Modeling capsid self-assembly: Design and analysis

TL;DR

This paper uses molecular dynamics simulations to explore the self-assembly of spherical virus capsids, revealing reversible growth pathways and key intermediate states that are difficult to observe experimentally.

Contribution

It introduces simplified models and simulation techniques to analyze capsid assembly, highlighting the role of reversibility and stable intermediates in the process.

Findings

Assembly proceeds via reversible stages

Few strongly bonded configurations dominate assembly

Intermediate states are crucial for understanding growth

Abstract

A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication of a common underlying design, motivating the use of simplified, low-resolution models in exploring the assembly process. Several versions of a molecular dynamics approach are described. Polyhedral shells of different sizes are involved, the assembly pathways are either irreversible or reversible, and an explicit solvent is optionally included. Model design, simulation methodology and analysis techniques are discussed. The analysis focuses on the growth pathways and the nature of the intermediate states, properties that are hard to access experimentally. Among the key observations are that efficient growth proceeds by means of a cascade of highly reversible stages, and that while there are a large variety of possible partial assemblies, only a relatively small number of strongly bonded configurations are actually encountered.