PubMed

Banerjee, Shubhadeep; Pal, Tapan K; Guha, Sujoy K

2012-03-01

To understand and maximize the therapeutic potential of poly(styrene-co-maleic acid) (SMA), a synthetic, pharmacologically-active co-polymer, its effect on conformation, phase behavior and stability of lipid matrix models of cell membranes were investigated. The modes of interaction between SMA and lipid molecules were also studied. While, attenuated total reflection-Fourier-transform infrared (ATR-FTIR) and static (31)P nuclear magnetic resonance (NMR) experiments detected SMA-induced conformational changes in the headgroup region, differential scanning calorimetry (DSC) studies revealed thermotropic phase behavior changes of the membranes. (1)H NMR results indicated weak immobilization of SMA within the bilayers. Molecular interpretation of the results indicated the role of hydrogen-bond formation and hydrophobic forces between SMA and zwitterionic phospholipid bilayers. The extent of membrane fluidization and generation of isotropic phases were affected by the surface charge of the liposomes, and hence suggested the role of electrostatic interactions between SMA and charged lipid headgroups. SMA was thus found to directly affect the structural integrity of model membranes. Copyright © 2011 Elsevier B.V. All rights reserved.

The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation

PubMed Central

Lee, Mihwa; Sadowska, Agata; Bekere, Indra; Ho, Diwei; Gully, Benjamin S.; Lu, Yanling; Iyer, K. Swaminathan; Trewhella, Jill; Fox, Archa H.; Bond, Charles S.

2015-01-01

SFPQ, (a.k.a. PSF), is a human tumor suppressor protein that regulates many important functions in the cell nucleus including coordination of long non-coding RNA molecules into nuclear bodies. Here we describe the first crystal structures of Splicing Factor Proline and Glutamine Rich (SFPQ), revealing structural similarity to the related PSPC1/NONO heterodimer and a strikingly extended structure (over 265 Å long) formed by an unusual anti-parallel coiled-coil that results in an infinite linear polymer of SFPQ dimers within the crystals. Small-angle X-ray scattering and transmission electron microscopy experiments show that polymerization is reversible in solution and can be templated by DNA. We demonstrate that the ability to polymerize is essential for the cellular functions of SFPQ: disruptive mutation of the coiled-coil interaction motif results in SFPQ mislocalization, reduced formation of nuclear bodies, abrogated molecular interactions and deficient transcriptional regulation. The coiled-coil interaction motif thus provides a molecular explanation for the functional aggregation of SFPQ that directs its role in regulating many aspects of cellular nucleic acid metabolism. PMID:25765647

Super-complexes of adhesion GPCRs and neural guidance receptors

NASA Astrophysics Data System (ADS)

Jackson, Verity A.; Mehmood, Shahid; Chavent, Matthieu; Roversi, Pietro; Carrasquero, Maria; Del Toro, Daniel; Seyit-Bremer, Goenuel; Ranaivoson, Fanomezana M.; Comoletti, Davide; Sansom, Mark S. P.; Robinson, Carol V.; Klein, Rüdiger; Seiradake, Elena

2016-04-01

Latrophilin adhesion-GPCRs (Lphn1-3 or ADGRL1-3) and Unc5 cell guidance receptors (Unc5A-D) interact with FLRT proteins (FLRT1-3), thereby promoting cell adhesion and repulsion, respectively. How the three proteins interact and function simultaneously is poorly understood. We show that Unc5D interacts with FLRT2 in cis, controlling cell adhesion in response to externally presented Lphn3. The ectodomains of the three proteins bind cooperatively. Crystal structures of the ternary complex formed by the extracellular domains reveal that Lphn3 dimerizes when bound to FLRT2:Unc5, resulting in a stoichiometry of 1:1:2 (FLRT2:Unc5D:Lphn3). This 1:1:2 complex further dimerizes to form a larger `super-complex' (2:2:4), using a previously undescribed binding motif in the Unc5D TSP1 domain. Molecular dynamics simulations, point-directed mutagenesis and mass spectrometry demonstrate the stability and molecular properties of these complexes. Our data exemplify how receptors increase their functional repertoire by forming different context-dependent higher-order complexes.

Lawrence Livermore National Laboratory Workshop Characterization of Pathogenicity, Virulence and Host-Pathogen Interactions

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

Krishnan, A

2006-08-30

The threats of bio-terrorism and newly emerging infectious diseases pose serious challenges to the national security infrastructure. Rapid detection and diagnosis of infectious disease in human populations, as well as characterizing pathogen biology, are critical for reducing the morbidity and mortality associated with such threats. One of the key challenges in managing an infectious disease outbreak, whether through natural causes or acts of overt terrorism, is detection early enough to initiate effective countermeasures. Much recent attention has been directed towards the utility of biomarkers or molecular signatures that result from the interaction of the pathogen with the host for improvingmore » our ability to diagnose and mitigate the impact of a developing infection during the time window when effective countermeasures can be instituted. Host responses may provide early signals in blood even from localized infections. Multiple innate and adaptive immune molecules, in combination with other biochemical markers, may provide disease-specific information and new targets for countermeasures. The presence of pathogen specific markers and an understanding of the molecular capabilities and adaptations of the pathogen when it interacts with its host may likewise assist in early detection and provide opportunities for targeting countermeasures. An important question that needs to be addressed is whether these molecular-based approaches will prove useful for early diagnosis, complement current methods of direct agent detection, and aid development and use of countermeasures. Lawrence Livermore National Laboratory (LLNL) will host a workshop to explore the utility of host- and pathogen-based molecular diagnostics, prioritize key research issues, and determine the critical steps needed to transition host-pathogen research to tools that can be applied towards a more effective national bio-defense strategy. The workshop will bring together leading researchers/scientists in the area of host-pathogen interactions as well as policy makers from federal agencies. The main objectives of the workshop are: (1) to assess the current national needs, capabilities, near-term technologies, and future challenges in applying various diagnostics tools to public health and bio-defense; (2) to evaluate the utility and feasibility of host-response and pathogen biomarker profiling in the diagnosis and management of infectious diseases; and (3) to create a comprehensive developmental strategy from proof-of-concept, through validation, to deployment of appropriate advanced technology for the clinical/public health and bio-defense environments.« less

Noncovalent interaction-assisted drug delivery system with highly efficient uptake and release of paclitaxel for anticancer therapy.

PubMed

Wei, Yuping; Ma, Liang; Zhang, Liang; Xu, Xia

2017-01-01

An effective drug delivery system requires efficient drug uptake and release inside cancer cells. Here, we report a novel drug delivery system, in which paclitaxel (PTX) interacts with a novel cell penetrating peptide (CPP) through noncovalent interaction designed based on molecular simulations. This CPP/PTX complex confers high efficiency in delivering PTX into cancer cells not by endocytosis but by an energy-independent pathway. Once inside cells, the noncovalent interaction between PTX and the CPP may allow fast release of PTX within cells due to the direct translocation of CPP/PTX. This drug delivery system exhibits strong capacity for inhibition of tumor growth and offers a new avenue for the development of advanced drug delivery systems for anticancer therapy.

A 90-Kilodalton Endothelial Cell Molecule Mediating Lymphocyte Binding in Humans

NASA Astrophysics Data System (ADS)

Salmi, Marko; Jalkanen, Sirpa

1992-09-01

Interactions between leukocyte surface receptors and their ligands on vascular endothelial cells control lymphocyte traffic between the blood and various lymphoid organs, as well as extravasation of leukocytes into sites of inflammation. A heretofore undescribed 90-kilodalton human endothelial cell adhesion molecule (VAP-1) defined by a monoclonal antibody 1B2 is described. The expression pattern, molecular mass, functional properties, and an amino-terminal amino acid sequence define VAP-1 as an endothelial ligand for lymphocytes. VAP-1 helps to elucidate the complex heterotypic cell interactions that direct tissue-selective lymphocyte migration in man.

Preface: Special Topic on Atomic and Molecular Layer Processing: Deposition, Patterning, and Etching

NASA Astrophysics Data System (ADS)

Engstrom, James R.; Kummel, Andrew C.

2017-02-01

Thin film processing technologies that promise atomic and molecular scale control have received increasing interest in the past several years, as traditional methods for fabrication begin to reach their fundamental limits. Many of these technologies involve at their heart phenomena occurring at or near surfaces, including adsorption, gas-surface reactions, diffusion, desorption, and re-organization of near-surface layers. Moreover many of these phenomena involve not just reactions occurring under conditions of local thermodynamic equilibrium but also the action of energetic species including electrons, ions, and hyperthermal neutrals. There is a rich landscape of atomic and molecular scale interactions occurring in these systems that is still not well understood. In this Special Topic Issue of The Journal of Chemical Physics, we have collected recent representative examples of work that is directed at unraveling the mechanistic details concerning atomic and molecular layer processing, which will provide an important framework from which these fields can continue to develop. These studies range from the application of theory and computation to these systems to the use of powerful experimental probes, such as X-ray synchrotron radiation, probe microscopies, and photoelectron and infrared spectroscopies. The work presented here helps in identifying some of the major challenges and direct future activities in this exciting area of research involving atomic and molecular layer manipulation and fabrication.

Preface: Special Topic on Atomic and Molecular Layer Processing: Deposition, Patterning, and Etching.

PubMed

Engstrom, James R; Kummel, Andrew C

2017-02-07

Thin film processing technologies that promise atomic and molecular scale control have received increasing interest in the past several years, as traditional methods for fabrication begin to reach their fundamental limits. Many of these technologies involve at their heart phenomena occurring at or near surfaces, including adsorption, gas-surface reactions, diffusion, desorption, and re-organization of near-surface layers. Moreover many of these phenomena involve not just reactions occurring under conditions of local thermodynamic equilibrium but also the action of energetic species including electrons, ions, and hyperthermal neutrals. There is a rich landscape of atomic and molecular scale interactions occurring in these systems that is still not well understood. In this Special Topic Issue of The Journal of Chemical Physics, we have collected recent representative examples of work that is directed at unraveling the mechanistic details concerning atomic and molecular layer processing, which will provide an important framework from which these fields can continue to develop. These studies range from the application of theory and computation to these systems to the use of powerful experimental probes, such as X-ray synchrotron radiation, probe microscopies, and photoelectron and infrared spectroscopies. The work presented here helps in identifying some of the major challenges and direct future activities in this exciting area of research involving atomic and molecular layer manipulation and fabrication.

Microscopic origin of electric-field-induced modulation of Curie temperature in cobalt

NASA Astrophysics Data System (ADS)

Ando, Fuyuki; Yamada, Kihiro T.; Koyama, Tomohiro; Ishibashi, Mio; Shiota, Yoichi; Moriyama, Takahiro; Chiba, Daichi; Ono, Teruo

2018-07-01

The Curie temperature T C is one of the most fundamental physical properties of ferromagnetic materials and can be described by the Weiss molecular field theory with the exchange interaction of neighboring atoms. Here, we demonstrate the electrical control of exchange coupling in cobalt films through direct magnetization measurements. We find that the reduction in magnetization with temperature, which is caused by thermal spin wave excitation and scales with Bloch’s law, clearly depends on the applied electric field. Furthermore, we confirm that the correlation between the electric-field-induced modulation of T C and that of exchange coupling follows the Weiss molecular field theory.

Restricted amide rotation with steric hindrance induced multiple conformations

NASA Astrophysics Data System (ADS)

Krishnan, V. V.; Vazquez, Salvador; Maitra, Kalyani; Maitra, Santanu

2017-12-01

The Csbnd N bond character is dependent directly upon the resonance-contributor structure population driven by the delocalized nitrogen lone-pair of electrons. In the case of N, N-dibenzyl-ortho-toluamide (o-DBET), the molecule adopts subpopulations of conformers with distinct NMR spectral features, particularly at low temperatures. This conformational adaptation is unique to o-DBET, while the corresponding meta- and para- forms do not show such behavior. Variable-temperature (VT) NMR, two-dimensional exchange spectroscopy (EXSY), and qualitative molecular modeling studies are used to demonstrate how multiple competing interactions such as restricted amide rotation and steric hindrance effects can lead to versatile molecular adaptations in the solution state.

Quantum tomography of a molecular bond in ice.

PubMed

Goldschleger, I U; Golschleger, I U; van Staveren, M N; Apkarian, V Ara

2013-07-21

We present the moving picture of a molecular bond, in phase-space, in real-time, at resolution limited by quantum uncertainty. The images are tomographically reconstructed Wigner distribution functions (WDF) obtained from four-wave mixing measurements on Br2-doped ice. The WDF completely characterizes the dissipative quantum evolution of the system, which despite coupling to the environment retains quantum coherence, as evidenced by its persistent negative Wigner hole. The spectral decomposition of the WDF allows a direct visualization of wavefunctions and spatiotemporal coherences of the system and the system-bath interaction. The measurements vividly illustrate nonclassical wave mechanics in a many-body system, in ordinary condensed matter.

FAST TRACK COMMUNICATION: Attosecond correlation dynamics during electron tunnelling from molecules

NASA Astrophysics Data System (ADS)

Walters, Zachary B.; Smirnova, Olga

2010-08-01

In this communication, we present an analytical theory of strong-field ionization of molecules, which takes into account the rearrangement of multiple interacting electrons during the ionization process. We show that such rearrangement offers an alternative pathway to the ionization of orbitals more deeply bound than the highest occupied molecular orbital. This pathway is not subject to the full exponential suppression characteristic of direct tunnel ionization from the deeper orbitals. The departing electron produces an 'attosecond correlation pulse' which controls the rearrangement during the tunnelling process. The shape and duration of this pulse are determined by the electronic structure of the relevant states, molecular orientation and laser parameters.

Bio-inspired algorithms applied to molecular docking simulations.

PubMed

Heberlé, G; de Azevedo, W F

2011-01-01

Nature as a source of inspiration has been shown to have a great beneficial impact on the development of new computational methodologies. In this scenario, analyses of the interactions between a protein target and a ligand can be simulated by biologically inspired algorithms (BIAs). These algorithms mimic biological systems to create new paradigms for computation, such as neural networks, evolutionary computing, and swarm intelligence. This review provides a description of the main concepts behind BIAs applied to molecular docking simulations. Special attention is devoted to evolutionary algorithms, guided-directed evolutionary algorithms, and Lamarckian genetic algorithms. Recent applications of these methodologies to protein targets identified in the Mycobacterium tuberculosis genome are described.

