Effect of Pregenomic\nRNA on the Mechanical Stability\nof HBV Capsid by Coarse-Grained Molecular Simulations

Hepatitis B virus (HBV) is a double-stranded DNA virus,\nbut its\nlife cycle involves an intermediate stage, during which pregenomic\nRNA (pgRNA) is encapsulated in the capsid and then reverse-transcribed\ninto the minus DNA strand. These immature HBV virions are the key\ntarget for antiviral drug discovery. In this study, we investigate\nthe flexibility and mechanical stability of the HBV capsid containing\npgRNA by employing residue-resolved coarse-grained molecular dynamics\nsimulations. The results showed that the presence of pgRNA tends to\ndecrease the overall flexibility of the capsid. In addition, the symmetrically\narranged subunits of the capsid show asymmetry in the dominant modes\nof the conformational fluctuations with or without the presence of\npgRNA. Furthermore, the simulations revealed that the presence of\npgRNA enhances the overall mechanical stability of the virion particle.\nElectrostatic interactions between the disordered CTD of capsid and\npgRNA were found to play a crucial role in modulating viral mechanical\nstability. Decreasing the electrostatic interactions by CTD phosphorylation\nor high salt concentration significantly reduces the mechanical stability\nof the HBV capsid containing pgRNA. Finally, the 2-fold symmetric\nsites have been proposed to be the most vulnerable to rupture during\nthe initial stages of capsid disassembly. These findings could enhance\nour understanding of the physical basis of viral invasion and provide\nvaluable insights into the development of antiviral drugs.