BPS2026 – The molecular mechanisms of HIV-1 capsid self-assembly using a multi-scale molecular dynamics framework

The HIV-1 capsid is a protein shell that delivers viral RNA into the nucleus of a host cell. Thousands of copies of the capsid protein (CA) self-assemble into hexamers and pentamers that form the building blocks of the final conical shape. Experimental and computational studies have shown that inositol-hexakiphosphate (IP 6 ) is an essential cofactor for a correct self-assembly, and that mutants of CA can self-assemble into capsids with tubular and icosahedral morphologies. However, the molecular mechanisms that underlie the self-assembly process remain unclear. Here, we show the formation of capsomers using multi-scale molecular dynamics (MD) simulations, and that pentamers are a metastable state of self-assembly characterized by extensive twisting motions of the individual CA that are stabilized in larger lattices. We simulated multiple copies of CA at different concentrations of IP 6 using all-atom (AA) MD simulations, and we were able to observe the formation of multimeric complexes of CA. Interestingly, we saw that IP 6 accelerates the rate of self-assembly of CA, in fact the subunits aggregated faster in models with higher concentrations of the small molecule. Using a bottom-up approach, we extended the AAMD trajectories by simulating a coarse-grained (CG) MD model of thousands of CA monomers that captured the self-assembly process of hexamers, pentamers, and larger lattices in its entirety. These results identify the critical residue-residue interactions driving CA self-assembly, elucidate the molecular pathway for capsid formation, and show metastable conformations of capsomers.