dorsal/arxiv
View SchemaAssembly Models for Papovaviridae based on Tiling Theory
| Authors | T. Keef, A. Taormina, R. Twarock |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0508031 |
| URL | https://arxiv.org/abs/q-bio/0508031 |
| DOI | 10.1088/1478-3975/2/3/005 |
| Journal | Phys. Biol. 2 (2005) 175-188 |
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 and Klug 1962), it can be modelled via tiling theory (Twarock 2004). 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 1994). 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.
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"abstract": "A vital constituent of a virus is its protein shell, called the viral capsid,\nthat encapsulates and hence provides protection for the viral genome. Assembly\nmodels are developed for viral capsids built from protein building blocks that\ncan assume different local bonding structures in the capsid. This situation\noccurs, for example, for viruses in the family of Papovaviridae, which are\nlinked to cancer and are hence of particular interest for the health sector.\nMore specifically, the viral capsids of the (pseudo-) T=7 particles in this\nfamily consist of pentamers that exhibit two different types of bonding\nstructures. While this scenario cannot be described mathematically in terms of\nCaspar-Klug Theory (Caspar and Klug 1962), it can be modelled via tiling theory\n(Twarock 2004). The latter is used to encode the local bonding environment of\nthe building blocks in a combinatorial structure, called the assembly tree,\nwhich is a basic ingredient in the derivation of assembly models for\nPapovaviridae along the lines of the equilibrium approach of Zlotnick (Zlotnick\n1994). A phase space formalism is introduced to characterize the changes in the\nassembly pathways and intermediates triggered by the variations in the\nassociation energies characterizing the bonds between the building blocks in\nthe capsid. Furthermore, the assembly pathways and concentrations of the\nstatistically dominant assembly intermediates are determined. The example of\nSimian Virus 40 is discussed in detail.",
"arxiv_id": "q-bio/0508031",
"authors": [
"T. Keef",
"A. Taormina",
"R. Twarock"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1088/1478-3975/2/3/005",
"journal_ref": "Phys. Biol. 2 (2005) 175-188",
"title": "Assembly Models for Papovaviridae based on Tiling Theory",
"url": "https://arxiv.org/abs/q-bio/0508031"
},
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