Direct Interaction between the Voltage Sensors Produces Cooperative Sustained Deactivation in Voltage-gated H+ Channel Dimers*

PubMed Central

Okuda, Hiroko; Yonezawa, Yasushige; Takano, Yu; Okamura, Yasushi; Fujiwara, Yuichiro

2016-01-01

The voltage-gated H+ channel (Hv) is a voltage sensor domain-like protein consisting of four transmembrane segments (S1–S4). The native Hv structure is a homodimer, with the two channel subunits functioning cooperatively. Here we show that the two voltage sensor S4 helices within the dimer directly cooperate via a π-stacking interaction between Trp residues at the middle of each segment. Scanning mutagenesis showed that Trp situated around the original position provides the slow gating kinetics characteristic of the dimer's cooperativity. Analyses of the Trp mutation on the dimeric and monomeric channel backgrounds and analyses with tandem channel constructs suggested that the two Trp residues within the dimer are functionally coupled during Hv deactivation but are less so during activation. Molecular dynamics simulation also showed direct π-stacking of the two Trp residues. These results provide new insight into the cooperative function of voltage-gated channels, where adjacent voltage sensor helices make direct physical contact and work as a single unit according to the gating process. PMID:26755722

Molecular complex of lumiflavin and 2-aminobenzoic acid: crystal structure, crystal spectra, and solution properties.

PubMed

Shieh, H S; Ghisla, S; Hanson, L K; Ludwig, M L; Nordman, C E

1981-08-04

The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N4O2.C7H7NO2.H2O) crystallizes from from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 A, c = 7.045 A, alpha = 95.44 degrees , beta = 95.86 degrees, and gamma = 105.66 degrees . The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating lumiflavin adn un-ionized (neutral) 2-aminobenzoic acid molecules. Two different modes of stacking interaction are observed. In one, 2-aminobenzoic acid overlaps all three of the isoalloxazine rings, at a mean distance of 3.36 A; in the other, 2-aminobenzoic acid interacts distance of 3.36 A; in the other, 2-aminobenzoic acid interacts with the pyrazine and dimethylbenzene moieties, at a distance of 3.42 A. Perpendicular to the stacking direction, the molecules form a continuous sheet. Each flavin is hydrogen bonded via O(2) and NH(3) to two symmetrically related aminobenzoates; the water of crystallization forms three hydrogen bonds, bridging two flavins, via O(4) and N(5), and one aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid molecules. Measurements of the polarized optical absorption spectra of crystals show that the transition moment direction for the long wavelength absorbance (beyond 530 nm) contains an out-of-plane component which can only arise from a charge-transfer interaction. Since the amino N does not make exceptionally close interactions with isoalloxazine atoms in either stacking mode (minimum interatomic distance 3.52 A), the charge transfer is presumed to involve pi orbitals of the 2-aminobenzoic acid donor.

Structures and properties of molecular torsion balances to decipher the nature of substituent effects on the aromatic edge-to-face interaction.

PubMed

Gardarsson, Haraldur; Schweizer, W Bernd; Trapp, Nils; Diederich, François

2014-04-14

Various recent computational studies initiated this systematic re-investigation of substituent effects on aromatic edge-to-face interactions. Five series of Tröger base derived molecular torsion balances (MTBs), initially introduced by Wilcox and co-workers, showing an aromatic edge-to-face interaction in the folded, but not in the unfolded form, were synthesized. A fluorine atom or a trifluoromethyl group was introduced onto the edge ring in ortho-, meta-, and para-positions to the C-H group interacting with the face component. The substituents on the face component were varied from electron-donating to electron-withdrawing. Extensive X-ray crystallographic data allowed for a discussion on the conformational behavior of the torsional balances in the solid state. While most systems adopt the folded conformation, some were found to form supramolecular intercalative dimers, lacking the intramolecular edge-to-face interaction, which is compensated by the gain of aromatic π-stacking interactions between four aryl rings of the two molecular components. This dimerization does not take place in solution. The folding free enthalpy ΔG(fold) of all torsion balances was determined by (1)H NMR measurements by using 10 mM solutions of samples in CDCl3 and C6D6. Only the ΔG(fold) values of balances bearing an edge-ring substituent in ortho-position to the interacting C-H show a steep linear correlation with the Hammett parameter (σ(meta)) of the face-component substituent. Thermodynamic analysis using van't Hoff plots revealed that the interaction is enthalpy-driven. The ΔG(fold) values of the balances, in addition to partial charge calculations, suggest that increasing the polarization of the interacting C-H group makes a favorable contribution to the edge-to-face interaction. The largest contribution, however, seems to originate from local direct interactions between the substituent in ortho-position to the edge-ring C-H and the substituted face ring. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vibrational cross-angles in condensed molecules: a structural tool.

PubMed

Chen, Hailong; Zhang, Yufan; Li, Jiebo; Liu, Hongjun; Jiang, De-En; Zheng, Junrong

2013-09-05

The fluctuations of three-dimensional molecular conformations of a molecule in different environments play critical roles in many important chemical and biological processes. X-ray diffraction (XRD) techniques and nuclear magnetic resonance (NMR) methods are routinely applied to monitor the molecular conformations in condensed phases. However, some special requirements of the methods have prevented them from exploring many molecular phenomena at the current stage. Here, we introduce another method to resolve molecular conformations based on an ultrafast MIR/T-Hz multiple-dimensional vibrational spectroscopic technique. The model molecule (4'-methyl-2'-nitroacetanilide, MNA) is prepared in two of its crystalline forms and liquid samples. Two polarized ultrafast infrared pulses are then used to determine the cross-angles of vibrational transition moment directions by exciting one vibrational band and detecting the induced response on another vibrational band of the molecule. The vibrational cross-angles are then converted into molecular conformations with the aid of calculations. The molecular conformations determined by the method are supported by X-ray diffraction and molecular dynamics simulation results. The experimental results suggest that thermodynamic interactions with solvent molecules are not altering the molecular conformations of MNA in the solutions to control their ultimate conformations in the crystals.

Confirming therapeutic target of protopine using immobilized β2 -adrenoceptor coupled with site-directed molecular docking and the target-drug interaction by frontal analysis and injection amount-dependent method.

PubMed

Liu, Guangxin; Wang, Pei; Li, Chan; Wang, Jing; Sun, Zhenyu; Zhao, Xinfeng; Zheng, Xiaohui

2017-07-01

Drug-protein interaction analysis is pregnant in designing new leads during drug discovery. We prepared the stationary phase containing immobilized β 2 -adrenoceptor (β 2 -AR) by linkage of the receptor on macroporous silica gel surface through N,N'-carbonyldiimidazole method. The stationary phase was applied in identifying antiasthmatic target of protopine guided by the prediction of site-directed molecular docking. Subsequent application of immobilized β 2 -AR in exploring the binding of protopine to the receptor was realized by frontal analysis and injection amount-dependent method. The association constants of protopine to β 2 -AR by the 2 methods were (1.00 ± 0.06) × 10 5 M -1 and (1.52 ± 0.14) × 10 4 M -1 . The numbers of binding sites were (1.23 ± 0.07) × 10 -7 M and (9.09 ± 0.06) × 10 -7 M, respectively. These results indicated that β 2 -AR is the specific target for therapeutic action of protopine in vivo. The target-drug binding occurred on Ser 169 in crystal structure of the receptor. Compared with frontal analysis, injection amount-dependent method is advantageous to drug saving, improvement of sampling efficiency, and performing speed. It has grave potential in high-throughput drug-receptor interaction analysis. Copyright © 2017 John Wiley & Sons, Ltd.

Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame.

PubMed

Deforges, Jules; de Breyne, Sylvain; Ameur, Melissa; Ulryck, Nathalie; Chamond, Nathalie; Saaidi, Afaf; Ponty, Yann; Ohlmann, Theophile; Sargueil, Bruno

2017-07-07

In the late phase of the HIV virus cycle, the unspliced genomic RNA is exported to the cytoplasm for the necessary translation of the Gag and Gag-pol polyproteins. Three distinct translation initiation mechanisms ensuring Gag production have been described with little rationale for their multiplicity. The Gag-IRES has the singularity to be located within Gag ORF and to directly interact with ribosomal 40S. Aiming at elucidating the specificity and the relevance of this interaction, we probed HIV-1 Gag-IRES structure and developed an innovative integrative modelling strategy to take into account all the gathered information. We propose a novel Gag-IRES secondary structure strongly supported by all experimental data. We further demonstrate the presence of two regions within Gag-IRES that independently and directly interact with the ribosome. Importantly, these binding sites are functionally relevant to Gag translation both in vitro and ex vivo. This work provides insight into the Gag-IRES molecular mechanism and gives compelling evidence for its physiological importance. It allows us to propose original hypotheses about the IRES physiological role and conservation among primate lentiviruses. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Profiling of 3696 Nuclear Receptor-Coregulator Interactions: A Resource for Biological and Clinical Discovery.

PubMed

Broekema, Marjoleine F; Hollman, Danielle A A; Koppen, Arjen; van den Ham, Henk-Jan; Melchers, Diana; Pijnenburg, Dirk; Ruijtenbeek, Rob; van Mil, Saskia W C; Houtman, René; Kalkhoven, Eric

2018-06-01

Nuclear receptors (NRs) are ligand-inducible transcription factors that play critical roles in metazoan development, reproduction, and physiology and therefore are implicated in a broad range of pathologies. The transcriptional activity of NRs critically depends on their interaction(s) with transcriptional coregulator proteins, including coactivators and corepressors. Short leucine-rich peptide motifs in these proteins (LxxLL in coactivators and LxxxIxxxL in corepressors) are essential and sufficient for NR binding. With 350 different coregulator proteins identified to date and with many coregulators containing multiple interaction motifs, an enormous combinatorial potential is present for selective NR-mediated gene regulation. However, NR-coregulator interactions have often been determined experimentally on a one-to-one basis across diverse experimental conditions. In addition, NR-coregulator interactions are difficult to predict because the molecular determinants that govern specificity are not well established. Therefore, many biologically and clinically relevant NR-coregulator interactions may remain to be discovered. Here, we present a comprehensive overview of 3696 NR-coregulator interactions by systematically characterizing the binding of 24 nuclear receptors with 154 coregulator peptides. We identified unique ligand-dependent NR-coregulator interaction profiles for each NR, confirming many well-established NR-coregulator interactions. Hierarchical clustering based on the NR-coregulator interaction profiles largely recapitulates the classification of NR subfamilies based on the primary amino acid sequences of the ligand-binding domains, indicating that amino acid sequence is an important, although not the only, molecular determinant in directing and fine-tuning NR-coregulator interactions. This NR-coregulator peptide interactome provides an open data resource for future biological and clinical discovery as well as NR-based drug design.

Centrobin–tubulin interaction is required for centriole elongation and stability

PubMed Central

Gudi, Radhika; Zou, Chaozhong; Li, Jun

2011-01-01

Centrobin is a daughter centriole protein that is essential for centrosome duplication. However, the molecular mechanism by which centrobin functions during centriole duplication remains undefined. In this study, we show that centrobin interacts with tubulin directly, and centrobin–tubulin interaction is pivotal for the function of centrobin during centriole duplication. We found that centrobin is recruited to the centriole biogenesis site via its interaction with tubulins during the early stage of centriole biogenesis, and its recruitment is dependent on hSAS-6 but not centrosomal P4.1–associated protein (CPAP) and CP110. The function of centrobin is also required for the elongation of centrioles, which is likely mediated by its interaction with tubulin. Furthermore, disruption of centrobin–tubulin interaction led to destabilization of existing centrioles and the preformed procentriole-like structures induced by CPAP expression, indicating that centrobin–tubulin interaction is critical for the stability of centrioles. Together, our study demonstrates that centrobin facilitates the elongation and stability of centrioles via its interaction with tubulins. PMID:21576394

Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations.

PubMed

Andrews, Casey T; Campbell, Brady A; Elcock, Adrian H

2017-04-11

Given the ubiquitous nature of protein-DNA interactions, it is important to understand the interaction thermodynamics of individual amino acid side chains for DNA. One way to assess these preferences is to perform molecular dynamics (MD) simulations. Here we report MD simulations of 20 amino acid side chain analogs interacting simultaneously with both a 70-base-pair double-stranded DNA and with a 70-nucleotide single-stranded DNA. The relative preferences of the amino acid side chains for dsDNA and ssDNA match well with values deduced from crystallographic analyses of protein-DNA complexes. The estimated apparent free energies of interaction for ssDNA, on the other hand, correlate well with previous simulation values reported for interactions with isolated nucleobases, and with experimental values reported for interactions with guanosine. Comparisons of the interactions with dsDNA and ssDNA indicate that, with the exception of the positively charged side chains, all types of amino acid side chain interact more favorably with ssDNA, with intercalation of aromatic and aliphatic side chains being especially notable. Analysis of the data on a base-by-base basis indicates that positively charged side chains, as well as sodium ions, preferentially bind to cytosine in ssDNA, and that negatively charged side chains, and chloride ions, preferentially bind to guanine in ssDNA. These latter observations provide a novel explanation for the lower salt dependence of DNA duplex stability in GC-rich sequences relative to AT-rich sequences.

End Groups of Functionalized Siloxane Oligomers Direct Block-Copolymeric or Liquid-Crystalline Self-Assembly Behavior

PubMed Central

2016-01-01

Monodisperse oligodimethylsiloxanes end-functionalized with the hydrogen-bonding ureidopyrimidinone (UPy) motif undergo phase separation between their aromatic end groups and dimethylsiloxane midblocks to form ordered nanostructures with domain spacings of <5 nm. The self-assembly behavior of these well-defined oligomers resembles that of high degree of polymerization (N)–high block interaction parameter (χ) linear diblock copolymers despite their small size. Specifically, the phase morphology varies from lamellar to hexagonal to body-centered cubic with increasing asymmetry in molecular volume fraction. Mixing molecules with different molecular weights to give dispersity >1.13 results in disorder, showing importance of molecular monodispersity for ultrasmall ordered phase separation. In contrast, oligodimethylsiloxanes end-functionalized with an O-benzylated UPy derivative self-assemble into lamellar nanostructures regardless of volume fraction because of the strong preference of the end groups to aggregate in a planar geometry. Thus, these molecules display more classically liquid-crystalline self-assembly behavior where the lamellar bilayer thickness is determined by the siloxane midblock. Here the lamellar nanostructure is tolerant to molecular polydispersity. We show the importance of end groups in high χ–low N block molecules, where block-copolymer-like self-assembly in our UPy-functionalized oligodimethylsiloxanes relies upon the dominance of phase separation effects over directional end group aggregation. PMID:27054381

Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes

PubMed Central

Nandy, Suman Kumar; Seal, Alpana

2016-01-01

Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases. PMID:27764212

DNA-binding and oxidative properties of cationic phthalocyanines and their dimeric complexes with anionic phthalocyanines covalently linked to oligonucleotides.

PubMed

Kuznetsova, A A; Lukyanets, E A; Solovyeva, L I; Knorre, D G; Fedorova, O S

2008-12-01

Design of chemically modified oligonucleotides for regulation of gene expression has attracted considerable attention over the past decades. One actively pursued approach involves antisense or antigene oligonucleotide constructs carrying reactive groups, many of these based on transition metal complexes. The complexes of Fe(II) and Co(II) with phthalocyanines are extremely good catalysts of oxidation of organic compounds with molecular oxygen and hydrogen peroxide. The binding of positively charged Fe(II) and Co(II) phthalocyanines with single- and double-stranded DNA was investigated. It was shown that these phthalocyanines interact with nucleic acids through an outside binding mode. The site-directed modification of single-stranded DNA by O2 and H2O2 in the presence of dimeric complexes of negatively and positively charged Fe(II) and Co(II) phthalocyanines was investigated. These complexes were formed directly on single-stranded DNA through interaction between negatively charged phthalocyanine in conjugate and positively charged phthalocyanine in solution. The resulting oppositely charged phthalocyanine complexes showed significant increase of catalytic activity compared with monomeric forms of phthalocyanines Fe(II) and Co(II). These complexes catalyzed the DNA oxidation with high efficacy and led to direct DNA strand cleavage. It was determined that oxidation of DNA by molecular oxygen catalyzed by complex of Fe(II)-phthalocyanines proceeds with higher rate than in the case of Co(II)-phthalocyanines but the latter led to a greater extent of target DNA modification.

Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain–Domain Interactions Mediating Protein–Protein Interactions

PubMed Central

Jothi, Raja; Cherukuri, Praveen F.; Tasneem, Asba; Przytycka, Teresa M.

2006-01-01

Recent advances in functional genomics have helped generate large-scale high-throughput protein interaction data. Such networks, though extremely valuable towards molecular level understanding of cells, do not provide any direct information about the regions (domains) in the proteins that mediate the interaction. Here, we performed co-evolutionary analysis of domains in interacting proteins in order to understand the degree of co-evolution of interacting and non-interacting domains. Using a combination of sequence and structural analysis, we analyzed protein–protein interactions in F1-ATPase, Sec23p/Sec24p, DNA-directed RNA polymerase and nuclear pore complexes, and found that interacting domain pair(s) for a given interaction exhibits higher level of co-evolution than the noninteracting domain pairs. Motivated by this finding, we developed a computational method to test the generality of the observed trend, and to predict large-scale domain–domain interactions. Given a protein–protein interaction, the proposed method predicts the domain pair(s) that is most likely to mediate the protein interaction. We applied this method on the yeast interactome to predict domain–domain interactions, and used known domain–domain interactions found in PDB crystal structures to validate our predictions. Our results show that the prediction accuracy of the proposed method is statistically significant. Comparison of our prediction results with those from two other methods reveals that only a fraction of predictions are shared by all the three methods, indicating that the proposed method can detect known interactions missed by other methods. We believe that the proposed method can be used with other methods to help identify previously unrecognized domain–domain interactions on a genome scale, and could potentially help reduce the search space for identifying interaction sites. PMID:16949097

Direct-Conversion Molecular Breast Imaging of Invasive Breast Cancer: Imaging Features, Extent of Invasive Disease, and Comparison Between Invasive Ductal and Lobular Histology.

PubMed

Conners, Amy Lynn; Jones, Katie N; Hruska, Carrie B; Geske, Jennifer R; Boughey, Judy C; Rhodes, Deborah J

2015-09-01

The purposes of this study were to compare the tumor appearance of invasive breast cancer on direct-conversion molecular breast imaging using a standardized lexicon and to determine how often direct-conversion molecular breast imaging identifies all known invasive tumor foci in the breast, and whether this differs for invasive ductal versus lobular histologic profiles. Patients with prior invasive breast cancer and concurrent direct-conversion molecular breast imaging examinations were retrospectively reviewed. Blinded review of direct-conversion molecular breast imaging examinations was performed by one of two radiologists, according to a validated lexicon. Direct-conversion molecular breast imaging findings were matched with lesions described on the pathology report to exclude benign reasons for direct-conversion molecular breast imaging findings and to document direct-conversion molecular breast imaging-occult tumor foci. Associations between direct-conversion molecular breast imaging findings and tumor histologic profiles were examined using chi-square tests. In 286 patients, 390 invasive tumor foci were present in 294 breasts. A corresponding direct-conversion molecular breast imaging finding was present for 341 of 390 (87%) tumor foci described on the pathology report. Invasive ductal carcinoma (IDC) tumor foci were more likely to be a mass (40% IDC vs 15% invasive lobular carcinoma [ILC]; p < 0.001) and to have marked intensity than were ILC foci (63% IDC vs 32% ILC; p < 0.001). Direct-conversion molecular breast imaging correctly revealed all pathology-proven foci of invasive disease in 79.8% of cases and was more likely to do so for IDC than for ILC (86.1% vs 56.7%; p < 0.0001). Overall, direct-conversion molecular breast imaging showed all known invasive foci in 249 of 286 (87%) patients. Direct-conversion molecular breast imaging features of invasive cancer, including lesion type and intensity, differ by histologic subtype. Direct-conversion molecular breast imaging is less likely to show all foci of ILC compared with IDC.

Complex molecular assemblies at hand via interactive simulations.

PubMed

Delalande, Olivier; Férey, Nicolas; Grasseau, Gilles; Baaden, Marc

2009-11-30

Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example. Copyright 2009 Wiley Periodicals, Inc.

MoCha: Molecular Characterization of Unknown Pathways.

PubMed

Lobo, Daniel; Hammelman, Jennifer; Levin, Michael

2016-04-01

Automated methods for the reverse-engineering of complex regulatory networks are paving the way for the inference of mechanistic comprehensive models directly from experimental data. These novel methods can infer not only the relations and parameters of the known molecules defined in their input datasets, but also unknown components and pathways identified as necessary by the automated algorithms. Identifying the molecular nature of these unknown components is a crucial step for making testable predictions and experimentally validating the models, yet no specific and efficient tools exist to aid in this process. To this end, we present here MoCha (Molecular Characterization), a tool optimized for the search of unknown proteins and their pathways from a given set of known interacting proteins. MoCha uses the comprehensive dataset of protein-protein interactions provided by the STRING database, which currently includes more than a billion interactions from over 2,000 organisms. MoCha is highly optimized, performing typical searches within seconds. We demonstrate the use of MoCha with the characterization of unknown components from reverse-engineered models from the literature. MoCha is useful for working on network models by hand or as a downstream step of a model inference engine workflow and represents a valuable and efficient tool for the characterization of unknown pathways using known data from thousands of organisms. MoCha and its source code are freely available online under the GPLv3 license.

Inhibition of plasminogen activator inhibitor-1 binding to endocytosis receptors of the low-density-lipoprotein receptor family by a peptide isolated from a phage display library

PubMed Central

Jensen, Jan K.; Malmendal, Anders; Schiøtt, Birgit; Skeldal, Sune; Pedersen, Katrine E.; Celik, Leyla; Nielsen, Niels Chr.; Andreasen, Peter A.; Wind, Troels

2006-01-01

The functions of the serpin PAI-1 (plasminogen activator inhibitor-1) are based on molecular interactions with its target proteases uPA and tPA (urokinase-type and tissue-type plasminogen activator respectively), with vitronectin and with endocytosis receptors of the low-density-lipoprotein family. Understanding the significance of these interactions would be facilitated by the ability to block them individually. Using phage display, we have identified the disulfide-constrained peptide motif CFGWC with affinity for natural human PAI-1. The three-dimensional structure of a peptide containing this motif (DVPCFGWCQDA) was determined by liquid-state NMR spectroscopy. A binding site in the so-called flexible joint region of PAI-1 was suggested by molecular modelling and validated through binding studies with various competitors and site-directed mutagenesis of PAI-1. The peptide with an N-terminal biotin inhibited the binding of the uPA–PAI-1 complex to the endocytosis receptors low-density-lipoprotein-receptor-related protein 1A (LRP-1A) and very-low-density-lipoprotein receptor (VLDLR) in vitro and inhibited endocytosis of the uPA–PAI-1 complex in U937 cells. We conclude that the isolated peptide represents a novel approach to pharmacological interference with the functions of PAI-1 based on inhibition of one specific molecular interaction. PMID:16813566

Self-evolving atomistic kinetic Monte Carlo simulations of defects in materials

DOE PAGES

Xu, Haixuan; Beland, Laurent K.; Stoller, Roger E.; ...

2015-01-29

The recent development of on-the-fly atomistic kinetic Monte Carlo methods has led to an increased amount attention on the methods and their corresponding capabilities and applications. In this review, the framework and current status of Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) are discussed. SEAKMC particularly focuses on defect interaction and evolution with atomistic details without assuming potential defect migration/interaction mechanisms and energies. The strength and limitation of using an active volume, the key concept introduced in SEAKMC, are discussed. Potential criteria for characterizing an active volume are discussed and the influence of active volume size on saddle point energies ismore » illustrated. A procedure starting with a small active volume followed by larger active volumes was found to possess higher efficiency. Applications of SEAKMC, ranging from point defect diffusion, to complex interstitial cluster evolution, to helium interaction with tungsten surfaces, are summarized. A comparison of SEAKMC with molecular dynamics and conventional object kinetic Monte Carlo is demonstrated. Overall, SEAKMC is found to be complimentary to conventional molecular dynamics, especially when the harmonic approximation of transition state theory is accurate. However it is capable of reaching longer time scales than molecular dynamics and it can be used to systematically increase the accuracy of other methods such as object kinetic Monte Carlo. Furthermore, the challenges and potential development directions are also outlined.« less

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations.

PubMed

Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

2012-04-14

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

NASA Astrophysics Data System (ADS)

Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

2012-04-01

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ17-42 protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ17-42 protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ17-42 are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ17-42 protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

Investigating Ebola virus pathogenicity using molecular dynamics.

PubMed

Pappalardo, Morena; Collu, Francesca; Macpherson, James; Michaelis, Martin; Fraternali, Franca; Wass, Mark N

2017-08-11

Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.

Expression of Cry1Ac toxin-binding region in Plutella xyllostella cadherin-like receptor and studying their interaction mode by molecular docking and site-directed mutagenesis.

PubMed

Hu, Xiaodan; Zhang, Xiao; Zhong, Jianfeng; Liu, Yuan; Zhang, Cunzheng; Xie, Yajing; Lin, Manman; Xu, Chongxin; Lu, Lina; Zhu, Qing; Liu, Xianjin

2018-05-01

Cadherin-like protein has been identified as the primary Bacillus thuringiensis (Bt) Cry toxin receptor in Lepidoptera pests and plays a key role in Cry toxin insecticidal. In this study, we successfully expressed the putative Cry1Ac toxin-binding region (CR7-CR11) of Plutella xylostella cadherin-like in Escherichia coli BL21 (DE3). The expressed CR7-CR11 fragment showed binding ability to Cry1Ac toxin under denaturing (Ligand blot) and non-denaturing (ELISA) conditions. The three-dimensional structure of CR7-CR11 was constructed by homology modeling. Molecular docking results of CR7-CR11 and Cry1Ac showed that domain II and domain III of Cry1Ac were taking part in binding to CR7-CR11, while CR7-CR8 was the region of CR7-CR11 in interacting with Cry1Ac. The interaction of toxin-receptor complex was found to arise from hydrogen bond and hydrophobic interaction. Through the computer-aided alanine mutation scanning, amino acid residues of Cry1Ac (Met341, Asn442 and Ser486) and CR7-CR11 (Asp32, Arg101 and Arg127) were predicted as the hot spot residues involved in the interaction of the toxin-receptor complex. At last, we verified the importance role of these key amino acid residues by binding assay. These results will lay a foundation for further elucidating the insecticidal mechanism of Cry toxin and enhancing Cry toxin insecticidal activity by molecular modification. Copyright © 2018 Elsevier B.V. All rights reserved.

Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4+ Interactions.

PubMed

Khan, Hanif M; Grauffel, Cédric; Broer, Ria; MacKerell, Alexander D; Havenith, Remco W A; Reuter, Nathalie

2016-11-08

Cation-π interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH 3 ) 3 ) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol-tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARMM36 and Drude polarizable force fields in modeling tyrosine-choline interactions. We show that the potential energy surface (PES) obtained using SAPT2+/aug-cc-pVDZ compares well with the large basis-set CCSD(T) PES when TMA approaches the phenol ring perpendicularly. Furthermore, the SAPT energy decomposition reveals comparable contributions from electrostatics and dispersion in phenol-TMA interactions. We then compared the SAPT2+/aug-cc-pVDZ PES obtained along various approach directions to the corresponding PES obtained with CHARMM, and we show that the force field accurately reproduces the minimum distances while the interaction energies are underestimated. The use of the Drude polarizable force field significantly improves the interaction energies but decreases the agreement on distances at energy minima. The best agreement between force field and QM PES is obtained by modifying the Lennard-Jones terms for atom pairs involved in the phenol-TMA cation-π interactions. This is further shown to improve the correlation between the occupancy of tyrosine-choline cation-π interactions obtained from molecular dynamics simulations of a bilayer-bound bacterial phospholipase and experimental affinity data of the wild-type protein and selected mutants.

Chirally directed formation of nanometer-scale proline clusters.

PubMed

Myung, Sunnie; Fioroni, Marco; Julian, Ryan R; Koeniger, Stormy L; Baik, Mu-Hyun; Clemmer, David E

2006-08-23

Ion mobility measurements, combined with molecular mechanics simulations, are used to study enantiopure and racemic proline clusters formed by electrospray ionization. Broad distributions of cluster sizes and charge states are observed, ranging from clusters containing only a few proline units to clusters that contain more than 100 proline units (i.e., protonated clusters of the form [xPro + nH](n+) with x = 1 to >100 and n = 1-7). As the sizes of clusters increase, there is direct evidence for nanometer scale, chirally induced organization into specific structures. For n = 4 and 5, enantiopure clusters of approximately 50 to 100 prolines assemble into structures that are more elongated than the most compact structure that is observed from the racemic proline clusters. A molecular analogue, cis-4-hydroxy-proline, displays significantly different behavior, indicating that in addition to the rigidity of the side chain ring, intermolecular interactions are important in the formation of chirally directed clusters. This is the first case in which assemblies of chirally selective elongated structures are observed in this size range of amino acid clusters. Relationships between enantiopurity, cluster shape, and overall energetics are discussed.

