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At least 343 records · Page 19Linked to original sources
PubMed1999

Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method.

Restrained and unrestrained aqueous solution molecular dynamics simulations applying the particle mesh Ewald (PME) method to DNA duplex structures previously determined via in vacuo restrained molecular dynamics with NMR-derived restraints are reported. Without experimental restraints, the DNA decamer, d(CATTTGCATC).d(GATGCAAATG) and trisdecamer, d(AGCTTGCCTTGAG).d(CTCAAGGCAAGCT), structures are stable on the nanosecond time scale and adopt conformations in the B-DNA family. These free DNA simulations exhibit behavior characteristic of PME simulations previously performed on DNA sequences, including a low helical twist, frequent sugar pucker transitions, BI-BII(epsilon-zeta) transitions and coupled crakshaft (alpha-gamma) motion. Refinement protocols similar to the original in vacuo restrained molecular dynamics (RMD) refinements but in aqueous solution using the Cornell et al. force field [Cornell et al. (1995) J. Am. Chem. Soc., 117, 5179-5197] and a particle mesh Ewald treatment produce structures which fit the restraints very well and are very similar to the original in vacuo NMR structure, except for a significant difference in the average helical twist. Figures of merit for the average structure found in the RMD PME decamer simulations in solution are equivalent to the original in vacuo NMR structure while the figures of merit for the free MD simulations are significantly higher. The free MD simulations with the PME method, however, lead to some sequence-dependent structural features in common with the NMR structures, unlike free MD calculations with earlier force fields and protocols. There is some suggestion that the improved handling of electrostatics by PME improves long-range structural aspects which are not well defined by the short-range nature of NMR restraints.

Algorithms↗
PubMed2004

Molecular dynamics investigations of modulated phases in organic materials.

In order to apply the molecular dynamics (MD) method to simulate modulated phases in organic materials, a compensating external pressure tensor is proposed to compensate for the deficiencies of the force field applied in the simulation. MD can well reproduce modulated phases that have been measured by diffraction. Mechanisms of incommensurate modulation are revealed from the simulations. Details of the structures relating to the origins and mechanisms giving rise to the formation of modulated phases are presented.

Journal Article↗
PubMed2005

Time series analysis of ion dynamics in glassy ionic conductors obtained by a molecular dynamics simulation.

We present several characteristics of ionic motion in glassy ionic conductors brought out by time series analysis of molecular dynamics (MD) simulation data. Time series analysis of data obtained by MD simulation can provide crucial information to describe, understand and predict the dynamics in many systems. The data have been treated by the singular spectrum analysis (SSA), which is a method to extract information from noisy short time series and thus provide insight into the unknown or partially unknown dynamics of the underlying system that generated the time series. Phase-space plot reconstructed using the principal components of SSA exhibited complex but clear structures, suggesting the deterministic nature of the dynamics.

Journal Article↗
PubMed1995

Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long-time molecular dynamics simulations.

Structural and dynamic properties of bovine pancreatic trypsin inhibitor (BPTI) in aqueous solution are investigated using two molecular dynamics (MD) simulations: one of 1.4 ns length and one of 0.8 ns length in which atom-atom distance bounds derived from NMR spectroscopy are included in the potential energy function to make the trajectory satisfy these experimental data more closely. The simulated properties of BPTI are compared with crystal and solution structures of BPTI, and found to be in agreement with the available experimental data. The best agreement with experiment was obtained when atom-atom distance restraints were applied in a time-averaged manner in the simulation. The polypeptide segments found to be most flexible in the MD simulations coincide closely with those showing differences between the crystal and solution structures of BPTI.

Animals↗
PubMed2005

Structure, energetics, and dynamics of water adsorbed on the muscovite (001) surface: a molecular dynamics simulation.

