Abstract
Viral capsids are prime biological examples of self-limited assembly, in which assembly terminates at a well-defined size and architecture. They are protein shells that enclose viral genomes and protect them from degradation. For many virus families, experiments show that during infection, viruses cause their hosts to synthesize additional proteins that undergo liquid-liquid phase separation to form membrane-less compartments. These are known as viral factories, viroplasms, negri bodies or inclusion bodies. It is hypothesized that selective localization of viral capsid proteins and genomic material within these compartments, offers a means to avoid the host immune response and coordinate events like viral genome replication, capsid protein translation, assembly and selective genome packaging. However, the physical principles governing condensate-mediated self-limiting assembly remain incompletely understood. In this work, we present a systematic analysis of this process using coarse-grained molecular dynamics simulations for icosahedral capsid assembly in the presence of a phase separated condensate. We present two different approaches to model the condensate. First we implicitly model the condensate using a potential, and second we explicitly include condensate constituent particles that undergo phase separation. Our work demonstrates agreement with existing thermodynamic and kinetic models for self-assembly coupled to liquid-liquid phase separation. Our results extend beyond these existing models by identifying new assembly pathways that can occur in a condensate, elucidating the role of excluded volume and off-pathway assemblies in determining optimal assembly conditions, and examining underlying assumptions of the equilibrium model. Our results are not only relevant to understanding how condensates guide viral self-assembly pathways, but also suggest how they can be used for achieving spatio-temporal control over the assembly of human-engineered nano-scale structures.