A molecular design principle of lyotropic liquid-crystalline conjugated polymers with directed alignment capability for plastic electronics

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

Kim, Bong-Gi; Jeong, Eun Jeong; Chung, Jong Won

Conjugated polymers with a one-dimensional p-orbital overlap exhibit optoelectronic anisotropy. Their unique anisotropic properties can be fully realized in device applications only when the conjugated chains are aligned. Here, we report a molecular design principle of conjugated polymers to achieve concentration-regulated chain planarization, self-assembly, liquid-crystal-like good mobility and non-interdigitated side chains. As a consequence of these intra- and intermolecular attributes, chain alignment along an applied flow field occurs. This liquid-crystalline conjugated polymer was realized by incorporating intramolecular sulphur–fluorine interactions and bulky side chains linked to a tetrahedral carbon having a large form factor. By optimizing the polymer concentration and themore » flow field, we could achieve a high dichroic ratio of 16.67 in emission from conducting conjugated polymer films. Two-dimensional grazing-incidence X-ray diffraction was performed to analyse a well-defined conjugated polymer alignment. Thin-film transistors built on highly aligned conjugated polymer films showed more than three orders of magnitude faster carrier mobility along the conjugated polymer alignment direction than the perpendicular direction.« less

Investigation of the Ligand-Nanoparticle Interface: A Cryogenic Approach for Preserving Surface Chemistry

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

Karakoti, Ajay S.; Yang, Ping; Wang, Weina

2018-02-15

Ligand functionalized nanoparticles have replaced bare nanoparticles from most biological applications. These applications require tight control over size and stability of nanoparticles in aqueous medium. Understanding the mechanism of interaction of nanoparticle surfaces with functional groups of different organic ligands such as carboxylic acids is confounding despite the two decades of research on nanoparticles because of the inability to characterize their surfaces in their immediate environment. Often the surface interaction is understood by correlating the information available, in a piecemeal approach, from surface sensitive spectroscopic information of ligands and the bulk and surface information of nanoparticles. In present study wemore » report the direct interaction of 5-7 nm cerium oxide nanoparticles surface with acetic acid. In-situ XPS study was carried out by freezing the aqueous solution of nanoparticles to liquid nitrogen temperatures. Analysis of data collected concurrently from the ligands as well as functionalized frozen cerium oxide nanoparticles show that the acetic acid binds to the ceria surface in both dissociated and molecular state with equal population over the surface. The cerium oxide surface was populated predominantly with Ce4+ ions consistent with the thermal hydrolysis synthesis. DFT calculations reveal that the acetate ions bind more strongly to the cerium oxide nanoparticles as compared to the water and can replace the hydration sphere of nanoparticles resulting in high acetate/acetic surface coverage. These findings reveal molecular level interaction between the nanoparticle surfaces and ligands giving a better understanding of how materials behave in their immediate aqueous environment. This study also proposes a simple and elegant methodology to directly study the surface functional groups attached to nanoparticles in their immediate aqueous environment.« less

Investigation of the Ligand–Nanoparticle Interface: A Cryogenic Approach for Preserving Surface Chemistry

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

Karakoti, Ajay S.; Yang, Ping; Wang, Weina

Ligand functionalized nanoparticles have replaced bare nanoparticles from most biological applications. These applications require tight control over size and stability of nanoparticles in aqueous medium. Understanding the mechanism of interaction of nanoparticle surfaces with functional groups of different organic ligands such as carboxylic acids is confounding despite the two decades of research on nanoparticles because of the inability to characterize their surfaces in their immediate environment. Often the surface interaction is understood by correlating the information available, in a piecemeal approach, from surface sensitive spectroscopic information of ligands and the bulk and surface information of nanoparticles. In present study wemore » report the direct interaction of 5-7 nm cerium oxide nanoparticles surface with acetic acid. In-situ XPS study was carried out by freezing the aqueous solution of nanoparticles to liquid nitrogen temperatures. Analysis of data collected concurrently from the ligands as well as functionalized frozen cerium oxide nanoparticles show that the acetic acid binds to the ceria surface in both dissociated and molecular state with equal population over the surface. The cerium oxide surface was populated predominantly with Ce4+ ions consistent with the thermal hydrolysis synthesis. DFT calculations reveal that the acetate ions bind more strongly to the cerium oxide nanoparticles as compared to the water and can replace the hydration sphere of nanoparticles resulting in high acetate/acetic surface coverage. These findings reveal molecular level interaction between the nanoparticle surfaces and ligands giving a better understanding of how materials behave in their immediate aqueous environment. This study also proposes a simple and elegant methodology to directly study the surface functional groups attached to nanoparticles in their immediate aqueous environment.« less

A simple model for electrical charge in globular macromolecules and linear polyelectrolytes in solution

NASA Astrophysics Data System (ADS)

Krishnan, M.

2017-05-01

We present a model for calculating the net and effective electrical charge of globular macromolecules and linear polyelectrolytes such as proteins and DNA, given the concentration of monovalent salt and pH in solution. The calculation is based on a numerical solution of the non-linear Poisson-Boltzmann equation using a finite element discretized continuum approach. The model simultaneously addresses the phenomena of charge regulation and renormalization, both of which underpin the electrostatics of biomolecules in solution. We show that while charge regulation addresses the true electrical charge of a molecule arising from the acid-base equilibria of its ionizable groups, charge renormalization finds relevance in the context of a molecule's interaction with another charged entity. Writing this electrostatic interaction free energy in terms of a local electrical potential, we obtain an "interaction charge" for the molecule which we demonstrate agrees closely with the "effective charge" discussed in charge renormalization and counterion-condensation theories. The predictions of this model agree well with direct high-precision measurements of effective electrical charge of polyelectrolytes such as nucleic acids and disordered proteins in solution, without tunable parameters. Including the effective interior dielectric constant for compactly folded molecules as a tunable parameter, the model captures measurements of effective charge as well as published trends of pKa shifts in globular proteins. Our results suggest a straightforward general framework to model electrostatics in biomolecules in solution. In offering a platform that directly links theory and experiment, these calculations could foster a systematic understanding of the interrelationship between molecular 3D structure and conformation, electrical charge and electrostatic interactions in solution. The model could find particular relevance in situations where molecular crystal structures are not available or rapid, reliable predictions are desired.

OsBRI1 Activates BR Signaling by Preventing Binding between the TPR and Kinase Domains of OsBSK3 via Phosphorylation.

PubMed

Zhang, Baowen; Wang, Xiaolong; Zhao, Zhiying; Wang, Ruiju; Huang, Xiahe; Zhu, Yali; Yuan, Li; Wang, Yingchun; Xu, Xiaodong; Burlingame, Alma L; Gao, Yingjie; Sun, Yu; Tang, Wenqiang

2016-02-01

Many plant receptor kinases transduce signals through receptor-like cytoplasmic kinases (RLCKs); however, the molecular mechanisms that create an effective on-off switch are unknown. The receptor kinase BR INSENSITIVE1 (BRI1) transduces brassinosteroid (BR) signal by phosphorylating members of the BR-signaling kinase (BSK) family of RLCKs, which contain a kinase domain and a C-terminal tetratricopeptide repeat (TPR) domain. Here, we show that the BR signaling function of BSKs is conserved in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) and that the TPR domain of BSKs functions as a "phospho-switchable" autoregulatory domain to control BSKs' activity. Genetic studies revealed that OsBSK3 is a positive regulator of BR signaling in rice, while in vivo and in vitro assays demonstrated that OsBRI1 interacts directly with and phosphorylates OsBSK3. The TPR domain of OsBSK3, which interacts directly with the protein's kinase domain, serves as an autoinhibitory domain to prevent OsBSK3 from interacting with bri1-SUPPRESSOR1 (BSU1). Phosphorylation of OsBSK3 by OsBRI1 disrupts the interaction between its TPR and kinase domains, thereby increasing the binding between OsBSK3's kinase domain and BSU1. Our results not only demonstrate that OsBSK3 plays a conserved role in regulating BR signaling in rice, but also provide insight into the molecular mechanism by which BSK family proteins are inhibited under basal conditions but switched on by the upstream receptor kinase BRI1. © 2016 American Society of Plant Biologists. All Rights Reserved.

Type I γ Phosphatidylinositol Phosphate 5-Kinase i5 Controls the Ubiquitination and Degradation of the Tumor Suppressor Mitogen-inducible Gene 6*

PubMed Central

Sun, Ming; Cai, Jinyang; Anderson, Richard A.; Sun, Yue

2016-01-01

Mitogen-inducible gene 6 (Mig6) is a tumor suppressor, and the disruption of Mig6 expression is associated with cancer development. Mig6 directly interacts with epidermal growth factor receptor (EGFR) to suppress the activation and downstream signaling of EGFR. Therefore, loss of Mig6 enhances EGFR-mediated signaling and promotes EGFR-dependent carcinogenesis. The molecular mechanism modulating Mig6 expression in cancer remains unclear. Here we demonstrate that type I γ phosphatidylinositol phosphate 5-kinase i5 (PIPKIγi5), an enzyme producing phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), stabilizes Mig6 expression. Knockdown of PIPKIγi5 leads to the loss of Mig6 expression, which dramatically enhances and prolongs EGFR-mediated cell signaling. Loss of PIPKIγi5 significantly promotes Mig6 protein degradation via proteasomes, but it does not affect the Mig6 mRNA level. PIPKIγi5 directly interacts with the E3 ubiquitin ligase neuronal precursor cell-expressed developmentally down-regulated 4-1 (NEDD4-1). The C-terminal domain of PIPKIγi5 and the WW1 and WW2 domains of NEDD4-1 are required for their interaction. The C2 domain of NEDD4-1 is required for its interaction with PtdIns(4,5)P2. By binding with NEDD4-1 and producing PtdIns(4,5)P2, PIPKIγi5 perturbs NEDD4-1-mediated Mig6 ubiquitination and the subsequent proteasomal degradation. Thus, loss of NEDD4-1 can rescue Mig6 expression in PIPKIγi5 knockdown cells. In this way, PIPKIγi5, NEDD4-1, and Mig6 form a novel molecular nexus that controls EGFR activation and downstream signaling. PMID:27557663

A Review of the Interactions between Alcohol and the Endocannabinoid System: Implications for Alcohol Dependence and Future Directions for Research

PubMed Central

Pava, Matthew J.; Woodward, John J.

2012-01-01

Over the past fifty years a significant body of evidence has been compiled suggesting an interaction between the endocannabinoid (EC) system and alcohol dependence. However, much of this work has been conducted only in the past two decades following the elucidation of the molecular constituents of the EC system that began with the serendipitous discovery of the cannabinoid 1 receptor (CB1). Since then, novel pharmacological and genetic tools have enabled researchers to manipulate select components of the EC system, to determine their contribution to the motivation to consume ethanol. From these preclinical studies, it is evident that CB1 contributes the motivational and reinforcing properties of ethanol, and chronic consumption of ethanol alters EC transmitter levels and CB1 expression in brain nuclei associated with addiction pathways. These results are augmented by in vitro and ex vivo studies showing that acute and chronic treatment with ethanol produces physiologically relevant alterations in the function of the EC system. This report provides a current and comprehensive review of the literature regarding the interactions between ethanol and the EC system. We begin be reviewing the studies published prior to the discovery of the EC system that compared the behavioral and physiological effects of cannabinoids with ethanol in addition to cross-tolerance between these drugs. Next, a brief overview of the molecular constituents of the EC system is provided as context for the subsequent review of more recent studies examining the interaction of ethanol with the EC system. These results are compiled into a summary providing a scheme for the known changes to the components of the EC system in different stages of alcohol dependence. Finally, future directions for research are discussed. PMID:22459871

Structural insights into pharmacophore-assisted in silico identification of protein-protein interaction inhibitors for inhibition of human toll-like receptor 4 - myeloid differentiation factor-2 (hTLR4-MD-2) complex.

PubMed

Mishra, Vinita; Pathak, Chandramani

2018-05-29

Toll-like receptor 4 (TLR4) is a member of Toll-Like Receptors (TLRs) family that serves as a receptor for bacterial lipopolysaccharide (LPS). TLR4 alone cannot recognize LPS without aid of co-receptor myeloid differentiation factor-2 (MD-2). Binding of LPS with TLR4 forms a LPS-TLR4-MD-2 complex and directs downstream signaling for activation of immune response, inflammation and NF-κB activation. Activation of TLR4 signaling is associated with various pathophysiological consequences. Therefore, targeting protein-protein interaction (PPI) in TLR4-MD-2 complex formation could be an attractive therapeutic approach for targeting inflammatory disorders. The aim of present study was directed to identify small molecule PPI inhibitors (SMPPIIs) using pharmacophore mapping-based approach of computational drug discovery. Here, we had retrieved the information about the hot spot residues and their pharmacophoric features at both primary (TLR4-MD-2) and dimerization (MD-2-TLR4*) protein-protein interaction interfaces in TLR4-MD-2 homo-dimer complex using in silico methods. Promising candidates were identified after virtual screening, which may restrict TLR4-MD-2 protein-protein interaction. In silico off-target profiling over the virtually screened compounds revealed other possible molecular targets. Two of the virtually screened compounds (C11 and C15) were predicted to have an inhibitory concentration in μM range after HYDE assessment. Molecular dynamics simulation study performed for these two compounds in complex with target protein confirms the stability of the complex. After virtual high throughput screening we found selective hTLR4-MD-2 inhibitors, which may have therapeutic potential to target chronic inflammatory diseases.

Structural Studies of the Nedd4 WW Domains and Their Selectivity for the Connexin43 (Cx43) Carboxyl Terminus.

PubMed

Spagnol, Gaelle; Kieken, Fabien; Kopanic, Jennifer L; Li, Hanjun; Zach, Sydney; Stauch, Kelly L; Grosely, Rosslyn; Sorgen, Paul L

2016-04-01

Neuronal precursor cell-expressed developmentally down-regulated 4 (Nedd4) was the first ubiquitin protein ligase identified to interact with connexin43 (Cx43), and its suppressed expression results in accumulation of gap junction plaques at the plasma membrane. Nedd4-mediated ubiquitination of Cx43 is required to recruit Eps15 and target Cx43 to the endocytic pathway. Although the Cx43 residues that undergo ubiquitination are still unknown, in this study we address other unresolved questions pertaining to the molecular mechanisms mediating the direct interaction between Nedd4 (WW1-3 domains) and Cx43 (carboxyl terminus (CT)). All three WW domains display a similar three antiparallel β-strand structure and interact with the same Cx43CT(283)PPXY(286)sequence. Although Tyr(286)is essential for the interaction, MAPK phosphorylation of the preceding serine residues (Ser(P)(279)and Ser(P)(282)) increases the binding affinity by 2-fold for the WW domains (WW2 > WW3 ≫ WW1). The structure of the WW2·Cx43CT(276-289)(Ser(P)(279), Ser(P)(282)) complex reveals that coordination of Ser(P)(282)with the end of β-strand 3 enables Ser(P)(279)to interact with the back face of β-strand 3 (Tyr(286)is on the front face) and loop 2, forming a horseshoe-shaped arrangement. The close sequence identity of WW2 with WW1 and WW3 residues that interact with the Cx43CT PPXY motif and Ser(P)(279)/Ser(P)(282)strongly suggests that the significantly lower binding affinity of WW1 is the result of a more rigid structure. This study presents the first structure illustrating how phosphorylation of the Cx43CT domain helps mediate the interaction with a molecular partner involved in gap junction regulation. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Molecular Basis of Autophagic Cell Death in Prostate Cancer

DTIC Science & Technology

2009-03-01

lipid-binding proteinwith high affinity for phosphatidic acid (PA) and cardiolipin (CL). Previously, it has been shown that PA directly interacted...lyceride), PI (phosphatidylinositol), DAG (diacylglycerol), PI4P (PtdIns(4)P), PA ( phosphatidic acid ), PI4,5P2 (PtdIns(4,5)P2), PS (phosphatidylserine...with high affinity for phosphatidic acid and cardiolipin and less affinity for various phosphoinositides. Functional genomics analysis identified 5

The Self-Assembly of Particles with Multipolar Interactions

DTIC Science & Technology

2004-01-01

the LATEX template in which this thesis has been written. I also thank Kevin Van Workum and Jack Douglas for contributing simulation work and some...of the computational expense of simulating such complex self-assembly systems at the molecular level and a desire to understand the self-assembly at...Dissertation directed by: Professor Wolfgang Losert Department of Physics In this thesis , we describe results from investigations of the self-assembly of

Molecular Mechanisms for Synaptic Modification in the Visual Cortex: Interaction between Theory and Experiment

DTIC Science & Technology

1989-02-03

known that the large majority of neurons in layers Ill, IV and VI receive direct monosynaptic input from the lateral geniculate nucleus (Toyama et al...1974; Ferster and Lindstrom, 1983; Martin, 1987). The receptive fields of lateral geniculate nucleus (LGN) neurons resemble those of retinal ganglion...the lateral geniculate nucleus only. The second stage of the theoretical analysis requires that relevant intracortical connections be incorporated

Local Bonding Influence on the Band Edge and Band Gap Formation in Quaternary Chalcopyrites.

