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
Guest-host coupling and anharmonicity in clathrate hydrates.
TL;DR: The vibrations of the guest molecules and their coupling to the cages is found to depend critically on the size, shape and electrostatic properties of the encaged guest.
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Observation of "ionic lock" formation in molecular dynamics simulations of wild-type beta 1 and beta 2 adrenergic receptors
TL;DR: Submicrosecond molecular dynamics simulations of wild-type beta(1) and beta(2) adrenergic receptors in a lipid bilayer under physiological conditions give access to structural and dynamic properties of the receptors in pseudo in vivo conditions, suggesting that the ligand binding mode is not affected by the introduced modifications.
Journal ArticleDOI
Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges.
TL;DR: The FEP algorithm is extended, which has been extensively applied to many drug discovery programs for relative binding free-energy calculations between ligands with the same net charge, to enable charge-changing perturbations and is found to be on par with the accuracy of charge-conserving perturbation.
Journal ArticleDOI
Biallelic Mutations in TBCD, Encoding the Tubulin Folding Cofactor D, Perturb Microtubule Dynamics and Cause Early-Onset Encephalopathy
Elisabetta Flex,Marcello Niceta,Serena Cecchetti,Isabelle Thiffault,Isabelle Thiffault,Margaret G. Au,Alessandro Capuano,Emanuela Piermarini,Anna A. Ivanova,Joshua W. Francis,Giovanni Chillemi,Balasubramanian Chandramouli,Giovanna Carpentieri,Giovanna Carpentieri,Charlotte A. Haaxma,Andrea Ciolfi,Simone Pizzi,Ganka Douglas,Kara L. Levine,Antonella Sferra,Maria Lisa Dentici,R. Pfundt,Jean Baptiste Le Pichon,Emily G. Farrow,Frank Baas,Fiorella Piemonte,Bruno Dallapiccola,John M. Graham,Carol J Saunders,Carol J Saunders,Enrico Bertini,Richard A. Kahn,David A. Koolen,Marco Tartaglia +33 more
TL;DR: This work reports that biallelic mutations in TBCD cause a disease with neurodevelopmental and neurodegenerative features characterized by early-onset cortical atrophy, secondary hypomyelination, microcephaly, thin corpus callosum, developmental delay, intellectual disability, seizures, optic atrophy and spastic quadriplegia.
Journal ArticleDOI
Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations
TL;DR: The method of “lagged RMSD-analysis” is suggested as a tool to judge if an MD simulation has not yet run long enough, based on R MSD values between pairs of configurations separated by variable time intervals Δt.
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.