Icosahedral packing of RNA viral genomes

The structural organisation of the viral genome within its protein container, called the viral capsid, is an important aspect of virus architecture. Many single-stranded (ss) RNA viruses organise a significant part of their genome in a dodecahedral cage as a RNA duplex structure that mirrors the symmetry of the capsid. Bruinsma and Rudnick have suggested a model for the structural organisation of the RNA in these cages. It is the purpose of this paper to further develop their...

The protein shells, or capsids, of all sphere-like viruses adopt icosahedral symmetry. In the present paper we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral capsids constructed from structurally identical protein subunits and that this symmetry requires (at least) two internal "switching" configurations of the protein. Our results indicate that icosahedral symmetry is not a generic consequence of...

The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundreds, or even thousands, of proteins assemble around the genome to form highly symmetrical structures remains an unresolved puzzle. In this paper, we design novel subunits and develop a model that enables us to explore the assembly pathways and genome packaging mechanism of icosahedral viruses, which...

Recent high resolution structures for viral capsids with 12, 32 and 72 subunits ($T1$, $T3$ and $T7$ viruses) have confirmed theoretical predictions of an icosadeltahedral structure with 12 subunits having five nearest neighbors (pentamers) and $(10T+2)-12$ subunits having six nearest neighbor subunits (hexamers). Here we note that theoretical considerations of energy strain for $T4$, $T9$ $T16$ and $T25$ viruses by aligned pentamers and energy strain along with the sheer num...

Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid, and in some cases surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which capsids assembles within their host cells and in vitro. We describe the thermodynamics and kinetics for assembly of protein subunits into icosahedral capsid shells, and how these are modified in cases where the capsid assembles around a nucleic...

The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomic sequences. Combining discrete direct and double Fourier transforms, we studied the quasi-regular large-scale segmentation in genomic sequences of different ssR...

Spherical viral shells with icosahedral symmetry have been considered as quasicrystalline tilings. Similarly to known Caspar-Klug quasi-equivalence theory, the presented approach also minimizes the number of conformations necessary for the protein molecule bonding with its neighbors in the shell, but is based on different geometrical principles. It is assumed that protein molecule centers are located at vertices of tiles with identical edges, and the number of different tile ...

The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral symmetry is a conspicuous feature, is a phenomenon whose dynamics remain unexplored; studying the growth process by means of computer simulation provides access to the mechanisms underlying assembly. In order to capture the more universal a...

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 up...

Many spherical viruses encapsulate their genome in protein shells with icosahedral symmetry. This process is spontaneous and driven by electrostatic interactions between positive domains on the virus coat proteins and the negative genome. We model the effect of the icosahedral charge distribution from the protein shell instead of uniform using a mean-field theory. We find that the non-uniform charge distribution strongly affects the optimal genome length, and that it can expl...