PubMed

Miglio, Anna; Heinrich, Christophe P; Tremel, Wolfgang; Hautier, Geoffroy; Zeier, Wolfgang G

2017-09-01

Quaternary chalcopyrites have shown to exhibit tunable band gaps with changing anion composition. Inspired by these observations, the underlying structural and electronic considerations are investigated using a combination of experimentally obtained structural data, molecular orbital considerations, and density functional theory. Within the solid solution Cu 2 ZnGeS 4- x Se x , the anion bond alteration parameter changes, showing larger bond lengths for metal-selenium than for metal-sulfur bonds. The changing bonding interaction directly influences the valence and conduction band edges, which result from antibonding Cu-anion and Ge-anion interactions, respectively. The knowledge of the underlying bonding interactions at the band edges can help design properties of these quaternary chalcopyrites for photovoltaic and thermoelectric applications.

Fermi orbital self-interaction corrected electronic structure of molecules beyond local density approximation

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

Hahn, T., E-mail: torsten.hahn@physik.tu-freiberg.de; Liebing, S.; Kortus, J.

2015-12-14

The correction of the self-interaction error that is inherent to all standard density functional theory calculations is an object of increasing interest. In this article, we apply the very recently developed Fermi-orbital based approach for the self-interaction correction [M. R. Pederson et al., J. Chem. Phys. 140, 121103 (2014) and M. R. Pederson, J. Chem. Phys. 142, 064112 (2015)] to a set of different molecular systems. Our study covers systems ranging from simple diatomic to large organic molecules. We focus our analysis on the direct estimation of the ionization potential from orbital eigenvalues. Further, we show that the Fermi orbitalmore » positions in structurally similar molecules appear to be transferable.« less

Determination of partial molar volumes from free energy perturbation theory†

PubMed Central

Vilseck, Jonah Z.; Tirado-Rives, Julian

2016-01-01

Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood–Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm3 mol−1. The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute–solvent interactions. PMID:25589343

Determination of partial molar volumes from free energy perturbation theory.

PubMed

Vilseck, Jonah Z; Tirado-Rives, Julian; Jorgensen, William L

2015-04-07

Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.

Subcellular Fractionation and Localization Studies Reveal a Direct Interaction of the Fragile X Mental Retardation Protein (FMRP) with Nucleolin

PubMed Central

Taha, Mohamed S.; Nouri, Kazem; Milroy, Lech G.; Moll, Jens M.; Herrmann, Christian; Brunsveld, Luc; Piekorz, Roland P.; Ahmadian, Mohammad R.

2014-01-01

Fragile X mental Retardation Protein (FMRP) is a well-known regulator of local translation of its mRNA targets in neurons. However, despite its ubiquitous expression, the role of FMRP remains ill-defined in other cell types. In this study we investigated the subcellular distribution of FMRP and its protein complexes in HeLa cells using confocal imaging as well as detergent-free fractionation and size exclusion protocols. We found FMRP localized exclusively to solid compartments, including cytosolic heavy and light membranes, mitochondria, nuclear membrane and nucleoli. Interestingly, FMRP was associated with nucleolin in both a high molecular weight ribosomal and translation-associated complex (≥6 MDa) in the cytosol, and a low molecular weight complex (∼200 kDa) in the nucleoli. Consistently, we identified two functional nucleolar localization signals (NoLSs) in FMRP that are responsible for a strong nucleolar colocalization of the C-terminus of FMRP with nucleolin, and a direct interaction of the N-terminus of FMRP with the arginine-glycine-glycine (RGG) domain of nucleolin. Taken together, we propose a novel mechanism by which a transient nucleolar localization of FMRP underlies a strong nucleocytoplasmic translocation, most likely in a complex with nucleolin and possibly ribosomes, in order to regulate translation of its target mRNAs. PMID:24658146

Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface.

PubMed

Wojcik, John; Lamontanara, Allan Joaquim; Grabe, Grzegorz; Koide, Akiko; Akin, Louesa; Gerig, Barbara; Hantschel, Oliver; Koide, Shohei

2016-04-15

Bcr-Abl is a constitutively active kinase that causes chronic myelogenous leukemia. We have shown that a tandem fusion of two designed binding proteins, termed monobodies, directed to the interaction interface between the Src homology 2 (SH2) and kinase domains and to the phosphotyrosine-binding site of the SH2 domain, respectively, inhibits the Bcr-Abl kinase activity. Because the latter monobody inhibits processive phosphorylation by Bcr-Abl and the SH2-kinase interface is occluded in the active kinase, it remained undetermined whether targeting the SH2-kinase interface alone was sufficient for Bcr-Abl inhibition. To address this question, we generated new, higher affinity monobodies with single nanomolar KD values targeting the kinase-binding surface of SH2. Structural and mutagenesis studies revealed the molecular underpinnings of the monobody-SH2 interactions. Importantly, the new monobodies inhibited Bcr-Abl kinase activity in vitro and in cells, and they potently induced cell death in chronic myelogenous leukemia cell lines. This work provides strong evidence for the SH2-kinase interface as a pharmacologically tractable site for allosteric inhibition of Bcr-Abl. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

PubMed Central

Kerrien, Samuel; Orchard, Sandra; Montecchi-Palazzi, Luisa; Aranda, Bruno; Quinn, Antony F; Vinod, Nisha; Bader, Gary D; Xenarios, Ioannis; Wojcik, Jérôme; Sherman, David; Tyers, Mike; Salama, John J; Moore, Susan; Ceol, Arnaud; Chatr-aryamontri, Andrew; Oesterheld, Matthias; Stümpflen, Volker; Salwinski, Lukasz; Nerothin, Jason; Cerami, Ethan; Cusick, Michael E; Vidal, Marc; Gilson, Michael; Armstrong, John; Woollard, Peter; Hogue, Christopher; Eisenberg, David; Cesareni, Gianni; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. Results The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. Conclusion The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel. PMID:17925023

Interaction of cationic surfactants with DNA: a single-molecule study

PubMed Central

Husale, Sudhir; Grange, Wilfried; Karle, Marc; Bürgi, Stephan; Hegner, Martin

2008-01-01

The interaction of cationic surfactants with single dsDNA molecules has been studied using force-measuring optical tweezers. For hydrophobic chains of length 12 and greater, pulling experiments show characteristic features (e.g. hysteresis between the pulling and relaxation curves, force-plateau along the force curves), typical of a condensed phase (compaction of a long DNA into a micron-sized particle). Depending on the length of the hydrophobic chain of the surfactant, we observe different mechanical behaviours of the complex (DNA-surfactants), which provide evidence for different binding modes. Taken together, our measurements suggest that short-chain surfactants, which do not induce any condensation, could lie down on the DNA surface and directly interact with the DNA grooves through hydrophobic–hydrophobic interactions. In contrast, long-chain surfactants could have their aliphatic tails pointing away from the DNA surface, which could promote inter-molecular interactions between hydrophobic chains and subsequently favour DNA condensation. PMID:18203749

Valence ionized states of iron pentacarbonyl and eta5-cyclopentadienyl cobalt dicarbonyl studied by symmetry-adapted cluster-configuration interaction calculation and collision-energy resolved Penning ionization electron spectroscopy.

PubMed

Fukuda, Ryoichi; Ehara, Masahiro; Nakatsuji, Hiroshi; Kishimoto, Naoki; Ohno, Koichi

2010-02-28

Valence ionized states of iron pentacarbonyl Fe(CO)(5) and eta(5)-cyclopentadienyl cobalt dicarbonyl Co(eta(5)-C(5)H(5))(CO)(2) have been studied by ultraviolet photoelectron spectroscopy, two-dimensional Penning ionization electron spectroscopy (2D-PIES), and symmetry-adapted cluster-configuration interaction calculations. Theory provided reliable assignments for the complex ionization spectra of these molecules, which have metal-carbonyl bonds. Theoretical ionization energies agreed well with experimental observations and the calculated wave functions could explain the relative intensities of PIES spectra. The collision-energy dependence of partial ionization cross sections (CEDPICS) was obtained by 2D-PIES. To interpret these CEDPICS, the interaction potentials between the molecules and a Li atom were examined in several coordinates by calculations. The relation between the slope of the CEDPICS and the electronic structure of the ionized states, such as molecular symmetry and the spatial distribution of ionizing orbitals, was analyzed. In Fe(CO)(5), an attractive interaction was obtained for the equatorial CO, while the interaction for the axial CO direction was repulsive. For Co(eta(5)-C(5)H(5))(CO)(2), the interaction potential in the direction of both Co-C-O and Co-Cp ring was attractive. These anisotropic interactions and ionizing orbital distributions consistently explain the relative slopes of the CEDPICS.

Structure and energetics of hydrogen-bonded networks of methanol on close packed transition metal surfaces

NASA Astrophysics Data System (ADS)

Murphy, Colin J.; Carrasco, Javier; Lawton, Timothy J.; Liriano, Melissa L.; Baber, Ashleigh E.; Lewis, Emily A.; Michaelides, Angelos; Sykes, E. Charles H.

2014-07-01

Methanol is a versatile chemical feedstock, fuel source, and energy storage material. Many reactions involving methanol are catalyzed by transition metal surfaces, on which hydrogen-bonded methanol overlayers form. As with water, the structure of these overlayers is expected to depend on a delicate balance of hydrogen bonding and adsorbate-substrate bonding. In contrast to water, however, relatively little is known about the structures methanol overlayers form and how these vary from one substrate to another. To address this issue, herein we analyze the hydrogen bonded networks that methanol forms as a function of coverage on three catalytically important surfaces, Au(111), Cu(111), and Pt(111), using a combination of scanning tunneling microscopy and density functional theory. We investigate the effect of intermolecular interactions, surface coverage, and adsorption energies on molecular assembly and compare the results to more widely studied water networks on the same surfaces. Two main factors are shown to direct the structure of methanol on the surfaces studied: the surface coverage and the competition between the methanol-methanol and methanol-surface interactions. Additionally, we report a new chiral form of buckled hexamer formed by surface bound methanol that maximizes the interactions between methanol monomers by sacrificing interactions with the surface. These results serve as a direct comparison of interaction strength, assembly, and chirality of methanol networks on Au(111), Cu(111), and Pt(111) which are catalytically relevant for methanol oxidation, steam reforming, and direct methanol fuel cells.

PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.

PubMed

Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E

2017-01-04

The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

ALS-linked mutant SOD1 proteins promote Aβ aggregates in ALS through direct interaction with Aβ.

PubMed

Jang, Ja-Young; Cho, Hyungmin; Park, Hye-Yoon; Rhim, Hyangshuk; Kang, Seongman

2017-11-04

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive degeneration of motor neurons. Aggregation of ALS-linked mutant Cu/Zn superoxide dismutase (SOD1) is a hallmark of a subset of familial ALS (fALS). Recently, intracellular amyloid-β (Aβ) is detected in motor neurons of both sporadic and familial ALS. We have previously shown that intracellular Aβ specifically interacts with G93A, an ALS-linked SOD1 mutant. However, little is known about the pathological and biological effect of this interaction in neurons. In this study, we have demonstrated that the Aβ-binding region is exposed on the SOD1 surface through the conformational changes due to misfolding of SOD1. Interestingly, we found that the intracellular aggregation of Aβ is enhanced through the direct interaction of Aβ with the Aβ-binding region exposed to misfolded SOD1. Ultimately, increased Aβ aggregation by this interaction promotes neuronal cell death. Consistent with this result, Aβ aggregates was three-fold higher in the brains of G93A transgenic mice than those of non Tg. Our study provides the first direct evidence that Aβ, an AD-linked factor, is associated to the pathogenesis of ALS and provides molecular clues to understand common aggregation mechanisms in the pathogenesis of neurodegenerative diseases. Furthermore, it will provide new insights into the development of therapeutic approaches for ALS. Copyright © 2017 Elsevier Inc. All rights reserved.

Lorentz-like force emerging from kinematic interactions between electrons and nuclei in molecules: A quantum mechanical origin of symmetry breaking that can trigger molecular chirality.

PubMed

Takatsuka, Kazuo

2017-02-28

The Longuet-Higgins (Berry) phase arising from nonadiabatic dynamics and the Aharonov-Bohm phase associated with the dynamics of a charged particle in the electromagnetic vector potential are well known to be individually a manifestation of a class of the so-called geometrical phase. We herein discuss another similarity between the force working on a charged particle moving in a magnetic field, the Lorentz force, and a force working on nuclei while passing across a region where they have a strong quantum mechanical kinematic (nonadiabatic) coupling with electrons in a molecule. This kinematic force is indeed akin to the Lorentz force in that its magnitude is proportional to the velocity of the relevant nuclei and works in the direction perpendicular to its translational motion. Therefore this Lorentz-like nonadiabatic force is realized only in space of more or equal to three dimensions, thereby highlighting a truly multi-dimensional effect of nonadiabatic interaction. We investigate its physical significance qualitatively in the context of breaking of molecular spatial symmetry, which is not seen otherwise without this force. This particular symmetry breaking is demonstrated in application to a coplanar collision between a planar molecule and an atom sharing the same plane. We show that the atom is guided by this force to the direction out from the plane, resulting in a configuration that distinguishes one side of the mirror plane from the other. This can serve as a trigger for the dynamics towards molecular chirality.

Warts phosphorylates Mud to promote Pins-mediated mitotic spindle orientation in Drosophila independent of Yorkie

PubMed Central

Dewey, Evan B.; Sanchez, Desiree; Johnston, Christopher A.

