Komeiji Y, Uebayasi M, Someya J, Yamato I
Department of Biology, Faculty of Science, University of Tokyo, Japan.
Proteins. 1993 Jul;16(3):268-77. doi: 10.1002/prot.340160305.
The solvent structure and behavior around a protein were examined by analyzing a trajectory of molecular dynamics simulation of the trp-holorepressor in a periodic box of water. The calculated self diffusion coefficient indicated that the solvent within 10 A of the protein had lower mobility. Examination of the solvent diffusion around different atoms of different kinds of residues showed no general tendency. This fact suggested that the solvent mobility is not influenced significantly by the kind of the atom or residue they solvated. Distribution analysis around the protein revealed two peaks of water oxygen: a sharp one at 2.8 A around polar and charged atoms and a broad one at approximately 3.4 A around apolar atoms. The former was stabilized by water-protein hydrogen bonds, and the latter was stabilized by water-water hydrogen bonds, suggesting the existence of a hydrophobic shell. An analysis of protein atom-water radial distribution functions confirmed these shell structures around polar or charged atoms and apolar ones.
通过分析色氨酸全阻遏蛋白在周期性水盒中的分子动力学模拟轨迹，研究了蛋白质周围的溶剂结构和行为。计算得到的自扩散系数表明，蛋白质周围10埃范围内的溶剂流动性较低。对不同种类残基的不同原子周围的溶剂扩散进行检查，未发现普遍趋势。这一事实表明，溶剂的流动性不受其溶剂化的原子或残基种类的显著影响。蛋白质周围的分布分析揭示了水氧的两个峰值：一个尖锐的峰值出现在极性和带电原子周围2.8埃处，一个较宽的峰值出现在非极性原子周围约3.4埃处。前者通过水-蛋白质氢键稳定，后者通过水-水氢键稳定，表明存在疏水壳。对蛋白质原子-水径向分布函数的分析证实了极性或带电原子以及非极性原子周围的这些壳结构。
