Yokogawa Daisuke, Sato Hirofumi, Imai Takashi, Sakaki Shigeyoshi
Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan.
J Chem Phys. 2009 Feb 14;130(6):064111. doi: 10.1063/1.3077209.
Three dimensional (3D) hydration structure is informative to clarify the functions of hydrated waters around a protein. We develop a new approach to calculate 3D solvation structure with reasonable computational cost. In the present method, the total solvation structure is obtained using conventional one dimensional reference interaction site model (RISM) followed by integrating the 3D fragment data, which are evaluated around each atom (site) of solute. Thanks to this strategy, time-consuming 3D fast Fourier transformation, which is required in 3D-RISM theory, can be avoided and high-parallel performance is achieved. The method is applied to small molecular systems for comparison with 3D-RISM. The obtained results by the present method and by 3D-RISM show good agreement. The hydration structures for a large protein computed by the present method are also consistent with those obtained by x-ray crystallography.
三维（3D）水化结构有助于阐明蛋白质周围水化水的功能。我们开发了一种新方法，以合理的计算成本计算3D溶剂化结构。在本方法中，使用传统的一维参考相互作用位点模型（RISM）获得总溶剂化结构，然后整合在溶质的每个原子（位点）周围评估的3D片段数据。由于这种策略，可以避免3D-RISM理论中所需的耗时的3D快速傅里叶变换，并实现高并行性能。该方法应用于小分子系统，以便与3D-RISM进行比较。本方法和3D-RISM获得的结果显示出良好的一致性。通过本方法计算的大型蛋白质的水化结构也与通过X射线晶体学获得的结构一致。
