Book ChapterDOI
Interaction Models for Water in Relation to Protein Hydration
Hjc Berendsen,J. P. M. Postma,W. F. van Gunsteren,Jan Hermans +3 more
- pp 331-342
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TLDR
In this article, a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6-12 potential on the oxygen positions only was developed, and parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion.Abstract:
For molecular dynamics simulations of hydrated proteins a simple yet reliable model for the intermolecular potential for water is required. Such a model must be an effective pair potential valid for liquid densities that takes average many-body interactions into account. We have developed a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6–12 potential on the oxygen positions only. Parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion. Both potential energy and pressure were required to coincide with experimental values. The model has very satisfactory properties, is easily incorporated into protein-water potentials, and requires only 0.25 sec computertime per dynamics step (for 216 molecules) on a CRAY-1 computer.read more
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Journal ArticleDOI
Spectroscopic and molecular dynamics characterization of glycyrrhizin membrane-modifying activity.
O. Yu. Selyutina,I.E. Apanasenko,A. V. Kim,Ekaterina A. Shelepova,S. S. Khalikov,Nikolay E. Polyakov +5 more
TL;DR: The interaction of GA with POPC liposomes and model DOPC, POPC and DPPC bilayers was investigated by NMR with addition of shift reagents and MD simulations to better understand the mechanism of enhanced drug bioavailability in the presence of GA.
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PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots.
TL;DR: While PPCheck can differentiate the generated decoys into native-like and non-native-like decoys with a fairly good accuracy, the results improve dramatically when features like conservation and accessibility are included.
Journal ArticleDOI
Lipid-II forms potential “landing terrain” for lantibiotics in simulated bacterial membrane
Anton O. Chugunov,Darya V. Pyrkova,Dmitry E. Nolde,Anton A. Polyansky,Anton A. Polyansky,Vladimir Pentkovsky,Roman G. Efremov,Roman G. Efremov +7 more
TL;DR: It is hypothesize that many lantibiotics exploit the conserved features of lipid-II along with characteristic modulation of the bacterial membrane as the “landing site”, which opens new opportunities for studies on lantIBiotics action and design of novel armament against resistant bacterial strains.
Journal ArticleDOI
Molecular dynamics simulations of polyglutamine aggregation using solvent-free multiscale coarse-grained models.
Yanting Wang,Gregory A. Voth +1 more
TL;DR: This work demonstrates that computer simulation of polypeptides self-assembly and aggregation, which is presently beyond the reach of all-atom MD simulations, is attainable using solvent-free MS-CG models.
Journal ArticleDOI
Water Replacement Hypothesis in Atomic Detail - Factors Determining the Structure of Dehydrated Bilayer Stacks
TL;DR: Molecular-dynamics simulations investigate the influence of trehalose on the area per lipid (APL) and related structural properties of dehydrated bilayers in atomic detail and confirm the water replacement hypothesis.
References
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TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.
Book
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David Eisenberg,Walter Kauzmann +1 more
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Journal ArticleDOI
Dynamics of folded proteins
TL;DR: The dynamics of a folded globular protein have been studied by solving the equations of motion for the atoms with an empirical potential energy function and suggest that the protein interior is fluid-like in that the local atom motions have a diffusional character.
Journal ArticleDOI
Algorithms for macromolecular dynamics and constraint dynamics
TL;DR: In this paper, the authors investigated the application of the computer simulation method of molecular dynamics to macromolecules and compared different algorithms for integrating the equations of motion, both theoretically and in practice.