Merzel Franci, Smith Jeremy C
National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
J Chem Inf Model. 2005 Nov-Dec;45(6):1593-9. doi: 10.1021/ci0502000.
A characterization of the physical properties of protein hydration water is critical for understanding protein structure and function. Recent small-angle X-ray and neutron scattering data indicate that the density of water on the surface of lysozyme is significantly higher than in bulk water. Here, we provide an interpretation of the scattering results using a molecular dynamics simulation, which allows us to make quantitative predictions about density variations in the first hydration shell. The perturbation relative to bulk water involves statistically significant changes in the average water structure in the first hydration layer. The water density in the first hydration shell is increased by 5% with respect to the bulk. In regions of higher water density, the water dipoles align more parallel to each other and the number of hydrogen bonds per water molecule is higher. Increased water density is found for water molecules interacting with hydrogen and carbon atoms in the backbone or with nonpolar or negatively charged side-chain groups.
对蛋白质水化水物理性质的表征对于理解蛋白质的结构和功能至关重要。最近的小角X射线和中子散射数据表明，溶菌酶表面的水密度明显高于本体水。在此，我们使用分子动力学模拟对散射结果进行解释，这使我们能够对第一水化层中的密度变化进行定量预测。相对于本体水的扰动涉及第一水化层中平均水结构的统计学显著变化。第一水化壳层中的水密度相对于本体增加了5%。在水密度较高的区域，水偶极子彼此更平行排列，每个水分子的氢键数量更多。发现与主链中的氢和碳原子或与非极性或带负电荷的侧链基团相互作用的水分子的水密度增加。
