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Implicit treatment of solvent dispersion forces in protein simulations
Author(s) -
Hassan Sergio A.
Publication year - 2014
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23655
Subject(s) - water model , dispersion (optics) , solvent , representation (politics) , ternary operation , work (physics) , london dispersion force , statistical physics , solvent models , molecular dynamics , chemical physics , chemistry , anisotropy , thermodynamics , binary number , materials science , molecule , computational chemistry , physics , computer science , mathematics , solvation , organic chemistry , van der waals force , law , arithmetic , optics , quantum mechanics , political science , programming language , politics
A model is proposed for the evaluation of dispersive forces in a continuum solvent representation for use in large‐scale computer simulations. The model captures the short‐ and long‐range effects of water‐exclusion in conditions of partial and anisotropic hydration. The model introduces three parameters, one of which represents the degree of hydration (water occupancy) at any point in the system, which depends on the solute conformation, and two that represent the strength of water–water and water–solute dispersive interactions. The model is optimized for proteins, using hydration data of a suboptimally hydrated binding site and results from dynamics simulations in explicit water. The model is applied to a series of aliphatic‐alcohol/protein complexes and a set of binary and ternary complexes of various sizes. Implications for weak and ultra‐weak protein‐protein association and for simulation in crowded media are discussed. Published 2014. This article is a U.S. Government work and is in the public domain in the USA