The Spanning Tree Model for the Assembly Kinetics of RNA Viruses

TL;DR

This paper introduces a kinetic model for RNA virus assembly that predicts RNA selection based on topological and interaction metrics, providing insights into viral packaging and nucleation processes.

Contribution

It presents a novel simple kinetic model that predicts RNA selection in virus assembly using topological invariants and explores the limits of nucleation theory in this context.

Findings

RNA molecules with minimal maximum ladder distance are favored

RNA with high wrapping number are preferred for assembly

The model explains the breakdown of nucleation theory at strong RNA-protein interactions

Abstract

We present a simple kinetic model for the assembly of small single-stranded RNA viruses that can be used to carry out analytical packaging contests between different types of RNA molecules. The RNA selection mechanism is purely kinetic and based on small differences between the assembly energy profiles. RNA molecules that win these packaging contests are characterized by having a minimum "Maximum Ladder Distance" and a maximum "Wrapping Number".The former is a topological invariant that measures the "branchiness" of the genome molecule while the latter measures the ability of the genome molecule to maximally associate with the capsid proteins. The model can also be used study the applicability of the theory of nucleation and growth to viral assembly, which breaks down with increasing strength of the RNA-protein interaction.