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

Abstract

Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between a ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! In this paper, we study the impact of genome stiffness on the encapsidation free energy of the complex of RNA and capsid proteins. We show 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. While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging.

References in corpus (21)

• Self-assembly of polyhedral shells: A molecular dynamics study
• Viral genome structures are optimal for capsid assembly
• A Precise Packing Sequence for Self-Assembled Convex Structures
• Recent advances in coarse-grained modeling of virus assembly
• Boosting capacitive blue-energy and desalination devices with waste heat
• Adsorption and Depletion of Polyelectrolytes from Charged Surfaces
• RNA topology remolds electrostatic stabilization of viruses
• In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway
• Quasi-Equilibrium Self-Assembly of Small RNA Viruses
• Statistical analysis of sizes and shapes of virus capsids and their resulting elastic properties
• Thermodynamics of nano-spheres encapsulated in virus capsids
• Effects of RNA branching on the electrostatic stabilization of viruses
• Impact of a non-uniform charge distribution on virus assembly
• Energetically favoured defects in dense packings of particles on spherical surfaces
• Impact of Charge Variation on the Encapsulation of Nanoparticles by Virus Coat Proteins
• Functional analysis of the N-terminal basic motif of a eukaryotic satellite RNA virus capsid protein in replication and packaging
• RNA Base Pairing Determines the Conformations of RNA Inside Spherical Viruses
• Radial distribution of RNA genome packaged inside spherical viruses
• Adsorption of annealed branched polymers on curved surfaces
• Role of Genome in the Formation of Conical Retroviral Shells
• The robust assembly of small symmetric nano-shells

Cited by in corpus (4)

• Impact of bending stiffness on ground-state conformations for semiflexible polymers
• Self Consistent Field Theory of Virus Assembly
• Secondary-Structure Phase Formation for Semifelxible Polymers by Bifurcation in Hyperphase Space
• Thermodynamic stability and kinetic control of capsid morphologies in hepatitis B virus