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
Journal ArticleDOI
Computational analysis of local membrane properties.
TL;DR: A collection of methods for an efficient local membrane property calculation, comprising bilayer thickness, area per lipid, deuterium order parameters, Gaussian and mean curvature, which proves to provide an intuitive and detailed view on the observables that are otherwise interpreted as averaged bilayer properties.
Journal ArticleDOI
Molecular dynamics simulation of nanoscale liquid flows
Yuxiu Li,Jinliang Xu,Dongqing Li +2 more
TL;DR: In this paper, a review of the methods and the applications of molecular dynamics simulation in liquid flows in nanochannels is presented, which is based on the Newton's second law to simulate the particles' interactions.
Journal ArticleDOI
Effect of surface polarity on the structure and dynamics of water in nanoscale confinement.
Santiago Romero-Vargas Castrillón,Nicolas Giovambattista,Ilhan A. Aksay,Pablo G. Debenedetti +3 more
TL;DR: A molecular dynamics simulation study of the structure and dynamics of water confined between silica surfaces using beta-cristobalite as a model template, which scale the surface Coulombic charges by means of a dimensionless number, k, and thereby can model systems ranging from hydrophobic apolar to hydrophilic, respectively.
Journal ArticleDOI
SARM1 is a metabolic sensor activated by an increased NMN/NAD+ ratio to trigger axon degeneration
Matthew D. Figley,W. Gu,Jeffrey D. Nanson,Yun Shi,Yo Sasaki,Katie Cunnea,Alpeshkumar K. Malde,Xinying Jia,Zhenyao Luo,Forhad Karim Saikot,Tamim Mosaiab,Veronika Masic,Stephanie Jane Holt,Lauren E. Hartley-Tassell,Helen Ying McGuinness,M.K. Manik,Todd Bosanac,Michael J. Landsberg,Philip S. Kerry,Mehdi Mobli,R.O. Hughes,Jeffrey Milbrandt,Bostjan Kobe,Aaron DiAntonio,Thomas Ve +24 more
TL;DR: In this paper, the authors demonstrate that SARM1 is activated by an increase in the ratio of nicotinamide mononucleotide (NMN) to NAD+ and show that both metabolites compete for binding to the auto-inhibitory N-terminal armadillo repeat (ARM) domain.
Journal ArticleDOI
Hydration Properties and Interlayer Organization of Water and Ions in Synthetic Na-Smectite with Tetrahedral Layer Charge. Part 2. Toward a Precise Coupling between Molecular Simulations and Diffraction Data
Eric Ferrage,Boris A. Sakharov,Laurent J. Michot,Alfred Delville,Allan Bauer,Bruno Lanson,Sylvain Grangeon,Gilles Frapper,Mónica Jiménez-Ruiz,Gabriel J. Cuello +9 more
TL;DR: Cygan et al. as mentioned in this paper developed a specific methodology to collate the interlayer configurations resulting from Grand-Canonical Monte Carlo (GCMC) simulations with experimental X-ray and neutron diffraction data for two synthetic Na-saturated saponites having contrasting layer charge.
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.