2015-01-01

SUMMARY Multicellular animals have evolved conserved signaling pathways that translate cell polarity cues into mitotic spindle positioning to control the orientation of cell division within complex tissue structures. These oriented cell divisions are essential for the development of cell diversity and the maintenance of tissue homeostasis. Despite intense efforts, the molecular mechanisms that control spindle orientation remain incompletely defined. Here we describe a role for the Hippo (Hpo) kinase complex in promoting Partner of Inscuteable (Pins)-mediated spindle orientation. Knockdown of Hpo, Salvador (Sav), or Warts (Wts) each result in a partial loss of spindle orientation, a phenotype previously described following loss of the Pins-binding protein Mushroom body defect (Mud). Similar to orthologs spanning yeast to mammals, Wts kinase localizes to mitotic spindle poles, a prominent site of Mud localization. Wts directly phosphorylates Mud in vitro within its C-terminal coiled-coil domain. This Mud coiled-coil domain directly binds the adjacent Pins-binding domain to dampen the Pins/Mud interaction, and Wts-mediated phosphorylation uncouples this intramolecular Mud interaction. Loss of Wts prevents cortical Pins/Mud association without affecting Mud accumulation at spindle poles, suggesting phosphorylation acts as a molecular switch to specifically activate cortical Mud function. Finally, loss of Wts in Drosophila imaginal disc epithelial cells results in diminished cortical Mud and defective planar spindle orientation. Our results provide new insights into the molecular basis for dynamic regulation of the cortical Pins/Mud spindle positioning complex and highlight a novel link with an essential, evolutionarily-conserved cell proliferation pathway. PMID:26592339

Warts phosphorylates mud to promote pins-mediated mitotic spindle orientation in Drosophila, independent of Yorkie.

PubMed

Dewey, Evan B; Sanchez, Desiree; Johnston, Christopher A

2015-11-02

Multicellular animals have evolved conserved signaling pathways that translate cell polarity cues into mitotic spindle positioning to control the orientation of cell division within complex tissue structures. These oriented cell divisions are essential for the development of cell diversity and the maintenance of tissue homeostasis. Despite intense efforts, the molecular mechanisms that control spindle orientation remain incompletely defined. Here, we describe a role for the Hippo (Hpo) kinase complex in promoting Partner of Inscuteable (Pins)-mediated spindle orientation. Knockdown of Hpo, Salvador (Sav), or Warts (Wts) each result in a partial loss of spindle orientation, a phenotype previously described following loss of the Pins-binding protein Mushroom body defect (Mud). Similar to orthologs spanning yeast to mammals, Wts kinase localizes to mitotic spindle poles, a prominent site of Mud localization. Wts directly phosphorylates Mud in vitro within its C-terminal coiled-coil domain. This Mud coiled-coil domain directly binds the adjacent Pins-binding domain to dampen the Pins/Mud interaction, and Wts-mediated phosphorylation uncouples this intramolecular Mud interaction. Loss of Wts prevents cortical Pins/Mud association without affecting Mud accumulation at spindle poles, suggesting phosphorylation acts as a molecular switch to specifically activate cortical Mud function. Finally, loss of Wts in Drosophila imaginal disc epithelial cells results in diminished cortical Mud and defective planar spindle orientation. Our results provide new insights into the molecular basis for dynamic regulation of the cortical Pins/Mud spindle positioning complex and highlight a novel link with an essential, evolutionarily conserved cell proliferation pathway. Copyright © 2015 Elsevier Ltd. All rights reserved.

H2O-CH4 and H2S-CH4 complexes: a direct comparison through molecular beam experiments and ab initio calculations.

PubMed

Cappelletti, David; Bartocci, Alessio; Frati, Federica; Roncaratti, Luiz F; Belpassi, Leonardo; Tarantelli, Francesco; Lakshmi, Prabha Aiswarya; Arunan, Elangannan; Pirani, Fernando

2015-11-11

New molecular beam scattering experiments have been performed to measure the total (elastic plus inelastic) cross sections as a function of the velocity in collisions between water and hydrogen sulfide projectile molecules and the methane target. Measured data have been exploited to characterize the range and strength of the intermolecular interaction in such systems, which are of relevance as they drive the gas phase molecular dynamics and the clathrate formation. Complementary information has been obtained by rotational spectra, recorded for the hydrogen sulfide-methane complex, with a pulsed nozzle Fourier transform microwave spectrometer. Extensive ab initio calculations have been performed to rationalize all the experimental findings. The combination of experimental and theoretical information has established the ground for the understanding of the nature of the interaction and allows for its basic components to be modelled, including charge transfer, in these weakly bound systems. The intermolecular potential for H2S-CH4 is significantly less anisotropic than for H2O-CH4, although both of them have potential minima that can be characterized as 'hydrogen bonded'.

Graphene defects induced by ion beam

NASA Astrophysics Data System (ADS)

Gawlik, Grzegorz; Ciepielewski, Paweł; Baranowski, Jacek; Jagielski, Jacek

2017-10-01

The CVD graphene deposited on the glass substrate was bombarded by molecular carbon ions C3+ C6+ hydrocarbon ions C3H4+ and atomic ions He+, C+, N+, Ar+, Kr+ Yb+. Size and density of ion induced defects were estimated from evolution of relative intensities of Raman lines D (∼1350 1/cm), G (∼1600 1/cm), and D‧ (∼1620 1/cm) with ion fluence. The efficiency of defect generation by atomic ions depend on ion mass and energy similarly as vacancy generation directly by ion predicted by SRIM simulations. However, efficiency of defect generation in graphene by molecular carbon ions is essentially higher than summarized efficiency of similar group of separate atomic carbon ions of the same energy that each carbon ion in a cluster. The evolution of the D/D‧ ratio of Raman lines intensities with ion fluence was observed. This effect may indicate evolution of defect nature from sp3-like at low fluence to a vacancy-like at high fluence. Observed ion graphene interactions suggest that the molecular ion interacts with graphene as single integrated object and should not be considered as a group of atomic ions with partial energy.

Direct evidence of three-body interactions in a cold {sup 85}Rb Rydberg gas

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

Han Jianing

2010-11-15

Cold Rydberg atoms trapped in a magneto-optical trap (MOT) are not isolated and they interact through dipole-dipole and multipole-multipole interactions. First-order dipole-dipole interactions and van der Waals interactions between two atoms have been intensively studied. However, the facts that the first-order dipole-dipole interactions and van der Waals interactions show the same size of broadening [A. Reinhard, K. C. Younge, T. C. Liebisch, B. Knuffman, P. R. Berman, and G. Raithel, Phys. Rev. Lett. 100, 233201 (2008)] and there are transitions between two dimer states [S. M. Farooqi, D. Tong, S. Krishnan, J. Stanojevic, Y. P. Zhang, J. R. Ensher, A.more » S. Estrin, C. Boisseau, R. Cote, E. E. Eyler, and P. L. Gould, Phys. Rev. Lett. 91, 183002 (2003); K. R. Overstreet, Arne Schwettmann, Jonathan Tallant, and James P. Shaffer, Phys. Rev. A 76, 011403(R) (2007)] cannot be explained by the two-atom picture. The purpose of this article is to show the few-body nature of a dense cold Rydberg gas by studying the molecular-state microwave spectra. Specifically, three-body energy levels have been calculated. Moreover, the transition from three-body energy levels to two-body coupled molecular energy levels and to isolated atomic energy levels as a function of the internuclear spacing is studied. Finally, single-body, two-body, and three-body interaction regions are estimated according to the experimental data. The results reported here provides useful information for plasma formation, further cooling, and superfluid formation.« less

Binding of integrin α1 to bone morphogenetic protein receptor IA suggests a novel role of integrin α1β1 in bone morphogenetic protein 2 signalling.

PubMed

Zu, Yan; Liang, Xudong; Du, Jing; Zhou, Shuai; Yang, Chun

2015-11-05

Here, we observed that integrin α1β1 and bone morphogenetic protein receptor (BMPR) IA formed a complex and co-localised in several cell types. However, the molecular interaction between these two molecules was not studied in detail to date and the role of the interaction in BMPR signalling remains unknown; thus, these were investigated here. In a steered molecular dynamics (SMD) simulation, the observed development of the rupture force related to the displacement between the A-domain of integrin α1 and the extracellular domain of BMPR IA indicated a strong molecular interaction within the integrin-BMPR complex. Analysis of the intermolecular forces revealed that hydrogen bonds, rather than salt bridges, are the major contributors to these intermolecular interactions. By using Enzyme-linked immunosorbent assay (ELISA) and co-immunoprecipitation (co-IP) experiments with site-directed mutants, we found that residues 85-89 in BMPR IA play the most important role for BMPR IA binding to integrin α1β1. These residues are the same as those responsible for bone morphogenetic protein 2 (BMP-2)/BMPR IA binding. In our experiments, we also found that the interference of integrin α1β1 up regulated the level of phosphorylated Smad1, 5, 8, which is the downstream of BMP/BMPR signalling. Therefore, our results suggest that integrin α1β1/BMPR IA may block BMP-2/BMPR IA complex information and interfere with the BMP-2 signalling pathway in cells. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation*

PubMed Central

Payne, Christina M.; Bomble, Yannick J.; Taylor, Courtney B.; McCabe, Clare; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.

2011-01-01

Proteins employ aromatic residues for carbohydrate binding in a wide range of biological functions. Glycoside hydrolases, which are ubiquitous in nature, typically exhibit tunnels, clefts, or pockets lined with aromatic residues for processing carbohydrates. Mutation of these aromatic residues often results in significant activity differences on insoluble and soluble substrates. However, the thermodynamic basis and molecular level role of these aromatic residues remain unknown. Here, we calculate the relative ligand binding free energy by mutating tryptophans in the Trichoderma reesei family 6 cellulase (Cel6A) to alanine. Removal of aromatic residues near the catalytic site has little impact on the ligand binding free energy, suggesting that aromatic residues immediately upstream of the active site are not directly involved in binding, but play a role in the glucopyranose ring distortion necessary for catalysis. Removal of aromatic residues at the entrance and exit of the Cel6A tunnel, however, dramatically impacts the binding affinity, suggesting that these residues play a role in chain acquisition and product stabilization, respectively. The roles suggested from differences in binding affinity are confirmed by molecular dynamics and normal mode analysis. Surprisingly, our results illustrate that aromatic-carbohydrate interactions vary dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, these results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for biomass utilization. Generally, these results suggest that nature employs aromatic-carbohydrate interactions with a wide range of binding affinities for diverse functions. PMID:21965672

Local structural ordering in surface-confined liquid crystals

NASA Astrophysics Data System (ADS)

Śliwa, I.; Jeżewski, W.; Zakharov, A. V.

2017-06-01

The effect of the interplay between attractive nonlocal surface interactions and attractive pair long-range intermolecular couplings on molecular structures of liquid crystals confined in thin cells with flat solid surfaces has been studied. Extending the McMillan mean field theory to include finite systems, it has been shown that confining surfaces can induce complex orientational and translational ordering of molecules. Typically, local smectic A, nematic, and isotropic phases have been shown to coexist in certain temperature ranges, provided that confining cells are sufficiently thick, albeit finite. Due to the nonlocality of surface interactions, the spatial arrangement of these local phases can display, in general, an unexpected complexity along the surface normal direction. In particular, molecules located in the vicinity of surfaces can still be organized in smectic layers, even though nematic and/or isotropic order can simultaneously appear in the interior of cells. The resulting surface freezing of smectic layers has been confirmed to occur even for rather weak surface interactions. The surface interactions cannot, however, prevent smectic layers from melting relatively close to system boundaries, even when molecules are still arranged in layers within the central region of the system. The internal interfaces, separating individual liquid-crystal phases, are demonstrated here to form fronts of local finite-size transitions that move across cells under temperature changes. Although the complex molecular ordering in surface confined liquid-crystal systems can essentially be controlled by temperature variations, specific thermal properties of these systems, especially the nature of the local transitions, are argued to be strongly conditioned to the degree of molecular packing.

Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

PubMed

Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

2018-03-13

Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

Relationship between the ability of oral streptococci to interact with platelet glycoprotein Ibalpha and with the salivary low-molecular-weight mucin, MG2.

PubMed

Plummer, Christopher; Douglas, Charles William Ian

2006-12-01

The oral streptococci Streptococcus sanguinis, Streptococcus gordonii and Streptococcus oralis are common aetiological agents of infective endocarditis, and their ability to adhere to and induce the aggregation of platelets is thought to be a virulence trait. The platelet glycoprotein GPIbalpha has been implicated as the adhesion receptor for S. sanguinis and S. gordonii, but it is not known if this is the case for S. oralis and other species. The aim of this study was to determine the GPIbalpha-interactive capability of a range of oral streptococci and to determine the relationship between this capability and their ability to interact with the salivary constituents that they would encounter in their normal habitat. All platelet-adhesive S. sanguinis strains and most S. gordonii strains adhered in a GPIbalpha-dependent manner, but strains of S. oralis, Streptococcus cristatus, Streptococcus parasanguinis and Streptococcus mitis had no direct affinity for platelets. Those strains that were able to bind GPIbalpha also bound to the low-molecular-weight submandibular salivary mucin, MG2, and this interaction was sialic acid-dependent. The data suggest that S. sanguinis and S. gordonii may be efficient colonizers of platelet vegetations because of their adaptation to recognize sialylated salivary mucins. In contrast, S. oralis does not interact with platelets and so is likely to colonize vegetations through an as yet unidentified mechanism.

Small Molecule Interactome Mapping by Photoaffinity Labeling Reveals Binding Site Hotspots for the NSAIDs.

PubMed

Gao, Jinxu; Mfuh, Adelphe; Amako, Yuka; Woo, Christina M

2018-03-28

Many therapeutics elicit cell-type specific polypharmacology that is executed by a network of molecular recognition events between a small molecule and the whole proteome. However, measurement of the structures that underpin the molecular associations between the proteome and even common therapeutics, such as the nonsteroidal anti-inflammatory drugs (NSAIDs), is limited by the inability to map the small molecule interactome. To address this gap, we developed a platform termed small molecule interactome mapping by photoaffinity labeling (SIM-PAL) and applied it to the in cellulo direct characterization of specific NSAID binding sites. SIM-PAL uses (1) photochemical conjugation of NSAID derivatives in the whole proteome and (2) enrichment and isotope-recoding of the conjugated peptides for (3) targeted mass spectrometry-based assignment. Using SIM-PAL, we identified the NSAID interactome consisting of over 1000 significantly enriched proteins and directly characterized nearly 200 conjugated peptides representing direct binding sites of the photo-NSAIDs with proteins from Jurkat and K562 cells. The enriched proteins were often identified as parts of complexes, including known targets of NSAID activity (e.g., NF-κB) and novel interactions (e.g., AP-2, proteasome). The conjugated peptides revealed direct NSAID binding sites from the cell surface to the nucleus and a specific binding site hotspot for the three photo-NSAIDs on histones H2A and H2B. NSAID binding stabilized COX-2 and histone H2A by cellular thermal shift assay. Since small molecule stabilization of protein complexes is a gain of function regulatory mechanism, it is conceivable that NSAIDs affect biological processes through these broader proteomic interactions. SIM-PAL enabled characterization of NSAID binding site hotspots and is amenable to map global binding sites for virtually any molecule of interest.

Prediction of luciferase inhibitors by the high-performance MIEC-GBDT approach based on interaction energetic patterns.

