Accessing the Viral Cargo: Capsid Dynamics and Disassembly

Abstract

Many viruses consist of a genome encapsulated in a protective, self-assembled protein capsid. Infection requires exposure of the genomic cargo to the host cellular machinery. Because the self-assembled capsid is thought to be in a free-energy minimum in the cellular environment, this exposure requires an external energy input or a chemical change in the environment. This thesis focuses on understanding how the cargo of a viral capsid can become exposed. In the first part, I study the uncoating of bacteriophage MS2 bound to its receptor in vivo using fluorescence imaging, and I find evidence of a new extracellular uncoating pathway, suggesting that the virus could have more than one uncoating pathway to balance different risks during the early stages of infection. In the second part, I use coarse-grained molecular dynamics simulations to understand the disassembly kinetics and intermediates of a generic virus-like particle. I find that disassembly is nucleated and investigate the factors that affect the nucleation barrier. In the third part, I develop a high-throughput measurement of capsid permeability and use it to investigate how MS2 and its virus-like particles respond to different environments, showing that increased capsid dynamics can help to expose the cargo even when the particle cannot disassemble completely. I also find that the size and structure of the cargo affects the permeability. The work presented here provides new insights into the viral disassembly process and the factors that contribute to the accessibility of a viral cargo.