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
Reads0
Chats0
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
More filters
Book ChapterDOI
Long-Term Dynamics
TL;DR: In this article, the long-term behavior of nonlinear ODEs is investigated in the context of numerical methods, and it is of great interest to know whether this behaviour is accurately captured when they are solved by numerical methods.
Journal ArticleDOI
A Fixed-Charge Model for Alcohol Polarization in the Condensed Phase, and Its Role in Small Molecule Hydration
TL;DR: In this paper, a simple optimization strategy for incorporating experimental dielectric response information on neat liquids in classical molecular models of alcohol is presented, and simple and transferable hydroxyl modulation rules are determined that, when applied to an existing molecular parameter set, result in a newly dielectoric corrected (DC) parameter set.
Journal ArticleDOI
Selective amino acid substitution reduces cytotoxicity of the antimicrobial peptide mastoparan.
Luz N. Irazazabal,William F. Porto,Suzana M. Ribeiro,Suzana M. Ribeiro,Sandra Casale,Vincent Humblot,Ali Ladram,Octavio L. Franco,Octavio L. Franco,Octavio L. Franco +9 more
TL;DR: The results indicate that hydrophobic moment modified by amino acid substitution may enhance MP selectivity and hypothesize that [I5, R8] MP follows a mechanism of action similar to that proposed for MP, where the pore-forming activity leads to cell death.
Journal ArticleDOI
Docking study and free energy simulation of the complex between p53 DNA-binding domain and azurin.
TL;DR: This work found that the highest scored docking conformation for the p53 DBD–AZ complex also yielded the most favorable free energy value, and this best three‐dimensional model for the complex was validated by using a computational mutagenesis strategy.
Journal ArticleDOI
Aqueous tert-butanol mixtures: A model for molecular-emulsions
Bernarda Kežić,Aurélien Perera +1 more
TL;DR: The issue of whether or not the Kirkwood-Buff integrals represent solely concentration fluctuations is settled by showing the contribution of the micro-heterogeneity to these integrals through the presence of an associated pre-peak in the structure factors.
References
More filters
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.