Molecular dynamics (MD) computer simulations of liquid water adsorbed on the muscovite (001) surface provide a greatly increased, atomistically detailed understanding of surface-related effects on the spatial variation in the structural and orientational ordering, hydrogen bond (H-bond) organization, and local density of H2O molecules at this important model phyllosilicate surface. MD simulations at constant temperature and volume (statistical NVT ensemble) were performed for a series of model systems consisting of a two-layer muscovite slab (representing 8 crystallographic surface unit cells of the substrate) and 0 to 319 adsorbed H2O molecules, probing the atomistic structure and dynamics of surface aqueous films up to 3 nm in thickness. The results do not demonstrate a completely liquid-like behavior, as otherwise suggested from the interpretation of X-ray reflectivity measurements and earlier Monte Carlo simulations. Instead, a more structurally and orientationally restricted behavior of surface H2O molecules is observed, and this structural ordering extends to larger distances from the surface than previously expected. Even at the largest surface water coverage studied, over 20% of H2O molecules are associated with specific adsorption sites, and another 50% maintain strongly preferred orientations relative to the surface. This partially ordered structure is also different from the well-ordered 2-dimensional ice-like structure predicted by ab initio MD simulations for a system with a complete monolayer water coverage. However, consistent with these ab initio results, our simulations do predict that a full molecular monolayer surface water coverage represents a relatively stable surface structure in terms of the lowest diffusional mobility of H2O molecules along the surface. Calculated energies of water adsorption are in good agreement with available experimental data.

Journal Article↗
PubMed2002

Molecular dynamics simulations of biological reactions.

This review considers the author perspective on the emergence of molecular dynamics (MD) simulations of biological processes. It starts with the 1976 simulation of the primary event in rhodopsin, moves to the earliest simulations of enzymatic reactions and electron transfer reactions and ends up with recent simulations of proton translocations and ion transport in proteins. The emphasis is placed on our progress in simulations of actual biological reactions and functional properties, rather than on studies of general properties such as structure and thermal motions. In most cases it has been possible to develop special strategies that capture the relevant dynamics of the given biological process. The predictive power of our early simulations of fast biological process (e.g. vision and photosynthesis) and the insight obtained from these studies is pointed out. Critical examinations of dynamical effects in different biological processes is reviewed. This includes the finding that dynamical effects are unlikely to contribute significantly to enzyme catalysis or to other processes with significant activation barriers. Even in the case of ion channels it is found that the most important effects are associated with energetics rather than dynamics. Nevertheless, MD simulations provide what is probably the most realistic description of the actual reactive events. The resulting insight is crucial in studies of fast photobiological reactions and instructive in cases of slower processes.

Carrier Proteins↗
PubMed2004

Computer simulations of adsorption and diffusion for binary mixtures of methane and hydrogen in titanosilicates.

Equilibrium molecular dynamics (MD) simulations of equimolar mixtures of hydrogen and methane were performed in three different titanosilicates: naturally occurring zorite and two synthetic titanosilicates, ETS-4 and ETS-10. In addition, single-component MD simulations and adsorption isotherms generated using grand canonical Monte Carlo simulations were performed to support the mixture simulations. The goal of this study was to determine the best membrane material to carry out hydrogen/methane separations. ETS-10 has a three-dimensional pore network. ETS-4 and zorite have two-dimensional pore networks. The simulations carried out in this study show that the increased porosity of ETS-10 results in self-diffusion coefficients for both hydrogen and methane that are higher in ETS-10 than in either ETS-4 or zorite. Methane only showed appreciable displacement in ETS-10. The ability of the methane molecules to move in all three directions in ETS-10 was demonstrated by the high degree of isotropy shown in the values of the x, y, and z components of the self-diffusion coefficient for methane in ETS-10. From our simulations we conclude that ETS-10 would be better suited for fast industrial separations of hydrogen and methane. However, the separation would not result in a pure hydrogen stream. In contrast, ETS-4 and zorite would act as true molecular sieves for separations of hydrogen and methane, as the methane would not move through membranes made of these materials. This was indicated by the near-zero self-diffusion coefficient of methane in ETS-4 and zorite.

Journal Article↗
PubMed2006

Simulation studies of the protein-water interface. II. Properties at the mesoscopic resolution.

