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A computational method to simulate global conformational changes of proteins induced by cosolvent
Author(s) -
Tanimoto Shoichi,
Tamura Koichi,
Hayashi Shigehiko,
Yoshida Norio,
Nakano Haruyuki
Publication year - 2021
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.26481
Subject(s) - denaturation (fissile materials) , molecular dynamics , chemistry , urea , biological system , computational chemistry , ubiquitin , thermodynamics , computer science , physics , biochemistry , biology , nuclear chemistry , gene
Abstract A computational method to investigate the global conformational change of a protein is proposed by combining the linear response path following (LRPF) method and three‐dimensional reference interaction site model (3D‐RISM) theory, which is referred to as the LRPF/3D‐RISM method. The proposed method makes it possible to efficiently simulate protein conformational changes caused by either solutions of varying concentrations or the presence of cosolvent species by taking advantage of the LRPF and 3D‐RISM. The proposed method is applied to the urea‐induced denaturation of ubiquitin. The LRPF/3D‐RISM trajectories successfully simulate the early stage of the denaturation process within the simulation time of 300 ns, whereas no significant structural change is observed even in the 1 μs standard MD simulation. The obtained LRPF/3D‐RISM trajectories reproduce the mechanism of the urea denaturation of ubiquitin reported in previous studies, and demonstrate the high efficiency of the method.