Effects of RNA branching on the electrostatic stabilization of viruses.

  title={Effects of RNA branching on the electrostatic stabilization of viruses.},
  author={Gonca Erdemci-Tandogan and Jef Wagner and Paul van der Schoot and R. Podgornik and Roya Zandi},
  journal={Physical review. E},
  volume={94 2-1},
Many single-stranded (ss) ribonucleic acid (RNA) viruses self-assemble from capsid protein subunits and the nucleic acid to form an infectious virion. It is believed that the electrostatic interactions between the negatively charged RNA and the positively charged viral capsid proteins drive the encapsidation, although there is growing evidence that the sequence of the viral RNA also plays a role in packaging. In particular, the sequence will determine the possible secondary structures that the… 

Figures from this paper

The effect of RNA stiffness on the self-assembly of virus particles

It is shown that an increase in effective chain stiffness because of base-pairing could be the reason why under certain conditions linear chains have an advantage over branched chains when it comes to encapsidation efficiency.

The different faces of mass action in virus assembly

The results rationalize a number of recent in vitro co-assembly experiments showing that short polyanions are less effective at attracting virus coat proteins to form virus-like particles than long ones do, even if both are present at equal weight concentrations in the assembly mixture.

Varieties of charge distributions in coat proteins of ssRNA+  viruses

This work provides two clear and complementary definitions of an N-terminal tail of a protein, and uses them to extract the tail sequences of a large number of CPs of ssRNA+  viruses, and examines the pH-dependent interplay of charge on both tails and CPs alike.

Assembly and Stability of Simian Virus 40 Polymorphs.

The C-terminal ligands control the dynamic assembly paths of SV40 polymorphs, allowing closed shells to continue growing via the pseudo-closed growth mechanism for which experimental evidence already exists.

RNA Structures and Their Role in Selective Genome Packaging

This review focuses on the role of viral encoded RNA structures in genome packaging and discusses how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs.

Length of encapsidated cargo impacts stability and structure of in vitro assembled alphavirus core-like particles

This work determined how the length of the cargo impacts the stability and structure of the assembled CLPs, and hypothesized that cargo neutralizes the basic region of the alphavirus capsid protein and if the cargo is long enough, it will also act to scaffold the CP monomers together.

Percolation Theory Reveals Biophysical Properties of Virus-like Particles

A comparative analysis of all alternative homogeneously tiled capsid structures of the same stoichiometry identifies evolutionary drivers favoring specific viral geometries in nature and offers a guide for virus-like particle design in nanotechnology.



Electrostatic origin of the genome packing in viruses

It is shown that nonspecific electrostatic interactions control both the length of the genome and genome conformations, and genomic nucleotides are predicted to occupy a radially symmetric spherical shell detached from the viral capsid, in agreement with experimental data.

Revealing the density of encoded functions in a viral RNA

Direct experimental evidence is presented that assembly of a single-stranded RNA virus occurs via a packaging signal-mediated mechanism, and it is shown that the sequences of coat protein recognition motifs within multiple, dispersed, putative RNA packaging signals, as well as their relative spacing within a genomic fragment, act collectively to influence the fidelity and yield of capsid self-assembly in vitro.

Packaging of a polymer by a viral capsid: the interplay between polymer length and capsid size.

It is suggested that the size of the encapsidated polymer cargo is the deciding factor for the selection of one distinct capsid size from several possible sizes with the same inherent symmetry.

Predicting the sizes of large RNA molecules

It is argued that there has been evolutionary pressure for the genome to have overall spatial properties—including an appropriate radius of gyration, Rg—that facilitate this assembly process, and it is predicted the Rg values of viral ssRNAs are smaller than those of nonviral sequences.

Classical nucleation theory of virus capsids.

expression for the size of the critical capsid, the lag time, and the steady-state nucleation rate of capsids, and how they depend on both protein concentration and binding energy are found, explaining why capsid nucleation is a sensitive function of the ambient conditions.

Role of Genome in the Formation of Conical Retroviral Shells.

This work models the role of the genome and its interaction with the capsid protein by modeling the genomic RNA through a mean-field theory and shows that the confinement free energy for a homopolymeric model genome confined in a conical capsid is lower than that in a cylindrical capsid.

The size of RNA as an ideal branched polymer.

The RNAs of icosahedral viruses are shown to be more compact than the random RNAs, and the scaling of ̂R(g) for ideal randomly branched polymers varies as N(1/3).

Thermodynamic basis for the genome to capsid charge relationship in viral encapsidation

An appropriate thermodynamic framework is established for determining the optimal genome length in electrostatically driven viral encapsidation that includes the electrostatic potential due to the Donnan equilibrium, which arises from the semipermeable nature of the viral capsid.

Phase diagram of self-assembled viral capsid protein polymorphs.

We present an experimental study of the self-assembly of capsid proteins of the cowpea chlorotic mosaic virus (CCMV), in the absence of the viral genome, as a function of pH and ionic strength. In