B M Hespenheide et al 2004 J. Phys.: Condens. Matter 16 S5055 doi:10.1088/0953-8984/16/44/003
B M Hespenheide1, D J Jacobs2 and M F Thorpe1
Show affiliationsThe cowpea chlorotic mottle virus (CCMV) has a protein cage, or capsid, which encloses its genetic material. The structure of the capsid consists of 180 copies of a single protein that self-assemble inside a cell to form a complete capsid with icosahedral symmetry. The icosahedral surface can be naturally divided into pentagonal and hexagonal faces, and the formation of either of these faces has been proposed to be the first step in the capsid assembly process. We have used the software FIRST to analyse the rigidity of pentameric and hexameric substructures of the complete capsid to explore the viability of certain capsid assembly pathways. FIRST uses the 3D pebble game to determine structural rigidity, and a brief description of this algorithm, as applied to body–bar networks, is given here. We find that the pentameric substructure, which corresponds to a pentagonal face on the icosahedral surface, provides the best structural properties for nucleating the capsid assembly process, consistent with experimental observations.
02.50.Le Decision theory and game theory
87.17.Aa Modeling, computer simulation of cell processes
87.15.B- Structure of biomolecules
91A80 Applications of game theory
92E10 Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
Issue 44 (10 November 2004)
Received 31 August 2004
Published 22 October 2004
B M Hespenheide et al 2004 J. Phys.: Condens. Matter 16 S5055
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