PubMed

Chen, Fu; Sun, Huiyong; Liu, Hui; Li, Dan; Li, Youyong; Hou, Tingjun

2017-04-12

High-throughput screening (HTS) is widely applied in many fields ranging from drug discovery to clinical diagnostics and toxicity assessment. Firefly luciferase is commonly used as a reporter to monitor the effect of chemical compounds on the activity of a specific target or pathway in HTS. However, the false positive rate of luciferase-based HTS is relatively high because many artifacts or promiscuous compounds that have direct interaction with the luciferase reporter enzyme are usually identified as active compounds (hits). Therefore, it is necessary to develop a rapid screening method to identify these compounds that can inhibit the luciferase activity directly. In this study, a virtual screening (VS) classification model called MIEC-GBDT (MIEC: Molecular Interaction Energy Components; GBDT: Gradient Boosting Decision Tree) was developed to distinguish luciferase inhibitors from non-inhibitors. The MIECs calculated by Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition were used to energetically characterize the binding pattern of each small molecule at the active site of luciferase, and then the GBDT algorithm was employed to construct the classifiers based on MIECs. The predictions to the test set show that the optimized MIEC-GBDT model outperformed molecular docking and MM/GBSA rescoring. The best MIEC-GBDT model based on the MIECs with the energy terms of ΔG ele , ΔG vdW , ΔG GB , and ΔG SA achieves the prediction accuracies of 87.2% and 90.3% for the inhibitors and non-inhibitors in the test sets, respectively. Moreover, the energetic analysis of the vital residues suggests that the energetic contributions of the vital residues to the binding of inhibitors are quite different from those to the binding of non-inhibitors. These results suggest that the MIEC-GBDT model is reliable and can be used as a powerful tool to identify potential interference compounds in luciferase-based HTS experiments.

Isoquinoline alkaloids and their binding with DNA: calorimetry and thermal analysis applications.

PubMed

Bhadra, Kakali; Kumar, Gopinatha Suresh

2010-11-01

Alkaloids are a group of natural products with unmatched chemical diversity and biological relevance forming potential quality pools in drug screening. The molecular aspects of their interaction with many cellular macromolecules like DNA, RNA and proteins are being currently investigated in order to evolve the structure activity relationship. Isoquinolines constitute an important group of alkaloids. They have extensive utility in cancer therapy and a large volume of data is now emerging in the literature on their mode, mechanism and specificity of binding to DNA. Thermodynamic characterization of the binding of these alkaloids to DNA may offer key insights into the molecular aspects that drive complex formation and these data can provide valuable information about the balance of driving forces. Various thermal techniques have been conveniently used for this purpose and modern calorimetric instrumentation provides direct and quick estimation of thermodynamic parameters. Thermal melting studies and calorimetric techniques like isothermal titration calorimetry and differential scanning calorimetry have further advanced the field by providing authentic, reliable and sensitive data on various aspects of temperature dependent structural analysis of the interaction. In this review we present the application of various thermal techniques, viz. isothermal titration calorimetry, differential scanning calorimetry and optical melting studies in the characterization of drug-DNA interactions with particular emphasis on isoquinoline alkaloid-DNA interaction.

Altered Cell Mechanics from the Inside: Dispersed Single Wall Carbon Nanotubes Integrate with and Restructure Actin

PubMed Central

Holt, Brian D.; Shams, Hengameh; Horst, Travis A.; Basu, Saurav; Rape, Andrew D.; Wang, Yu-Li; Rohde, Gustavo K.; Mofrad, Mohammad R. K.; Islam, Mohammad F.; Dahl, Kris Noel

2012-01-01

With a range of desirable mechanical and optical properties, single wall carbon nanotubes (SWCNTs) are a promising material for nanobiotechnologies. SWCNTs also have potential as biomaterials for modulation of cellular structures. Previously, we showed that highly purified, dispersed SWCNTs grossly alter F-actin inside cells. F-actin plays critical roles in the maintenance of cell structure, force transduction, transport and cytokinesis. Thus, quantification of SWCNT-actin interactions ranging from molecular, sub-cellular and cellular levels with both structure and function is critical for developing SWCNT-based biotechnologies. Further, this interaction can be exploited, using SWCNTs as a unique actin-altering material. Here, we utilized molecular dynamics simulations to explore the interactions of SWCNTs with actin filaments. Fluorescence lifetime imaging microscopy confirmed that SWCNTs were located within ~5 nm of F-actin in cells but did not interact with G-actin. SWCNTs did not alter myosin II sub-cellular localization, and SWCNT treatment in cells led to significantly shorter actin filaments. Functionally, cells with internalized SWCNTs had greatly reduced cell traction force. Combined, these results demonstrate direct, specific SWCNT alteration of F-actin structures which can be exploited for SWCNT-based biotechnologies and utilized as a new method to probe fundamental actin-related cellular processes and biophysics. PMID:24955540

Unraveling the complexity of the interactions of DNA nucleotides with gold by single molecule force spectroscopy

NASA Astrophysics Data System (ADS)

Bano, Fouzia; Sluysmans, Damien; Wislez, Arnaud; Duwez, Anne-Sophie

2015-11-01

Addressing the effect of different environmental factors on the adsorption of DNA to solid supports is critical for the development of robust miniaturized devices for applications ranging from biosensors to next generation molecular technology. Most of the time, thiol-based chemistry is used to anchor DNA on gold - a substrate commonly used in nanotechnology - and little is known about the direct interaction between DNA and gold. So far there have been no systematic studies on the direct adsorption behavior of the deoxyribonucleotides (i.e., a nitrogenous base, a deoxyribose sugar, and a phosphate group) and on the factors that govern the DNA-gold bond strength. Here, using single molecule force spectroscopy, we investigated the interaction of the four individual nucleotides, adenine, guanine, cytosine, and thymine, with gold. Experiments were performed in three salinity conditions and two surface dwell times to reveal the factors that influence nucleotide-Au bond strength. Force data show that, at physiological ionic strength, adenine-Au interactions are stronger, asymmetrical and independent of surface dwell time as compared to cytosine-Au and guanine-Au interactions. We suggest that in these conditions only adenine is able to chemisorb on gold. A decrease of the ionic strength significantly increases the bond strength for all nucleotides. We show that moderate ionic strength along with longer surface dwell period suggest weak chemisorption also for cytosine and guanine.Addressing the effect of different environmental factors on the adsorption of DNA to solid supports is critical for the development of robust miniaturized devices for applications ranging from biosensors to next generation molecular technology. Most of the time, thiol-based chemistry is used to anchor DNA on gold - a substrate commonly used in nanotechnology - and little is known about the direct interaction between DNA and gold. So far there have been no systematic studies on the direct adsorption behavior of the deoxyribonucleotides (i.e., a nitrogenous base, a deoxyribose sugar, and a phosphate group) and on the factors that govern the DNA-gold bond strength. Here, using single molecule force spectroscopy, we investigated the interaction of the four individual nucleotides, adenine, guanine, cytosine, and thymine, with gold. Experiments were performed in three salinity conditions and two surface dwell times to reveal the factors that influence nucleotide-Au bond strength. Force data show that, at physiological ionic strength, adenine-Au interactions are stronger, asymmetrical and independent of surface dwell time as compared to cytosine-Au and guanine-Au interactions. We suggest that in these conditions only adenine is able to chemisorb on gold. A decrease of the ionic strength significantly increases the bond strength for all nucleotides. We show that moderate ionic strength along with longer surface dwell period suggest weak chemisorption also for cytosine and guanine. Electronic supplementary information (ESI) available: Details of the data analysis; Fig. S1-S5 histograms of rupture lengths; histograms for Au-adenine and Au-amine interactions; Force-extension curve for MCH-Au interactions; normalized force-extension curves; theoretical length of the DNA oligomers. See DOI: 10.1039/c5nr05695k

Modeling molecular mixing in a spatially inhomogeneous turbulent flow

NASA Astrophysics Data System (ADS)

Meyer, Daniel W.; Deb, Rajdeep

2012-02-01

Simulations of spatially inhomogeneous turbulent mixing in decaying grid turbulence with a joint velocity-concentration probability density function (PDF) method were conducted. The inert mixing scenario involves three streams with different compositions. The mixing model of Meyer ["A new particle interaction mixing model for turbulent dispersion and turbulent reactive flows," Phys. Fluids 22(3), 035103 (2010)], the interaction by exchange with the mean (IEM) model and its velocity-conditional variant, i.e., the IECM model, were applied. For reference, the direct numerical simulation data provided by Sawford and de Bruyn Kops ["Direct numerical simulation and lagrangian modeling of joint scalar statistics in ternary mixing," Phys. Fluids 20(9), 095106 (2008)] was used. It was found that velocity conditioning is essential to obtain accurate concentration PDF predictions. Moreover, the model of Meyer provides significantly better results compared to the IECM model at comparable computational expense.

Molecular and kinetic determinants of local anaesthetic action on sodium channels.

PubMed

French, R J; Zamponi, G W; Sierralta, I E

1998-11-23

(1) Local anaesthetics (LA) rely for their clinical actions on state-dependent inhibition of voltage-dependent sodium channels. (2) Single, batrachoxin-modified sodium channels in planar lipid bilayers allow direct observation of drug-channel interactions. Two modes of inhibition of single-channel current are observed: fast block of the open channels and prolongation of a long-lived closed state, some of whose properties resemble those of the inactivated state of unmodified channels. (3) Analogues of different parts of the LA molecule separately mimic each blocking mode: amines--fast block, and water-soluble aromatics--closed state prolongation. (4) Interaction between a mu-conotoxin derivative and diethylammonium indicate an intrapore site of fast, open-state block. (5) Site-directed mutagenesis studies suggest that hydrophobic residues in transmembrane segment 6 of repeat domain 4 of sodium channels are critical for both LA binding and stabilization of the inactivated state.

Virtual screening of selective inhibitors of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis

NASA Astrophysics Data System (ADS)

Podshivalov, D. D.; Timofeev, V. I.; Sidorov-Biryukov, D. D.; Kuranova, I. P.

2017-05-01

Bacterial phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis (PPAT Mt) is a convenient target protein for the directed search for selective inhibitors as potent antituberculosis drugs. Four compounds suitable for the detailed investigation of their interactions with PPAT Mt were found by virtual screening. The active-site region of the enzyme was chosen as the ligand-binding site. The positions of the ligands found by the docking were refined by molecular dynamics simulation. The nearest environment of the ligands, the positions of which in the active site of the enzyme were found in a computational experiment, was analyzed. The compounds under consideration were shown to directly interact with functionally important active-site amino-acid residues and block access of substrates to the active site. Therefore, these compounds can be used for the design of selective inhibitors of PPAT Mt as potent antituberculosis drugs.

Peroxidasin contributes to lung host defense by direct binding and killing of gram-negative bacteria.

PubMed

Shi, Ruizheng; Cao, Zehong; Li, Hong; Graw, Jochen; Zhang, Guogang; Thannickal, Victor J; Cheng, Guangjie

2018-05-01

Innate immune recognition is classically mediated by the interaction of host pattern-recognition receptors and pathogen-associated molecular patterns; this triggers a series of downstream signaling events that facilitate killing and elimination of invading pathogens. In this report, we provide the first evidence that peroxidasin (PXDN; also known as vascular peroxidase-1) directly binds to gram-negative bacteria and mediates bactericidal activity, thus, contributing to lung host defense. PXDN contains five leucine-rich repeats and four immunoglobulin domains, which allows for its interaction with lipopolysaccharide, a membrane component of gram-negative bacteria. Bactericidal activity of PXDN is mediated via its capacity to generate hypohalous acids. Deficiency of PXDN results in a failure to eradicate Pseudomonas aeruginosa and increased mortality in a murine model of Pseudomonas lung infection. These observations indicate that PXDN mediates previously unrecognized host defense functions against gram-negative bacterial pathogens.

Stable chromosome condensation revealed by chromosome conformation capture

PubMed Central

Eagen, Kyle P.; Hartl, Tom A.; Kornberg, Roger D.

2015-01-01

SUMMARY Chemical cross-linking and DNA sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to ten-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes. PMID:26544940

Interplay of weak interactions in the atom-by-atom condensation of xenon within quantum boxes

PubMed Central

Nowakowska, Sylwia; Wäckerlin, Aneliia; Kawai, Shigeki; Ivas, Toni; Nowakowski, Jan; Fatayer, Shadi; Wäckerlin, Christian; Nijs, Thomas; Meyer, Ernst; Björk, Jonas; Stöhr, Meike; Gade, Lutz H.; Jung, Thomas A.

2015-01-01

Condensation processes are of key importance in nature and play a fundamental role in chemistry and physics. Owing to size effects at the nanoscale, it is conceptually desired to experimentally probe the dependence of condensate structure on the number of constituents one by one. Here we present an approach to study a condensation process atom-by-atom with the scanning tunnelling microscope, which provides a direct real-space access with atomic precision to the aggregates formed in atomically defined ‘quantum boxes’. Our analysis reveals the subtle interplay of competing directional and nondirectional interactions in the emergence of structure and provides unprecedented input for the structural comparison with quantum mechanical models. This approach focuses on—but is not limited to—the model case of xenon condensation and goes significantly beyond the well-established statistical size analysis of clusters in atomic or molecular beams by mass spectrometry. PMID:25608225

Spatially-Interactive Biomolecular Networks Organized by Nucleic Acid Nanostructures

PubMed Central

Fu, Jinglin; Liu, Minghui; Liu, Yan; Yan, Hao

2013-01-01

Conspectus Living systems have evolved a variety of nanostructures to control the molecular interactions that mediate many functions including the recognition of targets by receptors, the binding of enzymes to substrates, and the regulation of enzymatic activity. Mimicking these structures outside of the cell requires methods that offer nanoscale control over the organization of individual network components. Advances in DNA nanotechnology have enabled the design and fabrication of sophisticated one-, two- and three-dimensional (1D, 2D and 3D) nanostructures that utilize spontaneous and sequence specific DNA hybridization. Compared to other self-assembling biopolymers, DNA nanostructures offer predictable and programmable interactions, and surface features to which other nanoparticles and bio-molecules can be precisely positioned. The ability to control the spatial arrangement of the components while constructing highly-organized networks will lead to various applications of these systems. For example, DNA nanoarrays with surface displays of molecular probes can sense noncovalent hybridization interactions with DNA, RNA, and proteins and covalent chemical reactions. DNA nanostructures can also align external molecules into well-defined arrays, which may improve the resolution of many structural determination methods, such as X-ray diffraction, cryo-EM, NMR, and super-resolution fluorescence. Moreover, by constraining target entities to specific conformations, self-assembled DNA nanostructures can serve as molecular rulers to evaluate conformation-dependent activities. This Account describes the most recent advances in the DNA nanostructure directed assembly of biomolecular networks and explores the possibility of applying this technology to other fields of study. Recently, several reports have demonstrated the DNA nanostructure directed assembly of spatially-interactive biomolecular networks. For example, researchers have constructed synthetic multi-enzyme cascades by organizing the position of the components using DNA nanoscaffolds in vitro, or by utilizing RNA matrices in vivo. These structures display enhanced efficiency compared to the corresponding unstructured enzyme mixtures. Such systems are designed to mimic cellular function, where substrate diffusion between enzymes is facilitated and reactions are catalyzed with high efficiency and specificity. In addition, researchers have assembled multiple choromophores into arrays using a DNA nanoscaffold that optimizes the relative distance between the dyes and their spatial organization. The resulting artificial light harvesting system exhibits efficient cascading energy transfers. Finally, DNA nanostructures have been used as assembly templates to construct nanodevices that execute rationally-designed behaviors, including cargo loading, transportation and route control. PMID:22642503

Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

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

Wang, Hao; Yang, Weitao, E-mail: weitao.yang@duke.edu; Department of Physics, Duke University, Durham, North Carolina 27708

We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniformmore » external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics’ force fields and nontransferable molecule-specific atomic polarizabilities.« less

Study on the Characteristics of Gas Molecular Mean Free Path in Nanopores by Molecular Dynamics Simulations

PubMed Central

Liu, Qixin; Cai, Zhiyong

2014-01-01

This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale. PMID:25046745

Biopython: freely available Python tools for computational molecular biology and bioinformatics

PubMed Central

Cock, Peter J. A.; Antao, Tiago; Chang, Jeffrey T.; Chapman, Brad A.; Cox, Cymon J.; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J. L.

