9 research outputs found
Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly
We simulate the assembly dynamics of icosahedral capsids from subunits that
interconvert between different conformations (or quasi-equivalent states). The
simulations identify mechanisms by which subunits form empty capsids with only
one morphology but adaptively assemble into different icosahedral morphologies
around nanoparticle cargoes with varying sizes, as seen in recent experiments
with brome mosaic virus (BMV) capsid proteins. Adaptive cargo encapsidation
requires moderate cargo-subunit interaction strengths; stronger interactions
frustrate assembly by stabilizing intermediates with incommensurate curvature.
We compare simulation results to experiments with cowpea chlorotic mottle virus
empty capsids and BMV capsids assembled on functionalized nanoparticles and
suggest new cargo encapsidation experiments. Finally, we find that both empty
and templated capsids maintain the precise spatial ordering of subunit
conformations seen in the crystal structure even if interactions that preserve
this arrangement are favored by as little as the thermal energy, consistent
with experimental observations that different subunit conformations are highly
similar
Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition
Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available