We report molecular dynamics (MD) simulations of three protein-water systems (ubiquitin, apo-calbindin D(9K), and the C-terminal SH2 domain of phospholipase C-gamma1), from which we compute the dielectric properties of the solutions. Since two of the proteins studied have a net charge, we develop the necessary theory to account for the presence of charged species in a form suitable for computer simulations. In order to ensure convergence of the time correlation functions needed for the analysis, the minimum length of the MD simulations was 20 ns. The system sizes (box length, number of waters) were chosen so that the resulting protein concentrations are comparable to experimental conditions. A dielectric component analysis was carried out to analyze the contributions from protein and water to the frequency-dependent dielectric susceptibility chi(omega) of the solutions. Additionally, an even finer decomposition into protein, two solvation shells, and the remaining water (bulk water) was carried out. The results of these dielectric decompositions were used to study protein solvation at mesoscopic resolution, i.e., in terms of protein, first and second solvation layers, and bulk water. This study, therefore, complements the structural and dynamical analyses at molecular resolution that are presented in the companion paper. The dielectric component contributions from the second shell and bulk water are very similar in all three systems. We find that the proteins influence the dielectric properties of water even beyond the second solvation shell, in agreement with what was observed for the mean residence times of water molecules in protein solutions. By contrast, the protein contributions, as well as the contributions of the first solvation shell, are system specific. Most importantly, the protein and the first water shell around ubiquitin and apo-calbindin are anticorrelated, whereas the first water shell around the SH2 domain is positively correlated.

Amino Acids↗
PubMed2006

Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase.

Solution NMR spin relaxation experiments and classical MD simulations are used to study the dynamics of triosephosphate isomerase (TIM) in complex with glycerol 3-phosphate (G3P). Three regions in TIM exhibit conformational transitions on the micros-ms time scale as detected by chemical exchange broadening effects in NMR spectroscopy: residue Lys 84 on helix C, located at the dimeric interface; active site loop 6; and helix G. The results indicate that the conformational exchange process affecting the residues of loop 6 is the correlated opening and closing of the loop. Distinct processes are responsible for the chemical exchange linebroadening observed in the other regions of TIM. MD simulations confirm that motions of individual residues within the active site loop are correlated and suggest that the chemical exchange processes observed for residues in helix G arise from transitions between 3(10)- and alpha-helical structures. The results of the joint NMR and MD study provide global insight into the role of conformational dynamic processes in the function of TIM.

Binding Sites↗
PubMed2006

Molecular dynamics simulation of polymer electrolytes based on poly(ethylene oxide) and ionic liquids. I. Structural properties.

Molecular dynamics (MD) simulations have been performed for prototype models of polymer electrolytes in which the salt is an ionic liquid based on 1-alkyl-3-methylimidazolium cations and the polymer is poly(ethylene oxide), PEO. The MD simulations were performed by combining the previously proposed models for pure ionic liquids and polymer electrolytes containing simple inorganic ions. A systematic investigation of ionic liquid concentration, temperature, and the 1-alkyl- chain length, [1,3-dimethylimidazolium]PF6, and [1-butyl-3-methylimidazolium]PF6, effects on resulting equilibrium structure is provided. It is shown that the ionic liquid is dispersed in the polymeric matrix, but ionic pairs remain in the polymer electrolyte. Imidazolium cations are coordinated by both the anions and the oxygen atoms of PEO chains. Probability density maps of occurrences of nearest neighbors around imidazolium cations give a detailed physical picture of the environment experienced by cations. Conformational changes on PEO chains upon addition of the ionic liquid are identified. The equilibrium structure of simulated systems is also analyzed in reciprocal space by using the static structure factor, S(k). Calculated S(k) display a low wave-vector peak, indicating that spatial correlation in an extended-range order prevail in the ionic liquid polymer electrolytes. Long-range correlations are assigned to nonuniform distribution of ionic species within the simulation box.

Journal Article↗
PubMed1996

VMD: visual molecular dynamics.

VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.

Computer Graphics↗
PubMed2001

Molecular dynamics simulations of the rehydration of folded and unfolded cytochrome C ions in the vapor phase.

