Effects of RNA branching on the electrostatic stabilization of viruses

Abstract

Many single-stranded (ss) 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 ssRNA will take in solution. In this work, we use a mean field theory to investigate how the secondary structure of the RNA combined with electrostatic interactions affects the efficiency of assembly and stability of the assembled virions. We show that the secondary structure of RNA may result in negative osmotic pressures while a linear polymer causes positive osmotic pressures for the same conditions. This may suggest that the branched structure makes the RNA more effectively packaged and the virion more stable.

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

“…While previous theoretical studies have focused on the scaling behavior of linear and branched flexible polymers [32,34,35,48,[56][57][58], in this paper we study the impact of the stiffness or Kuhn length on the encapsidation of RNA by capsid proteins. In general the duplexed segments of viral RNA contain on average about five to six base-pairs [11].…”

“…Following these experiments a number of simulation studies, using quenched (fixed) branched polymers as a model for RNA, have shown that the optimal length of encapsidated RNA increases when accounting for its secondary structure [12,33]. Mean-field calculations using annealed (equilibrium) branched polymers as model RNAs have also shown that the length of encapsidated polymer increases as the propensity to form larger numbers of branched points increases [32,34,35]. More importantly, these calculations show that a higher level of branching considerably increases the depth of the freeenergy gain associated with the encapsulation of RNA by a positively charged shell.…”

“…Above-mentioned theoretical and experimental studies indicate that in a head-to-head competition between two different types of RNAs, the RNA with a larger number of branching junctions or branch points should have a competitive edge over others [32,34,35]. A naive physical explanation is that branching causes RNA molecules to become more compact than structureless linear polymers of similar chain length, which are then easier to accommodate in the limited space provided by the cavity of a capsid.…”

Impact of a nonuniform charge distribution on virus assembly

“…In summary, we have studied the phenomena of overcharging observed in many viruses. Previous mean-field theories as well as the experimental studies of CCMV capsid proteins with short linear polymers have indicated the resulting VLPs are undercharged [24,25,[37][38][39][40]. However, MD simulations revealed overcharging can happen even for linear polymers and the question is why [22].…”

Self consistent field theory of virus assembly

“…where ∆ = E 1 − E 0 is the energy gap, and the function R(r, s) is the remainder of the expansion. When s∆ 1, the second term above becomes exponentially negligible, and we may write q(r, s) = e −E0s q 0 ψ 0 (r) (22) and then Eqs. 20, 19 and 7 become respectively equal to…”