2009-01-01

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk. PMID:19304878

Catenanes: Fifty Years of Molecular Links

PubMed Central

Gil-Ramírez, Guzmán; Leigh, David A; Stephens, Alexander J

2015-01-01

Half a century after Schill and Lüttringhaus carried out the first directed synthesis of a [2]catenane, a plethora of strategies now exist for the construction of molecular Hopf links (singly interlocked rings), the simplest type of catenane. The precision and effectiveness with which suitable templates and/or noncovalent interactions can arrange building blocks has also enabled the synthesis of intricate and often beautiful higher order interlocked systems, including Solomon links, Borromean rings, and a Star of David catenane. This Review outlines the diverse strategies that exist for synthesizing catenanes in the 21st century and examines their emerging applications and the challenges that still exist for the synthesis of more complex topologies. PMID:25951013

Fluid Physics and Macromolecular Crystal Growth in Microgravity

NASA Technical Reports Server (NTRS)

Pusey, M.; Snell, E.; Judge, R.; Chayen, N.; Boggon, T.; Helliwell, J.; Rose, M. Franklin (Technical Monitor)

2000-01-01

The molecular structure of biological macromolecules is important in understanding how these molecules work and has direct application to rational drug design for new medicines and for the improvement and development of industrial enzymes. In order to obtain the molecular structure, large, well formed, single macromolecule crystals are required. The growth of macromolecule crystals is a difficult task and is often hampered on the ground by fluid flows that result from the interaction of gravity with the crystal growth process. One such effect is the bulk movement of the crystal through the fluid due to sedimentation. A second is buoyancy driven convection close to the crystal surface. On the ground the crystallization process itself induces both of these flows.

Vibrational inelastic scattering effects in molecular electronics

NASA Astrophysics Data System (ADS)

Ness, H.; Fisher, A. J.

2005-06-01

We describe how to treat the interaction of traveling electrons with localized vibrational modes in nanojunctions. We present a multichannel scattering technique, which can be applied to calculate the transport properties for realistic systems, and we show how it is related to other methods that are useful in particular cases. We apply our technique to describe recent experiments on the conductance through molecular junctions. Author contributions: H.N. and A.J.F. designed research and wrote the paper; and H.N. performed research and analyzed data.This paper was submitted directly (Track II) to the PNAS office.Abbreviations: IETS, inelastic electron tunneling spectroscopy; SSSM, single-site, single-vibrational mode; e-ph, electron-phonon.

Paramaterization of a coarse-grained model for linear alkylbenzene sulfonate surfactants and molecular dynamics studies of their self-assembly in aqueous solution

NASA Astrophysics Data System (ADS)

He, Xibing; Shinoda, Wataru; DeVane, Russell; Anderson, Kelly L.; Klein, Michael L.

2010-02-01

A coarse-grained (CG) forcefield for linear alkylbenzene sulfonates (LAS) was systematically parameterized. Thermodynamic data from experiments and structural data obtained from all-atom molecular dynamics were used as targets to parameterize CG potentials for the bonded and non-bonded interactions. The added computational efficiency permits one to employ computer simulation to probe the self-assembly of LAS aqueous solutions into different morphologies starting from a random configuration. The present CG model is shown to accurately reproduce the phase behavior of solutions of pure isomers of sodium dodecylbenzene sulfonate, despite the fact that phase behavior was not directly taken into account in the forcefield parameterization.

Simulation and display of macromolecular complexes

NASA Technical Reports Server (NTRS)

Nir, S.; Garduno, R.; Rein, R.; Macelroy, R. D.

1977-01-01

In association with an investigation of the interaction of proteins with DNA and RNA, an interactive computer program for building, manipulating, and displaying macromolecular complexes has been designed. The system provides perspective, planar, and stereoscopic views on the computer terminal display, as well as views for standard and nonstandard observer locations. The molecule or its parts may be rotated and/or translated in any direction; bond connections may be added or removed by the viewer. Molecular fragments may be juxtaposed in such a way that given bonds are aligned, and given planes and points coincide. Another subroutine provides for the duplication of a given unit such as a DNA or amino-acid base.

Fluid/Solid Boundary Conditions in Non-Isothermal Systems

NASA Technical Reports Server (NTRS)

Rosner, Daniel E.

1999-01-01

The existing theoretical research concerned with thermal creep at fluid/solid interfaces is briefly reviewed, and the importance of microgravity-based experimental data is then discussed. It is noted that the ultimate goal of this research is a rational molecular level theory that predicts the dependence of a dimensionless thermal creep coefficient, Ctc, on relevant dimensionless parameters describing the way fluid molecules interact with the solid surface and how they interact among themselves. The discussion covers thermophoresis of isolated solid spheres and aggregates in gases; solid sphere thermophoresis in liquids and dense vapors; thermophoresis of small immiscible liquid droplets; and applications of the direct simulation Monte Carlo method.

Amino Acid Side Chain Interactions in the Presence of Salts

PubMed Central

Hassan, Sergio A.

2005-01-01

The effects of salt on the intermolecular interactions between polar/charged amino acids are investigated through molecular dynamics simulations. The mean forces and associated potentials are calculated for NaCl salt in the 0–2 M concentration range at 298 K. It is found that the addition of salt may stabilize or destabilize the interactions, depending on the nature of the interacting molecules. The degree of (de)stabilization is quantified, and the origin of the salt-dependent modulation is discussed based upon an analysis of solvent density profiles. To gain insight into the molecular origin of the salt modulation, spatial distribution functions (sdf’s) are calculated, revealing a high degree of solvent structuredness in all cases. The peaks in the sdf’s are consistent with long-range hydrogen-bonding networks connecting the solute hydrophilic groups, and that contribute to their intermolecular solvent-induced forces. The restructuring of water around the solutes as they dissociate from close contact is analyzed. This analysis offers clues on how the solvent structure modulates the effective intermolecular interactions in complex solutes. This modulation results from a critical balance between bulk electrostatic forces and those exerted by (i) the water molecules in the structured region between the monomers, which is disrupted by ions that transiently enter the hydration shells, and (ii) the ions in the hydration shells in direct interactions with the solutes. The implications of these findings in protein/ligand (noncovalent) association/dissociation mechanisms are briefly discussed. PMID:16479276

Allosteric Fine-Tuning of the Binding Pocket Dynamics in the ITK SH2 Domain by a Distal Molecular Switch: An Atomistic Perspective.

PubMed

Momin, Mohamed; Xin, Yao; Hamelberg, Donald

2017-06-29

Although the regulation of function of proteins by allosteric interactions has been identified in many subcellular processes, molecular switches are also known to induce long-range conformational changes in proteins. A less well understood molecular switch involving cis-trans isomerization of a peptidyl-prolyl bond could induce a conformational change directly to the backbone that is propagated to other parts of the protein. However, these switches are elusive and hard to identify because they are intrinsic to biomolecules that are inherently dynamic. Here, we explore the conformational dynamics and free energy landscape of the SH2 domain of interleukin-2-inducible T-cell or tyrosine kinase (ITK) to fully understand the conformational coupling between the distal cis-trans molecular switch and its binding pocket of the phosphotyrosine motif. We use multiple microsecond-long all-atom molecular dynamics simulations in explicit water for over a total of 60 μs. We show that cis-trans isomerization of the Asn286-Pro287 peptidyl-prolyl bond is directly coupled to the dynamics of the binding pocket of the phosphotyrosine motif, in agreement with previous NMR experiments. Unlike the cis state that is localized and less dynamic in a single free energy basin, the trans state samples two distinct conformations of the binding pocket-one that recognizes the phosphotyrosine motif and the other that is somewhat similar to that of the cis state. The results provide an atomic-level description of a less well understood allosteric regulation by a peptidyl-prolyl cis-trans molecular switch that could aid in the understanding of normal and aberrant subcellular processes and the identification of these elusive molecular switches in other proteins.

Hepatitis C virus NS5A protein is a substrate for the peptidyl-prolyl cis/trans isomerase activity of cyclophilins A and B.

PubMed

Hanoulle, Xavier; Badillo, Aurélie; Wieruszeski, Jean-Michel; Verdegem, Dries; Landrieu, Isabelle; Bartenschlager, Ralf; Penin, François; Lippens, Guy

2009-05-15

We report here a biochemical and structural characterization of domain 2 of the nonstructural 5A protein (NS5A) from the JFH1 Hepatitis C virus strain and its interactions with cyclophilins A and B (CypA and CypB). Gel filtration chromatography, circular dichroism spectroscopy, and finally NMR spectroscopy all indicate the natively unfolded nature of this NS5A-D2 domain. Because mutations in this domain have been linked to cyclosporin A resistance, we used NMR spectroscopy to investigate potential interactions between NS5A-D2 and cellular CypA and CypB. We observed a direct molecular interaction between NS5A-D2 and both cyclophilins. The interaction surface on the cyclophilins corresponds to their active site, whereas on NS5A-D2, it proved to be distributed over the many proline residues of the domain. NMR heteronuclear exchange spectroscopy yielded direct evidence that many proline residues in NS5A-D2 form a valid substrate for the enzymatic peptidyl-prolyl cis/trans isomerase (PPIase) activity of CypA and CypB.

RNA extraction from self-assembling peptide hydrogels to allow qPCR analysis of encapsulated cells.

PubMed

Burgess, Kyle A; Workman, Victoria L; Elsawy, Mohamed A; Miller, Aline F; Oceandy, Delvac; Saiani, Alberto

2018-01-01

Self-assembling peptide hydrogels offer a novel 3-dimensional platform for many applications in cell culture and tissue engineering but are not compatible with current methods of RNA isolation; owing to interactions between RNA and the biomaterial. This study investigates the use of two techniques based on two different basic extraction principles: solution-based extraction and direct solid-state binding of RNA respectively, to extract RNA from cells encapsulated in four β-sheet forming self-assembling peptide hydrogels with varying net positive charge. RNA-peptide fibril interactions, rather than RNA-peptide molecular complexing, were found to interfere with the extraction process resulting in low yields. A column-based approach relying on RNA-specific binding was shown to be more suited to extracting RNA with higher purity from these peptide hydrogels owing to its reliance on strong specific RNA binding interactions which compete directly with RNA-peptide fibril interactions. In order to reduce the amount of fibrils present and improve RNA yields a broad spectrum enzyme solution-pronase-was used to partially digest the hydrogels before RNA extraction. This pre-treatment was shown to significantly increase the yield of RNA extracted, allowing downstream RT-qPCR to be performed.

Molecular basis for the interplay of apoptosis and proliferation mediated by Bcl-xL:Bim interactions in pancreatic cancer cells

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

Abrol, Ravinder, E-mail: abrol@wag.caltech.edu; Edderkaoui, Mouad; Goddard, William A.

2012-06-15

Highlights: Black-Right-Pointing-Pointer Direct role of Bcl-2 protein interactions in cell proliferation is not clear. Black-Right-Pointing-Pointer Designed Bcl-xL mutants show opposite effects on apoptosis and proliferation. Black-Right-Pointing-Pointer Disrupting Bcl-xL:Bim interaction increased apoptosis in pancreatic cancer. Black-Right-Pointing-Pointer Disrupting Bcl-xL:Bim interaction decreased proliferation in pancreatic cancer. Black-Right-Pointing-Pointer Bcl-xL:Bim interaction can control both apoptosis and proliferation. -- Abstract: A major mechanism through which cancer cells avoid apoptosis is by promoting the association of anti-apoptotic members of the pro-survival Bcl-2 protein family (like Bcl-2 and Bcl-xL) with BH{sub 3} domain-only proteins (like Bim and Bid). Apoptosis and cell proliferation have been shown to be linkedmore » for many cancers but the molecular basis for this link is far from understood. We have identified the Bcl-xL:Bim protein-protein interface as a direct regulator of proliferation and apoptosis in pancreatic cancer cells. We were able to predict and subsequently verify experimentally the effect of various Bcl-xL single-point mutants (at the position A142) on binding to Bim by structural analysis and computational modeling of the inter-residue interactions at the Bcl-xL:Bim protein-protein interface. The mutants A142N, A142Q, and A142Y decreased binding of Bim to Bcl-xL and A142S increased this binding. The Bcl-xL mutants, with decreased affinity for Bim, caused an increase in apoptosis and a corresponding decrease in cell proliferation. However, we could prevent these effects by introducing a small interfering RNA (siRNA) targeted at Bim. These results show a novel role played by the Bcl-xL:Bim interaction in regulating proliferation of pancreatic cancer cells at the expense of apoptosis. This study presents a physiologically relevant model of the Bcl-xL:Bim interface that can be used for rational therapeutic design for the inhibition of proliferation and cancer cell resistance to apoptosis.« less

Phase behavior of Langmuir monolayers with ionic molecular heads: Molecular simulations

NASA Astrophysics Data System (ADS)

González-Castro, Carlos A.; Ramírez-Santiago, Guillermo

2015-03-01

We carried out Monte Carlo simulations in the N ,Π,T ensemble of a Langmuir monolayer coarse-grained molecular model. Considering that the hydrophilic groups can be ionized by modulating acid-base interactions, here we study the phase behavior of a model that incorporates the short-range steric and long-range ionic interactions. The simulations were carried out in the reduced temperature range 0.1 ≤T*<4.0 , where there is a competition of these interactions. Different order parameters were calculated and analyzed for several values of the reduced surface pressure in the interval, 1 ≤Π*≤40. For most of the surface pressures two directions of molecular tilt were found: (i) towards the nearest neighbor (NN) at low temperatures, T*<0.7, and most of the values of Π* and (ii) towards next-nearest neighbors (NNN) in the temperature interval 0.7 ≤T*<1.1 for Π*<25. We also found the coexistence of the NN and NNN at intermediate temperatures and Π*>25 . A low-temperature reentrant disorder-order-disorder transition in the positions of the molecular heads and in the collective tilt of the tails was found for all the surface pressure values. It was also found that the molecular tails arranged forming "rotating patterns" in the temperature interval, 0.5