Electrostatics of capsid-induced viral RNA organization

Abstract

We have addressed the role of electrostatics in the formation of genome structure in the Pariacoto virus, where substantial experimental data are available. We have used Langevin dynamics simulation of a coarse-grained model, based on the published crystal structure of the rigid portion of the Pariacoto capsid and including flexible N-terminal protein arms, attached to the rigid capsid at the appropriate locations. The inclusion of charged residues in our model was dictated solely by the location of charges inherent in the Pariacoto sequence itself. Although the viral genome and other exogenous RNA sequences used in experimental studies can assume secondary structures, we have intentionally used uniformly charged flexible polyelectrolyte lacking predetermined secondary structures as the substitute for the viral genome, in order to see whether the same final assembled genome structure emerges without invoking secondary RNA structures. The intent of our study was to investigate the internal environment presented by the capsid proteins of Pariacoto virus, specifically whether the topological features and electrostatic potential at the inner capsid surface can induce complexation of generic negatively charged polyelectrolyte into structures similar to those observed experimentally with packaged RNA. We find that the charge decoration on the interior of the capsid templates the assembly of the flexible polyelectrolyte, allowing hybridizationlike folding of similarly charged strands, and eventually organizing dodecahedral assembly of the polymer. Our results from a generic flexible polyelectrolyte for the assembled structure and bimodal monomer distribution are remarkably matched to that of the viral RNA found experimentally. Results of our work can be interpreted primarily as a consequence of electrostatics, as consideration of base-pairing has been omitted. We propose that our work supports the growing body of evidence that electrostatic interactions play a crucial role in RNA viral assembly and structure.

Solving a Levinthal's paradox for virus assembly identifies a unique antiviral strategy

“…This contrasts with what is observed in nature; assembly of capsids is highly efficient and robust to kinetic trapping. Previous models that exemplify the roles of CP-CP interactions and, where applicable, interactions with genomic RNAs, only partially address these issues (7)(8)(9)(10). We show here that a vital step in resolving the viral assembly paradox lies in the timing of viral CP production, the protein "ramp," i.e., the accumulation of CP that would naturally occur in the in vivo process.…”

“…In these studies genome encapsidation is often nonspecific with noncognate RNA and even anionic polymers being encapsidated (6)(7)(8)(9)(10), leading to an interpretation that CPs alone have the ability to form capsids identical to those formed in vivo. However, these studies fail to address the efficiency, fidelity, and speed of assembly in vivo and also the observation that in cells genome encapsidation is highly specific (11).…”

Electrostatic interactions in biological DNA-related systems

“…[407][408][409] Many ss-RNA viruses compact their genomes using strongly basic flexible protein arms on the inner side of capsid proteins that provoke adsorption of flexible ss-RNA genome. [410][411][412][413] All these facts underline the importance of ES forces for DNA/RNA packaging and capsid self-assembly, producing a growing number of theoretical studies on this hot topic in the last years. [414][415][416][417][418][419] A number of theoretical [420][421][422] and computational [423][424][425][426] models exist for the capsid self-assembly.…”

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

“…If the RNA are sufficiently large, and on account of their electrostatic repulsion with each other, the likelihood of multiple RNA nucleating one capsid is low and, for the optimal length question, we may confine ourselves to the population of single RNA-encapsidated viral particles. Also, following previous theoretical works (3,(5)(6)(7)(10)(11)(12)(13)(14)(15), we treat the RNA as a linear polyelectrolyte, and ignore the secondary structures (16). This approximation is in part a computational necessity and in part guided by the motivation to elucidate the generic features of electrostatically driven viral assembly by using simple models.…”