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Biophys J, December 1998, p. 2626-2636, Vol. 75, No. 6
*Laboratory for Computer Science and ¶Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; #AT&T Labs, Florham Park, New Jersey 07932, and §Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
A computer model is described for studying the kinetics
of the self-assembly of icosahedral viral capsids. Solution of this problem is crucial to an understanding of the viral life cycle, which
currently cannot be adequately addressed through laboratory techniques.
The abstract simulation model employed to address this is based on the
local rules theory of Berger et al. (1994. Proc. Natl. Acad. Sci.
USA. 91:7732-7736). It is shown that the principle of local
rules, generalized with a model of kinetics and other extensions, can
be used to simulate complicated problems in self-assembly. This
approach allows for a computationally tractable molecular dynamics-like
simulation of coat protein interactions while retaining many relevant
features of capsid self-assembly. Three simple simulation experiments
are presented to illustrate the use of this model. These show the
dependence of growth and malformation rates on the energetics of
binding interactions, the tolerance of errors in binding positions, and
the concentration of subunits in the examples. These experiments
demonstrate a tradeoff within the model between growth rate and
fidelity of assembly for the three parameters. A detailed discussion of
the computational model is also provided.
Biophys J, December 1998, p. 2626-2636, Vol. 75, No. 6
© 1998 by the Biophysical Society 0006-3495/98/12/2626/11 $2.00
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