Markus Dittrich, Jin Yu, and Klaus Schulten.
PcrA helicase, a molecular motor studied from the electronic to the
functional level.
Topics in Current Chemistry, 268:319-347, 2006.
DITT2006A
Molecular motors are adenosine tri-phosphate (ATP) hydrolysis-driven,
cellular proteins responsible for a wide variety of different
tasks, such as transport, energy metabolism, and DNA processing.
Their operation cycle spans a wide range of length and time scales,
from the localized and fast chemical reaction in the catalytic site(s)
to the large scale and much slower conformational motions involved
in the motors' physiological function. From a computational point
of view, this means that currently there exists no single approach
capable of capturing the whole spectrum of events during
molecular motor function. In the present review, we show for
PcrA helicase, a molecular motor involved in the unwinding
of double stranded DNA, how a combination of computational approaches
can be used to examine PcrA's function in its entirety as well as
in detail. Combined quantum mechanical/molecular mechanical
simulations are used to study the catalytic ATP hydrolysis event
and its coupling to protein conformational changes. Molecular
dynamics simulations then provide a means of studying overall PcrA
function on a nanosecond time scale. Finally, to reach
physiologically relevant time scales, i.e., milliseconds, stochastic
simulations are employed. We show that by combining the three stated
approaches one can obtain insight into PcrA helicase function.
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