Assembly of an Unenveloped Icosahedral RNA Viruses using Coarse-Grained Models

Abstract

We investigate the assembly of Satellite Tobacco Mosaic Virus (STMV) in a coarse-grained model. We use multi-level coarse-grained representations to decrease the computational expenses and adequately represent the different parts of the viral structure. The RNA coarse grain model was generated from a combination of an idealized RNA secondary structure based on the X-ray crystal and a proposed tRNA-like secondary structure at the 3’ end. The RNA model has one pseudo atom (bead) per residue. The coarse-grained model for the capsid contains 20 triangular units, each of which also contains three flexible positively charged protein tails. The assembly process as well as the stability of the virus mainly depends on RNA-protein and protein-protein interactions. The protein tails are attracted to the RNA by electrostatic interactions while the capsid proteins are weakly attracted with each other by hydrophobic interactions. We modeled RNA-protein interactions with a Debye-Huckel potential and protein-protein interaction with a Lennard-Jones potential. We varied values of these two interactions to find regions where the virus is stable and will self-assemble, and construct a phase diagram of viral stability. Finally we investigated the assembly of the virus using molecular dynamics. These simulations help us understand the individual roles of these two interactions on viral assembly.