Linking Capsomere Elasticity with Virus Capsid Size and Patterning

Self-limiting spontaneous assembly of proteins gives rise to many structures, including virus capsids. Often copies of a single type of protein are capable of assembling into an empty shell. Higher T-number viruses of this type, such as Hepatitis B virus (HBV), present an interesting challenge to model. Though these capsids exhibit a ubiquitous icosahedral symmetry, they can display distinct tiling patterns resulting from individual capsomeres in quasi-equivalent states. In order to model the assembly of these capsids, rigid-body models either use multiple monomeric subunits with different geometries or pre-formed pentamers and hexamers with fine-tuned interactions. We introduce SOUFFLE, a molecular dynamics simulation method with elastic capsomeres, to investigate capsid assembly. The method is used to study a model T1 system as well as nucleating tiling patterns associated with T3 and T4 HBV capsids. The assembly of full T3 and T4 capsids using pentamers and hexamers pre-formed with elastic capsomeres is also probed. Based on tiling-patterns and assembly diagrams, we propose that the heterogeneity of HBV capsids can be attributed to relatively low bending modulus of its capsomeres (10-15 kB T).