Matsuoka Daisuke, Nakasako Masayoshi
Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
J Phys Chem B. 2009 Aug 13;113(32):11274-92. doi: 10.1021/jp902459n.
Hydration structures on protein surfaces are visualized by high-resolution cryogenic X-ray crystallography. We calculated the probability distributions of 4,831,570 hydration water molecules found around the 4,214,227 polar atoms in main chains and hydrophilic side chains from the 17,984 crystal structures in the Protein Data Bank. The structures are refined using the diffraction data collected below 150 K and at resolutions of better than 2.2 A. The calculated distributions were nonrandom but condensed into a few clusters. The clusters were decomposed into the distance and angular distributions by viewing from the polar coordinate system. The major peaks in the clusters were almost located along the directions of the N-H and O-H bonds or the lone pairs of oxygen atoms. The Gaussian fitting method was applied for the distribution profiles to evaluate quantitatively the peak positions and the widths. The parameters characterizing the distributions apparently depended on the hydrogen-bond partners of water molecules and on the modes whether the water molecules acted as donors or acceptors of protons. This led to propose the different roles of NH(n) (n = 1, 3), OH, and CO groups in protein hydration and possible in protein-ligand and protein-protein interaction: While C horizontal lineO groups appear to control the H-bond distances, NH(n) groups likely limit the angular range of H-bonds. The OH groups have both characteristics. In addition, it was also demonstrated that polar protein atoms were arranged to satisfy the tetrahedral hydrogen-bond geometry of water molecules, suggesting essential roles of water molecules in the folding process and in the stabilization of protein structures. These probability distributions are probably one of fundamental data to better understand the roles of hydration water molecules in the folding process and the stability of proteins in solution.
通过高分辨率低温X射线晶体学可视化蛋白质表面的水合结构。我们从蛋白质数据库中的17984个晶体结构计算了在主链和亲水侧链中4214227个极性原子周围发现的4831570个水合水分子的概率分布。这些结构使用在150K以下收集且分辨率优于2.2埃的衍射数据进行精修。计算得到的分布是非随机的，而是凝聚成几个簇。通过从极坐标系观察，将簇分解为距离和角度分布。簇中的主要峰值几乎沿着N-H和O-H键的方向或氧原子的孤对方向定位。对分布轮廓应用高斯拟合方法以定量评估峰值位置和宽度。表征分布的参数显然取决于水分子的氢键伙伴以及水分子作为质子供体或受体的模式。这导致提出NH(n)（n = 1, 3）、OH和CO基团在蛋白质水合以及蛋白质-配体和蛋白质-蛋白质相互作用中可能具有的不同作用：虽然C=O基团似乎控制氢键距离，但NH(n)基团可能限制氢键的角度范围。OH基团具有这两种特征。此外，还证明极性蛋白质原子的排列满足水分子的四面体氢键几何结构，这表明水分子在折叠过程和蛋白质结构稳定中的重要作用。这些概率分布可能是更好理解水合水分子在折叠过程中的作用以及蛋白质在溶液中的稳定性的基础数据之一。
