Gallery of Biomolecular Simulations
Schematic illustration of Brownian dynamics simulation
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This polymerization of actin both within the cell and in vitro
has been studied experimentally for many years. One of the most
interesting facts about actin polymerization is that the two ends of
the filament do not grow at the same rate, but the barbed
polymerizes 5-20 times faster than the pointed end. The basis
for this asymmetry has never truly been understood.
With advances in computational power in the past years, it has
become possible to simulate the interaction of larger biomolecules,
the polymerization of actin being one such system. Using Brownian
dynamics simulations, the binding of a monomer to the end of a
filament was simulated over a range of ionic strengths. The animation
depicts two `fictional' trajectories intended to illustrate the basic
concepts behind the simulations. For each trajectory, the monomer was
started with a random orientation on a sphere surrounding the
filament. By keeping track of the number of successful binding events
at each end of the filament, a rate constant for binding can be
calculated. This study showed that electrostatic interactions in fact
lead to an asymmetry in polymerization rates between the two ends.
More details and analysis of the simulations will be published in:
D. Sept, A.H. Elcock and J.A. McCammon, Computer simulations
of actin polymerization can explain the barbed-pointed end asymmetry, to
appear in J. Mol. Biol., 1999
or you can contact Dave Sept directly.
McCammon Group, UCSD (http://mccammon.ucsd.edu/)
Created by Cameron Mura on Sat Jun 7 17:55:12 PDT 2003.
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