Modeling capsid self-assembly: Design and analysis

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.

27 pages, 18 figs

References in corpus (7)

• Virus shapes and buckling transitions in spherical shells
• Reversible self-assembly of patchy particles into monodisperse icosahedral clusters
• Role of reversibility in viral capsid growth: A paradigm for self-assembly
• A Precise Packing Sequence for Self-Assembled Convex Structures
• Modelling the Self-Assembly of Virus Capsids
• Stochastic kinetics of viral capsid assembly based on detailed protein structures
• Studies of reversible capsid shell growth

Cited by in corpus (9)

• Learning to grow: control of material self-assembly using evolutionary reinforcement learning
• Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly
• Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles
• Minimal positive design for self-assembly of the Archimedean tilings
• Neuroevolutionary learning of particles and protocols for self-assembly
• Design Strategies for Self-Assembly of Discrete Targets
• Emergent rhombus tilings from molecular interactions with $M$-fold rotational symmetry
• Role of dynamic capsomere supply for viral capsid self-assembly
• Molecular dynamics simulation: a tool for exploration and discovery using simple models