Molecular dynamics (MD) simulations have been performed to study the rehydration of compact and unfolded cytochrome c ions in the vapor phase. Experimental studies have shown that the compact conformations adsorb many more water molecules than unfolded ones when exposed to water vapor. MD simulations performed with up to 150 water molecules reproduce the key experimental observations, including a partial refolding caused by hydration. According to the calculations it is more energetically favorable to hydrate the compact conformation in the initial stages of hydration, because it is easier for a water molecule to interact simultaneously with several polar groups (due to their proximity). The protonated side chains are not favored hydration sites in the simulations because they have "self-solvation" shells which must be disrupted for the water to penetrate. For both conformations, the adsorbed water molecules are mainly located in surface crevices.

Computer Simulation↗
PubMed1991

Mass-weighted molecular dynamics simulation and conformational analysis of polypeptide.

Atomic motions in protein molecules have been studied by molecular dynamics (MD) simulations; dynamics simulation methods have also been employed in conformational studies of polypeptide molecules. It was found that when atomic masses are weighted, the molecular dynamics method can significantly increase the sampling of dihedral conformation space in such studies, compared to a conventional MD simulation of the same total simulation time length. Herein the theoretical study of molecular conformation sampling by the molecular dynamics-based simulation method in which atomic masses are weighted is reported in detail; moreover, a numerical scheme for analyzing the extensive conformational sampling in the simulation of a tetrapeptide amide molecule is presented. From numerical analyses of the mass-weighted molecular dynamics trajectories of backbone dihedral angles, low-resolution structures covering the entire backbone dihedral conformation space of the molecule were determined, and the distribution of rotationally stable conformations in this space were analyzed quantitatively. The theoretical analyses based on the computer simulation and numerical analytical methods suggest that distinctive regimes in the conformational space of the peptide molecule can be identified.

Amino Acid Sequence↗
PubMed2004

Conformation of prion protein repeat peptides probed by FRET measurements and molecular dynamics simulations.

We report the combined use of steady-state fluorescence resonance energy transfer (FRET) experiments and molecular dynamics (MD) simulations to investigate conformational distributions of the prion protein (PrP) repeat system. FRET was used for the first time to probe the distance, as a function of temperature and pH, between a donor Trp residue and an acceptor dansyl group attached to the N-terminus in seven model peptides containing one to three repeats of the second decarepeat of PrP from marsupial possum (PHPGGSNWGQ)nG, and one and two human PrP consensus octarepeats (PHGGGWGQ)nG. In multirepeat peptides, single-Trp mutants were made by replacing other Trp(s) with Phe. As previous work has shown PrP repeats do not adopt a single preferred stable conformation, the FRET values are averages reflecting heterogeneity in the donor-acceptor distances. The T-dependence of the conformational distributions, and derived average dansyl-Trp distances, were obtained directly from MD simulation of the marsupial dansyl-PHPGGSNWGQG peptide. The results show excellent agreement between the FRET and MD T-dependent distances, and demonstrate the remarkable sensitivity and reproducibility of the FRET method in this first-time use for a set of disordered peptides. Based on the results, we propose a model involving cation-pi or pi-pi His-Trp interactions to explain the T- (5-85 degrees C) and pH- (6.0, 7.2) dependencies on distance, with HW i, i + 4 or WH i, i + 4 separations in sequence being more stable than HW i, i + 6 or WH i, i + 6 separations. The model has peptides adopting loosely folded conformations, with dansyl-Trp distances very much less than estimates for fully extended conformations, for example, approximately 16 vs. 33, approximately 21 vs. 69, and approximately 22 vs. 106 A for 1-3 decarepeats, and approximately 14 vs. 25 and approximately 19 vs. 54 A for 1-2 octarepeats, respectively. The study demonstrates the usefulness of combining FRET with MD, a combination reported only once previously. Initial "mapping" of the conformational distribution of flexible peptides by simulation can assist in designing and interpreting experiments using steady-state intensity methods, and indicating how time-resolved or anisotropy methods might be used.

Amino Acid Sequence↗
PubMed2006

Neutron diffraction and simulation studies of CsNO3 and Cs2CO3 solutions.

Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to study the structuring in aqueous solution of two cesium salts, cesium carbonate, and cesium nitrate. As was previously found for guanidinium salts of carbonate, mesoscopic-scale clusters were seen to form in the Cs2CO3 solution both in the MD simulations and in the diffraction experiments. No such large scale ion clusters were found in the CsNO3 solutions in either the modeling or experiments. The results are dominated by the strength and geometry of the direct first-neighbor interactions, which explain the differences in the clustering behavior between the two solutions without need to refer to longer-range water-water structuring.

