A new method for finding the minimum free energy pathway of ions and small molecule transportation through protein based on 3D-RISM theory and the string method

被引：2

作者：

Yoshida, Norio ^{[1
]}

机构：

[1] Kyushu Univ, Grad Sch Sci, Dept Chem, Nishi Ku, 744 Motooka, Fukuoka 8190395, Japan

来源：

CHEMICAL PHYSICS LETTERS | 2018年 / 699卷

关键词：

3D-RISM; String method; Ion channel; Molecular transportation; INTEGRAL-EQUATION THEORY; INTERACTION SITE MODEL; SOLVATION; MYOGLOBIN; DYNAMICS; FORCE; WATER; SIMULATION; DIFFUSION; SOLVENT;

D O I：

10.1016/j.cplett.2018.03.034

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

A new method for finding the minimum free energy pathway (MFEP) of ions and small molecule transportation through a protein based on the three-dimensional reference interaction site model (3D-RISM) theory combined with the string method has been proposed. The 3D-RISM theory produces the distribution function, or the potential of mean force (PMF), for transporting substances around the given protein structures. By applying the string method to the PMF surface, one can readily determine the MFEP on the PMF surface. The method has been applied to consider the Na+ conduction pathway of channelrhodopsin as an example. (C) 2018 Elsevier B.V. All rights reserved.

引用

页码：22 / 27

页数：6

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