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Assembly models for Papovaviridae based on tiling theory

Keef, T., Taormina, A. and Twarock, R. (2005) Assembly models for Papovaviridae based on tiling theory. Physical Biology, 2 (3). pp. 175-188. ISSN 1478-3975

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Abstract

A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Assembly models are developed for viral capsids built from protein building blocks that can assume different local bonding structures in the capsid. This situation occurs, for example, for viruses in the family of Papovaviridae, which are linked to cancer and are hence of particular interest for the health sector. More specifically, the viral capsids of the (pseudo-) T = 7 particles in this family consist of pentamers that exhibit two different types of bonding structures. While this scenario cannot be described mathematically in terms of Caspar–Klug theory (Caspar D L D and Klug A 1962 Cold Spring Harbor Symp. Quant. Biol. 27 1), it can be modelled via tiling theory (Twarock R 2004 J. Theor. Biol. 226 477). The latter is used to encode the local bonding environment of the building blocks in a combinatorial structure, called the assembly tree, which is a basic ingredient in the derivation of assembly models for Papovaviridae along the lines of the equilibrium approach of Zlotnick (Zlotnick A 1994 J. Mol. Biol. 241 59). A phase space formalism is introduced to characterize the changes in the assembly pathways and intermediates triggered by the variations in the association energies characterizing the bonds between the building blocks in the capsid. Furthermore, the assembly pathways and concentrations of the statistically dominant assembly intermediates are determined. The example of Simian virus 40 is discussed in detail.

Item Type: Article
Academic Units: The University of York > Biology (York)
The University of York > Mathematics (York)
Depositing User: York RAE Import
Date Deposited: 26 Feb 2009 14:12
Last Modified: 26 Feb 2009 14:12
Published Version: http://dx.doi.org/10.1088/1478-3975/2/3/005
Status: Published
Publisher: Institute of Physics and IOP Publishing Limited
Refereed: Yes
Identification Number: 10.1088/1478-3975/2/3/005
URI: http://eprints.whiterose.ac.uk/id/eprint/7173

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