Abhishek Singharoy and Christophe Chipot.
Methodology for the simulation of molecular motors at different
scales.
Journal of Physical Chemistry B, 121:3502-3514, 2017.
(PMC: PMC5518690)
SING2016-CC
Millisecond-scale conformational transitions represent
a seminal challenge for traditional molecular dynamics
simulations, even with the help of
high-end supercomputer architectures.
Such events are particularly relevant to the study of molecular motors -
proteins or abiological constructs that convert chemical energy into mechanical
work.
Here, we present a hybrid-simulation scheme combining an array of
methods including elastic network models, transition path sampling and
advanced
free-energy methods possibly in conjunction with generalized-ensemble
schemes to deliver
a viable option for capturing the millisecond-scale motor steps of biological
motors.
The methodology is already implemented
in large measure
in popular molecular dynamics programs,
and can leverage the massively parallel capabilities of petascale computers.
Applicability of the hybrid method is demonstrated with two examples, namely
cyclodextrin-based motors and V-type ATPases.
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