  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.
