Impact of the RNA Binding Domain Localization of the Protein Shell on Virus Particle Stability

TL;DR

This study uses molecular dynamics simulations to explore how the specific localization of RNA-binding domains on virus shells influences virus particle stability and encapsulation efficiency, highlighting the importance of charge distribution.

Contribution

The paper demonstrates that localized charge interactions significantly affect virus encapsulation, providing insights beyond traditional uniform charge models.

Findings

Localized charge positions impact optimal polymer length

Simulations align with experimental trends

Quantitative differences exist between models and simulations

Abstract

The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat proteins and the negatively charged polyanions. Theoretically, this interaction is often modeled by coarse-graining the charge distribution of the binding domains, either by projecting the charges onto the inner surface of the protein shell or by spreading them across a region representing the capsid lumen where the binding domains are located. In practice, however, the positive charges are not uniformly distributed across the binding domains, which themselves are positioned at discrete, specific sites on the shell surface. Here, we use molecular dynamics simulations to investigate the impact of localized interactions on the most probable or optimal length of the encapsulated polymer, revealing that the specific location of charges along the binding domains plays a significant role, consistent with experimental observations. Comparing the simulations with predictions from a simple mean-field theory taken from the literature, we find that while the general trends are reasonably well captured, quantitative discrepancies arise between the two approaches.