蛋白质模拟中溶剂色散力的隐式处理。
Implicit treatment of solvent dispersion forces in protein simulations.
机构信息
Center for Molecular Modeling, DCB, CIT, National Institutes of Health, Bethesda, Maryland, 20892.
出版信息
J Comput Chem. 2014 Aug 15;35(22):1621-9. doi: 10.1002/jcc.23655. Epub 2014 Jun 12.
Abstract
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.
摘要
提出了一种用于连续溶剂表示中分散力评估的模型，可用于大规模计算机模拟。该模型捕获了部分和各向异性水合条件下水排斥的短程和长程效应。该模型引入了三个参数，其中一个参数表示系统中任意点的水合度（水占有率），该参数取决于溶质构象，另外两个参数表示水-水和水-溶质分散相互作用的强度。该模型针对蛋白质进行了优化，使用了一个亚最佳水合结合位点的水合数据和在显式水中进行的动力学模拟的结果。该模型应用于一系列脂肪醇/蛋白质复合物以及各种大小的二元和三元复合物。讨论了对弱和超弱蛋白质-蛋白质相互作用以及在拥挤介质中模拟的影响。
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