Useful scars: Physics of the capsids of archaeal viruses

Abstract

We propose a physical model for the capsids of tailed archaeal viruses as viscoelastic membranes under tension. The fluidity is generated by thermal motion of scarlike structures that are an intrinsic feature of the ground state of large particle arrays covering surfaces with nonzero Gauss curvature. The tension is generated by a combination of the osmotic pressure of the enclosed genome and an extension force generated by filamentous structure formation that drives the formation of the tails. In continuum theory, the capsid has the shape of a surface of constant mean curvature: an unduloid. Particle arrays covering unduloids are shown to exhibit pronounced subdiffusive and diffusive single-particle transport at temperatures that are well below the melting temperature of defect-free particle arrays on a surface with zero Gauss curvature.

Kirigami and the Caspar-Klug construction for viral shells with negative Gauss curvature

“…As more pairs are introduced, they begin to connect and develop into pentamer-heptamer "scars" along the capsid. We observed similar pentamer-heptamer scar-like structures on the surface of an unduloid representing the ATV capsid [16]. By using five pentamer-heptamer pairs for each step in the radius change, it is possible for each section to preserves five-fold symmetry.…”

Physics of viral dynamics

“…A particularly interesting case is the family of archaeal viruses 155 . Certain archaeal viruses, whose capsids bear no resemblance to the classical rod and sphere viral geometries, can smoothly transform the Gaussian curvature of their capsids, which suggests that these capsids are in a liquid state [153][154][155][156][157] .…”

Smectic viral capsids and the aneurysm instability

“…To obtain an idea of the positioning of capsid proteins in the smectic state on an unduloid surface, we can populate these concentric spirals with small spheres representing the capsid proteins (see also [13]). Figure 7-borrowed from [13]-shows the result of the application of the Voronoi construction to the particle positions.…”

“…In particular, three viral families (Fuselloviridae, Bicaudaviridae, Salterprovirus) are characterized by spindleshaped (lemon-shaped) capsids [3,12]. In terms of physical virology this presents us with a fundamental challenge: these capsids cannot be a positionally-ordered protein shells because the spindle shape necessitates the introduction of a large number of five-fold and seven-fold topological defects [13].…”

“…We performed in [13] a finite temperature Monte-Carlo simulation of interacting particles located on the surface of an unduloid. The simulation revealed (i) that the negative Gauss curvature of an unduloid covered by a particle array automatically generates a plethora of dislocations, disclinations, and strings of dislocations and (ii) that these topological defects remain mobile at temperatures well below the nominal melting temperature of the particle array.…”