Role of reversibility in viral capsid growth: A paradigm for self-assembly

Abstract

Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells. Molecular dynamics simulation of shell formation in the presence of an atomistic solvent provides new insight into the self-assembly mechanism, notably that growth proceeds via a cascade of strongly reversible steps and, despite the large variety of possible intermediates, only a small fraction of highly bonded forms appear on the pathway.

arXiv comment4 pages, 4 figures (slightly shorter version, new Fig.2); further minor changes

References in corpus (5)

• Virus shapes and buckling transitions in spherical shells
• Dynamic Pathways for Viral Capsid Assembly
• Self-assembly of polyhedral shells: A molecular dynamics study
• An irreversible growth model for virus capsid assembly
• Stochastic kinetics of viral capsid assembly based on detailed protein structures

Cited by in corpus (47)

• Mechanisms of virus assembly
• The Statistical Mechanics of Dynamic Pathways to Self-assembly
• Equilibrium mechanisms of self-limiting assembly
• Viral genome structures are optimal for capsid assembly
• Mechanisms of kinetic trapping in self-assembly and phase transformation
• Understanding the Concentration Dependence of Viral Capsid Assembly Kinetics - the Origin of the Lag Time and Identifying the Critical Nucleus Size
• Control of pathways and yields of protein crystallization through the interplay of nonspecific and specific attractions
• Modelling the Self-Assembly of Virus Capsids
• Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules
• A theory for viral capsid assembly around electrostatic cores
• Monodisperse self-assembly in a model with protein-like interactions
• Robust nonequilibrium pathways to microcompartment assembly
• Self-assembly of monodisperse clusters: Dependence on target geometry
• Mechanisms of viral capsid assembly around a polymer
• Using Markov State Models to Study Self-Assembly
• Extracting bulk properties of self-assembling systems from small simulations
• 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
• Geometric frustration in small colloidal clusters
• Modeling capsid self-assembly: Design and analysis
• Analyzing mechanisms and microscopic reversibility of self-assembly
• Predicting the self-assembly of a model colloidal crystal
• Thermodynamics of nano-spheres encapsulated in virus capsids
• Design rules for the self-assembly of a protein crystal
• The dynamics of viruslike capsid assembly and disassembly
• The self-assembly of DNA Holliday junctions studied with a minimal model
• Controlling crystal self-assembly using a real-time feedback scheme
• Do hierarchical structures assemble best via hierarchical pathways?
• Self-assembly of artificial microtubules
• Studies of reversible capsid shell growth
• 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
• Hierarchical assembly may be a way to make large information-rich structures
• Role of dynamic capsomere supply for viral capsid self-assembly
• Similarity of ensembles of trajectories of reversible and irreversible growth processes
• Molecular dynamics simulation: a tool for exploration and discovery using simple models
• Optimising self-assembly through time-dependent interactions
• Self-assembly of model proteins into virus capsids
• Quantifying reversibility in a phase-separating lattice gas: an analogy with self-assembly
• Optimizing Event-Driven Simulations
• Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis
• Effects of non-pairwise repulsion on nanoparticle assembly
• 2D capsid formation within an oscillatory energy landscape: orderly self-assembly depends on the interplay between a dynamic potential and intrinsic relaxation times
• Virus Assembly on a Membrane is Facilitated by Membrane Microdomains
• Pathways for virus assembly around nucleic acids
• The role of packaging sites in efficient and specific virus assembly