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Biophys J, August 2001, p. 667-674, Vol. 81, No. 2
*Center for Computational Biology, and Department of Biomedical
Engineering, Washington University, St. Louis, Missouri 63130-4899 and
Howard Hughes Medical Institute, Department of Chemistry
and Biochemistry, and Department of Pharmacology, University of
California, San Diego, La Jolla, California 92093-0365 USA
We have performed computer simulations and free energy
calculations to determine the thermodynamics and kinetics of actin nucleation and thus identify a probable nucleation pathway and critical
nucleus size. The binding free energies of structures along the
nucleation pathway are found through a combination of electrostatic
calculations and estimates of the entropic and surface area
contributions. The association kinetics for the formation of each
structure are determined through a series of Brownian dynamics
simulations. The combination of the binding free energies and the
association rate constants determines the dissociation rate constants,
allowing for a complete characterization of the nucleation and
polymerization kinetics. The results indicate that the trimer is the
size of the critical nucleus, and the rate constants produce
polymerization plots that agree very well with experimental results
over a range of actin monomer concentrations.
Biophys J, August 2001, p. 667-674, Vol. 81, No. 2
© 2001 by the Biophysical Society 0006-3495/01/08/667/08 $2.00
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