Role of genome topology in the stability of viral capsids

Abstract

We explore how the stability of RNA viruses depends on genome topology and interactions between RNA and the capsid proteins. RNA is modeled as a branched polymer with 12 attractive sites (packaging signals) that can form bonds with 12 icosahedrally distributed capsid sites. The genome topology is encoded as a graph by mapping pairs of adjacent packaging signals to edges. We perform replica exchange molecular dynamics simulations and evaluate the osmotic pressure of all unique branched topologies of encapsulated RNA. We find that virion stability depends in a complex fashion on both genome topology and degree of confinement, and predict that MS2 bacteriophage should prefer a more linear genome topology.