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
Multiple C2 domains and transmembrane region proteins (MCTPs) tether membranes at plasmodesmata.
Marie L Brault,Jules D. Petit,Jules D. Petit,Françoise Immel,William J Nicolas,Marie Glavier,Lysiane Brocard,Amèlia Gaston,Mathieu Fouché,Timothy J. Hawkins,Jean-Marc Crowet,Magali S. Grison,Véronique Germain,Marion Rocher,Max E. Kraner,Vikram Alva,Stéphane Claverol,Andrea Paterlini,Yrjö Helariutta,Magali Deleu,Laurence Lins,Jens Tilsner,Jens Tilsner,Emmanuelle Bayer +23 more
TL;DR: It is shown that the multiple C2 domains and transmembrane region protein (MCTP) family, key regulators of cell‐to‐cell signalling in plants, act as ER‐PM tethers specifically at plasmodesmata.
Journal ArticleDOI
Entropic Contributions in Cosolvent Binding to Hydrophobic Solutes in Water
TL;DR: In this article, the authors investigated the contribution of small hydrophobic solutes and studied the dependence of the entropy cost of solute insertion on solvent−solvent interactions in cosolvent/water mixtures by means of molecular dynamics simulations.
Journal ArticleDOI
A dynamic pharmacophore drives the interaction between Psalmotoxin-1 and the putative drug target acid-sensing ion channel 1a.
Natalie J. Saez,Mehdi Mobli,Michael Bieri,Irène R. Chassagnon,Alpeshkumar K. Malde,Roland Gamsjaeger,Alan E. Mark,Paul R. Gooley,Lachlan D. Rash,Glenn F. King +9 more
TL;DR: An efficient bacterial expression system is developed to produce a panel of π-TRTX-Pc1a mutants for probing structure-activity relationships as well as isotopically labeled toxin for determination of its solution structure and dynamics, and it is demonstrated that the toxin pharmacophore resides in a β-hairpin loop that was revealed to be mobile over a wide range of time scales.
Journal ArticleDOI
Interlayer structure and dynamics of Cl-bearing hydrotalcite: far infrared spectroscopy and molecular dynamics modeling
TL;DR: In this article, a comparison of the observed far-infrared (FIR) spectrum of Cl−-containing hydrotalcite, [Mg3Al(OH)8]Cl·3H2O, to a power spectrum calculated using molecular dynamics (MD) computer simulation, provides a greatly increased understanding of the structure and vibrational dynamics in the interlayers of layered double hydroxides.
Journal ArticleDOI
Nonequilibrium molecular dynamics study of electric and low-frequency microwave fields on hen egg white lysozyme.
TL;DR: Nonequilibrium molecular dynamics simulations of various mutants of hen egg white lysozyme have been performed in the presence of both external static electric and low-frequency microwave fields of varying intensity, finding substantial differences in behavior for proteins with and without overall net charges.
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.