@article{96b608295833478baaa1fb72a3b8e97a,
title = "A computational method to simulate global conformational changes of proteins induced by cosolvent",
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.",
author = "Shoichi Tanimoto and Koichi Tamura and Shigehiko Hayashi and Norio Yoshida and Haruyuki Nakano",
note = "Funding Information: The authors are grateful for the financial support from the Japan Society for the Promotion of Science (JSPS) KAKENHI (Grant nos. 18K05036 and 19H02677). NY acknowledges the Toyota Riken Scholar from the Toyota Physical and Chemical Research Institute. ST acknowledges the financial support of JSPS Grants-in-Aid for JSPS Fellows (Grant no. 19J11525). Numerical calculations were conducted, in part, at the Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences. Molecular graphics were depicted with the UCSF Chimera, developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco.66 Funding Information: The authors are grateful for the financial support from the Japan Society for the Promotion of Science (JSPS) KAKENHI (Grant nos. 18K05036 and 19H02677). NY acknowledges the Toyota Riken Scholar from the Toyota Physical and Chemical Research Institute. ST acknowledges the financial support of JSPS Grants‐in‐Aid for JSPS Fellows (Grant no. 19J11525). Numerical calculations were conducted, in part, at the Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences. Molecular graphics were depicted with the UCSF Chimera, developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco. 66 Publisher Copyright: {\textcopyright} 2021 Wiley Periodicals LLC.",
year = "2021",
month = mar,
day = "30",
doi = "10.1002/jcc.26481",
language = "English",
volume = "42",
pages = "552--563",
journal = "Journal of Computational Chemistry",
issn = "0192-8651",
publisher = "John Wiley and Sons Inc.",
number = "8",
}