DOMINANT SALVATION EFFECTS FROM THE PRIMARY SHELL OF HYDRATION - APPROXIMATION FOR MOLECULAR-DYNAMICS SIMULATIONS

被引:68
作者
BEGLOV, D
ROUX, B
机构
[1] Department of Chemistry, University of Montreal, Montreal, Quebec, H3C 3J7, CP 6128, succ A
关键词
D O I
10.1002/bip.360350205
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
A simple approximation is developed to account for the dominant effects of solvation in molecular dynamics simulations of biopolymers. A small number of water molecules are induced explicitly in the primary hydration shell around the biopolymer. A nonspherical confining potential responding dynamically to the conformational changes of the biopolymer is applied to prevent evaporation and to approximate the conditions of constant pressure of a bulk solution. Simulations of a spherical system of 25 water molecules are used to adjust the empirical restraining potential to yield a uniform density distribution close to that in the bulk liquid. The primary hydration shell approach is tested with molecular dynamics simulations of simple hydrated peptides. The conformational equilibrium of alanine dipeptide and alanine tripeptide is examined using umbrella sampling calculations. The relative free energies of the C-7ax (phi = 60, psi = -80) and alpha(L) (phi = 60, psi = 60) conformations of the alanine dipeptide and the opened and closed conformations of a reversed beta-turn modeled with the alanine tripeptide were calculated. The results indicate that the primary, hydration shell can reproduce the influence of solvent on small peptides that was observed in simulations involving a much larger number of Mater molecules. (C) 1995 John Wiley & Sons, Inc.
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页码:171 / 178
页数:8
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