Modelling the Self-Assembly of Virus Capsids

Abstract

We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of thermodynamic and geometric factors can be qualitatively related to the potential energy landscape structure of the assembling system. Even though the model is strongly coarse-grained, it exhibits a number of features also observed in experiments, such as sigmoidal assembly dynamics, hysteresis in capsid formation and numerous kinetic traps. We also investigate the effect of macromolecular crowding on the assembly dynamics. Crowding agents generally reduce capsid yields at optimal conditions for non-crowded assembly, but may increase yields for parameter regimes away from the optimum. Finally, we generalize the model to a larger triangulation number T = 3, and observe more complex assembly dynamics than that seen for the original T = 1 model.

16 pages, 11 figures

References in corpus (8)

• Hydrodynamic interactions and Brownian forces in colloidal suspensions: Coarse-graining over time and length-scales
• Reversible self-assembly of patchy particles into monodisperse icosahedral clusters
• Role of reversibility in viral capsid growth: A paradigm for self-assembly
• Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly
• Monodisperse self-assembly in a model with protein-like interactions
• Self-assembly of monodisperse clusters: Dependence on target geometry
• Use of the Metropolis algorithm to simulate the dynamics of protein chains
• Simulation studies of a phenomenological model for elongated virus capsid formation

Cited by in corpus (22)

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• Using Markov State Models to Study Self-Assembly
• Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly
• Templated self-assembly of patchy particles
• Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles
• Modeling capsid self-assembly: Design and analysis
• The role of the encapsulated cargo in microcompartment assembly
• Designing the self-assembly of arbitrary shapes using minimal complexity building blocks
• Studying protein assembly with reversible Brownian dynamics of patchy particles
• Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble
• Influence of Fluctuating Membranes on Self-Assembly of Patchy Colloids
• Dynamics of Self-Assembly of Model Viral Capsids in the Presence of a Fluctuating Membrane
• Role of dynamic capsomere supply for viral capsid self-assembly
• Molecular dynamics simulation: a tool for exploration and discovery using simple models
• Self-assembly of model proteins into virus capsids
• Self-assembly of a dimer system
• Derangement model of ligand-receptor binding