Switchable Conformation in Protein Subunits: Unveiling Assembly Dynamics of Icosahedral Viruses

TL;DR

This study uses molecular dynamics simulations and experimental data to explore the assembly pathways of icosahedral virus capsids, revealing how proteins and RNA interact during virus formation.

Contribution

We developed a novel model and simulation approach to investigate virus assembly dynamics, providing new insights into the role of RNA topology and protein interactions.

Findings

Capsid fragments assemble at different genome locations

Disordered structures merge into symmetric capsids

RNA packaging offers advantages over linear polymers

Abstract

The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundreds, or even thousands, of proteins assemble around the genome to form highly symmetrical structures remains an unresolved puzzle. In this paper, we design novel subunits and develop a model that enables us to explore the assembly pathways and genome packaging mechanism of icosahedral viruses, which were previously inaccessible. Using molecular dynamics (MD) simulations, we observe capsid fragments, varying in protein number and morphology, assembling at different locations along the genome. Initially, these fragments create a disordered structure that later merges to form a perfect symmetric capsid. The model demonstrates remarkable strength in addressing numerous unresolved issues surrounding virus assembly. For instance, it enables us to explore the advantages of RNA packaging by capsid proteins over linear polymers. Our MD simulations are in excellent agreement with our experimental findings from small-angle X-ray scattering and cryo-transmission electron microscopy, carefully analyzing the assembly products of viral capsid proteins around RNAs with distinct topologies.