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Multiscale molecular dynamics simulations of rotary motor proteins
#MMPMID29204882
Ekimoto T
; Ikeguchi M
Biophys Rev
2018[Apr]; 10
(2
): 605-615
PMID29204882
show ga
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.
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