Imai Takashi, Kovalenko Andriy, Hirata Fumio
Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
J Phys Chem B. 2005 Apr 14;109(14):6658-65. doi: 10.1021/jp045667c.
The three-dimensional reference interaction site model (3D-RISM) theory is applied to the analysis of hydration effects on the partial molar volume of proteins. For the native structure of some proteins, the partial molar volume is decomposed into geometric and hydration contributions using the 3D-RISM theory combined with the geometric volume calculation. The hydration contributions are correlated with the surface properties of the protein. The thermal volume, which is the volume of voids around the protein induced by the thermal fluctuation of water molecules, is directly proportional to the accessible surface area of the protein. The interaction volume, which is the contribution of electrostatic interactions between the protein and water molecules, is apparently governed by the charged atomic groups on the protein surface. The polar atomic groups do not make any contribution to the interaction volume. The volume differences between low- and high-pressure structures of lysozyme are also analyzed by the present method.
三维参考相互作用位点模型（3D-RISM）理论被应用于分析水合作用对蛋白质偏摩尔体积的影响。对于一些蛋白质的天然结构，利用3D-RISM理论结合几何体积计算，将偏摩尔体积分解为几何贡献和水合贡献。水合贡献与蛋白质的表面性质相关。热体积是由水分子的热涨落引起的蛋白质周围空隙的体积，它与蛋白质的可及表面积成正比。相互作用体积是蛋白质与水分子之间静电相互作用的贡献，显然由蛋白质表面的带电原子基团决定。极性原子基团对相互作用体积没有任何贡献。本文方法还分析了溶菌酶低压和高压结构之间的体积差异。
