Saher A. Shaikh, Jing Li, Giray Enkavi, Po-Chao Wen, Zhijian Huang, and Emad
Tajkhorshid.
Visualizing functional motions of membrane transporters with
molecular dynamics simulations.
Biochemistry, 52:569-587, 2013.
(PMC: PMC3560430)
SHAI2013-ET
Computational modeling and molecular simulation techniques have become an integral
part of modern molecular research. Various areas of molecular sciences continue to benefit
from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these
technologies, to provide a more complete picture of the molecular problems at hand.
Because of the continuous development of more efficient algorithms harvesting ever-
expanding computational resources, and the emergence of more advanced and novel
theories and methodologies, the scope of computational studies has expanded
significantly over the past decade, now including much larger molecular systems and far
more complex molecular phenomena. Among the various computer modeling techniques,
the application of molecular dynamics (MD) simulation and related techniques has
particularly drawn attention in biomolecular research, because of the ability of the method
to describe the dynamical nature of the molecular systems and thereby to provide a more
realistic representation, which is often needed for understanding fundamental molecular
properties. The method has proven to be remarkably successful in capturing molecular
events and structural transitions highly relevant to the function and/or physicochemical
properties of biomolecular systems. Herein, after a brief introduction to the method of MD,
we use a number of membrane transport proteins studied in our laboratory as examples to
showcase the scope and applicability of the method and its power in characterizing
molecular motions of various magnitudes and time scales that are involved in the function
of this important class of membrane proteins.
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