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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Journal ArticleDOI
Bending of the calmodulin central helix: A theoretical study
TL;DR: The results of the molecular dynamics simulations reproduce the experimentally determined location of the bend in a simulation of only the CaM central helix, indicating that the bending point is an intrinsic property of the α‐helix, for which the remainder of the protein is not important.
Journal ArticleDOI
Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups.
Beat Vögeli,Takuya F. Segawa,Dominik Leitz,Alexander Sobol,Alexandra Choutko,Daniel Trzesniak,Wilfred F. van Gunsteren,Roland Riek +7 more
TL;DR: It is demonstrated that the measurement of NOE buildups between amide protons in perdeuterated human ubiquitin using a designed (15)N-resolved HMQC-NOESY experiment enables the determination of (1)H(N)-(1) H(N) distances up to 5 A with high accuracy and precision.
Journal ArticleDOI
Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains.
TL;DR: The description of carbohydrate chains afforded by 56A6CARBO_R suggests a significant extent of ring flexibility, i.e., small but often non‐negligible equilibrium populations of inverted chairs, and challenges the “textbook” picture of conformationally locked carbohydrate rings.
Journal ArticleDOI
Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperatures.
TL;DR: The results demonstrate that salt bridge interactions are extremely resilient to temperature increases and, as such, are uniquely suited to promoting protein stability at high temperatures.
Journal ArticleDOI
Effect of high exogenous electric pulses on protein conformation: myoglobin as a case study.
TL;DR: This paper shows results from molecular dynamics simulations of a single myoglobin molecule in water exposed to pulsed and static electric fields, finding that the highest intensity produced a fast transition between folded and unfolded states, as inferred by secondary structures and geometrical analysis.
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.