A computational method to simulate global conformational changes of proteins induced by cosolvent

Shoichi Tanimoto, Koichi Tamura, Shigehiko Hayashi, Norio Yoshida, Haruyuki Nakano

研究成果: Contribution to journalArticle査読

抄録

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.

本文言語英語
ページ(範囲)552-563
ページ数12
ジャーナルJournal of Computational Chemistry
42
8
DOI
出版ステータス出版済み - 3 30 2021

All Science Journal Classification (ASJC) codes

  • 化学 (全般)
  • 計算数学

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