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• W2772226369 abstract "Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations." @default.
• W2772226369 created "2017-12-22" @default.
• W2772226369 creator A5067499258 @default.
• W2772226369 creator A5069786759 @default.
• W2772226369 date "2017-12-04" @default.
• W2772226369 modified "2023-10-16" @default.
• W2772226369 title "Multiscale molecular dynamics simulations of rotary motor proteins" @default.
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• W2772226369 doi "https://doi.org/10.1007/s12551-017-0373-4" @default.
• W2772226369 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/5899732" @default.
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• W2772226369 hasPublicationYear "2017" @default.
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