How a Virus Circumvents Energy Barriers to Form Symmetric Shells

Abstract

Previous self-assembly experiments on a model icosahedral plant virus have shown that, under physiological conditions, capsid proteins initially bind to the genome through an en masse mechanism and form nucleoprotein complexes in a disordered state, which raises the questions as to how virions are assembled into a highly ordered structure in the host cell. Using small-angle X-ray scattering, we find out that a disorder-order transition occurs under physiological conditions upon an increase in capsid protein concentrations. Our cryo-transmission electron microscopy reveals closed spherical shells containing in vitro transcribed viral RNA even at pH 7.5, in marked contrast with the previous observations. We use Monte Carlo simulations to explain this disorder-order transition and find that, as the shell grows, the structures of disordered intermediates in which the distribution of pentamers does not belong to the icosahedral subgroups become energetically so unfavorable that the caps can easily dissociate and reassemble overcoming the energy barriers for the formation of perfect icosahedral shells. In addition, we monitor the growth of capsids under the condition that the nucleation and growth is the dominant pathway and show that the key for the disorder-order transition in both en masse and nucleation and growth pathways lies in the strength of elastic energy compared to the other forces in the system including protein-protein interactions and the chemical potential of free subunits. Our findings explain, at least in part, why perfect virions with icosahedral order form under different conditions including physiological ones.

Visualization of Single Molecules Building a Viral Capsid Protein Lattice through Stochastic Pathways

“…Those features include reversibility and nucleation 4 , 5 , 8 − 10 , 63 , 64 and also multinucleation. 38 The experimental results obtained also verify several key predictions of CG simulations of mature HIV capsid assembly in particular. 66 − 70 The combination of high spatial and temporal resolution provided by HS-AFM confirmed such features at the single-molecule level.…”

Virus Assembly Pathways: Straying Away but Not Too Far

“…In support of the idea of metastability of lower‐symmetry particles, we note that Tresset and collaborators have recently observed by Monte Carlo simulations that the cost of elastic energy of a non‐symmetric shell assembling around a genomic template is so high that the partial capsids formed under non‐equilibrium conditions will eventually repair themselves and form equilibrated symmetric structures. [ 42 ]…”

“…[41] In support of the idea of metastability of lower-symmetry particles, we note that Tresset and collaborators have recently observed by Monte Carlo simulations that the cost of elastic energy of a non-symmetric shell assembling around a genomic template is so high that the partial capsids formed under nonequilibrium conditions will eventually repair themselves and form equilibrated symmetric structures. [42] In the context of fragmentation products of the metastable H8 and H15 particles, we note that the top or bottom halves of H15 have a structure that is very similar to that of a T = 3 icosahedral particle. Therefore, the angle between the pentameric-hexameric capsomers and hexameric-hexameric capsomers are similar with those encountered in wt BMV ( Figure S12, Supporting Information).…”

In Vitro Assembly of Virus-Like Particles and Their Applications

“…Understanding capsid self-assembly pathways will help to tailor the mechanisms of virus infection and replication for therapeutic applications. Different methods have been used to characterize intermediate assemblies and the assembly pathways of virus capsids, such as electron microscopy [83][84][85][86], X-ray crystallography [57], atomic force microscopy [57,58,85], small-angle X-ray scattering [87][88][89][90][91][92], mass spectrometry [93][94][95], size-exclusion chromatography [84], resistive-pulse sensing [84,96], interferometric scattering microscopy [97], single-molecule fluorescence correlation spectroscopy [98], optical tweezers in combination with confocal fluorescence microscopy and acoustic force spectroscopy [58,99]. Recently, high-speed atomic force microscopy (HS-AFM), a powerful single-molecule technique for real-time visualization of biomolecules in dynamic action [100], has been used to visualize self-assembly of HIV capsid protein lattice [81].…”