Carbonates↗
PubMed1993

Molecular dynamics simulation of the stability of a 22-residue alpha-helix in water and 30% trifluoroethanol.

A molecular dynamics (MD) simulation was performed on the alpha-helix H8-HC5, the C-terminal part of myoglobin (residue 132-153), under periodic boundary conditions in two different solutions, water and water with 30% (v/v) 2,2,2-trifluoroethanol (TFE), at 300 K to investigate the stability of the helix. In both simulations, the initial configuration was a canonical right-handed alpha-helix. In the course of the MD trajectory in water (200 ps), the helix clearly destabilized and began to unfold after 100 ps. In the TFE solution, two stable parts of helical regions were observed after 70 ps of a 200-ps MD simulation, supporting the notion that TFE acts as a structure-forming solvent.

Amino Acid Sequence↗
PubMed1987

Molecular dynamics simulations of cyclosporin A: the crystal structure and dynamic modelling of a structure in apolar solution based on NMR data.

The conformation of the immunosuppressive drug cyclosporin A (CPA), both in apolar solution and in crystalline state, has been studied by computer simulation techniques. Three molecular dynamics (MD) simulations have been performed: one modelling the crystal structure and two modelling the structure in apolar solution, using a restrained MD approach in which data from nuclear magnetic resonance (NMR) and infrared (IR) spectroscopy are taken into account. The simulation of the crystalline state (MDC) concerns a system of 4 unit cells containing 16 cyclosporin A molecules and 22 water molecules, which is simulated using crystalline periodic boundary conditions. The simulations modelling the apolar solvent conformation (MDS) concern one isolated cyclosporin A molecule. In these simulations an extra term in the interatomic potential function is used, which forces the molecule to satisfy a set of 57 atom-atom distance constraints originating from nuclear Overhauser effects (NOEs) obtained from NMR spectroscopy and one distance constraint deduced from IR spectroscopy. From a comparison of the results of the crystal simulation to those of the X-ray experiment in terms of structure, atomic fluctuations, hydrogen bond pattern, etc., it is concluded that the force field that is used yields an adequate representation of crystalline cyclosporin A. Secondly, it is shown that the dynamic modelling technique that is used to obtain a structure in a polar solution from NMR distance information works well. Starting from initial conformations which have a root mean square difference of 0.14 nm both distance restrained MD simulations converge to the same final solution structure. A comparison of the crystal structure of cyclosporin A and the one in apolar solution shows that there are significant differences. The overall difference in atomic positions is 0.09 nm for the C alpha atoms and 0.17 nm for all atoms. In apolar solution, the molecule is slightly more bent and the side chains of 1 MeBmt and 10 MeLeu adopt a different conformation.

Computer Simulation↗
PubMed2001

Molecular dynamics simulation of thymine glycol-lesioned DNA reveals specific hydration at the lesion.

One nanosecond molecular dynamics (MD) simulation of a thymine glycol (TG)-lesioned part of human lymphoblast AG9387 was performed to determine structural changes in DNA molecule caused by the presence of a lesion. These changes can be significant for proper recognition of lesions by a repair enzyme. Thymine glycol is the DNA oxidative lesion formed by addition of OH radicals to C5 and C6 atoms of the thymine base. This lesion is known as causing Cockayne Syndrome-inherited genetic disorder. Distribution of water molecules in a hydration shell around the DNA molecule was analyzed for its contribution to the recognition of the TG lesion by the repair enzyme. The results of MD simulation show there is a specific DNA structural configuration formed at the lesion. After 500 ps the DNA is bent in a kink at the TG site. This change dislocates the glycosyl bond at C5' to a position closer to the DNA surface, and thus its atoms are more exposed to the surrounding water shell. The increased number of water molecules that are close to the TG site indicates that the glycosyl bond may be easily contacted by the repair enzyme. In addition, the higher number of water molecules at the TG site substantiates the importance of water-mediated hydrogen bonds created between the repair enzyme and the DNA upon formation of the complex. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1723-1731, 2001

Journal Article↗