The role of packaging sites in efficient and specific virus assembly

TL;DR

This study uses computational modeling to investigate how packaging sites influence the efficiency and specificity of viral capsid assembly, revealing mechanisms that promote selective assembly and potential kinetic traps.

Contribution

Developed a coarse-grained simulation model to analyze the role of packaging sites in viral RNA assembly, linking computational predictions with experimental assays.

Findings

Packaging sites can enhance assembly specificity through different mechanisms.

Certain conditions lead to kinetic traps during assembly.

Simulation results align with in vitro competition assays.

Abstract

During the lifecycle of many single-stranded RNA viruses, including many human pathogens, a protein shell called the capsid spontaneously assembles around the viral genome. Understanding the mechanisms by which capsid proteins selectively assemble around the viral RNA amidst diverse host RNAs is a key question in virology. In one proposed mechanism, sequence elements (packaging sites) within the genomic RNA promote rapid and efficient assembly through specific interactions with the capsid proteins. In this work we develop a coarse-grained particle-based computational model for capsid proteins and RNA which represents protein-RNA interactions arising both from non-specific electrostatics and specific packaging sites interactions. Using Brownian dynamics simulations, we explore how the efficiency and specificity of assembly depend on solution conditions (which control protein-protein and nonspecific protein-RNA interactions) as well as the strength and number of packaging sites. We identify distinct regions in parameter space in which packaging sites lead to highly specific assembly via different mechanisms, and others in which packaging sites lead to kinetic traps. We relate these computational predictions to in vitro assays for specificity in which cognate viral RNAs are compete against non-cognate RNAs for assembly by capsid proteins.