Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

被引:11
作者
Bao Linh Nguyen [1 ]
Pettitt, B. Montgomery [1 ]
机构
[1] Univ Texas Med Branch, Sealy Ctr Struct Biol & Mol Biophys, Galveston, TX 77555 USA
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
MOLECULAR-DYNAMICS; WATER; HYDRATION; SOLVENT; SOLVATION; MODEL;
D O I
10.1021/ct501116v
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.
引用
收藏
页码:1399 / 1409
页数:11
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