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
Citations
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Impact of point mutation P29S in RAC1 on tumorigenesis.
TL;DR: The overall results strongly implied that the changes in atomic conformation of the switch I and II regions in mutant RAC1 protein were a significant reason for its malignant transformation and tumorigenesis.
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Grand canonical monte carlo simulation study of water adsorption in silicalite at 300 K.
TL;DR: It is shown, on the basis of periodic ab initio calculations, that confined water molecules in silicalite have a dipole value roughly 10% smaller than that in the bulk liquid phase, indicating that the environment felt by a confined water molecule insilicalite pores is not equivalent to that inThe bulk liquid.
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Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation
TL;DR: The one‐step perturbation approach is applied and is shown to yield accurate results based on only two 2‐ns molecular dynamics simulations of an unphysical, judiciously chosen, reference state.
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Interfacial Connection Mechanisms in Calcium-Silicate-Hydrates/Polymer Nanocomposites: A Molecular Dynamics Study.
Yang Zhou,Yang Zhou,Dongshuai Hou,Hegoi Manzano,Carlos A. Orozco,Guoqing Geng,Paulo J.M. Monteiro,Paulo J.M. Monteiro,Jiaping Liu +8 more
TL;DR: Molecular dynamics, using pair-potential-based force fields, was employed to investigate the structure, dynamics, and stability of interfacial connections between calcium-silicate-hydrates (C-S-H) and organic functional groups of three different polymer species to give fundamental insights into the polymer modification of C-s-H.
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Structural Basis of Substrate Recognition in Human Nicotinamide N-Methyltransferase
TL;DR: The crystal structure of human NNMT is determined as a ternary complex bound to both the demethylated donor S-adenosyl-l-homocysteine and the acceptor substrate nicotinamide, to 2.7 Å resolution, revealing the structural basis for Nicotinamide binding and highlighting several residues in the active site which may play roles in nicotinamia recognition and NN MT catalysis.
References
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Journal ArticleDOI
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
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
The Structure and Properties of Water
David Eisenberg,Walter Kauzmann +1 more
TL;DR: The Water Molecule 2 The Real Vapour 3. Ice 4. Properties of Liquid Water 5. Models for Liquid Water Addendum as mentioned in this paper, which is an extension of the model presented in this paper.
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.