Abstract
The high mutation rate in retroviruses is one of the leading causes of rampant drug resistance and the emergence of novel infectious diseases. In human immunodeficiency virus type-1 (HIV-1), synergistic mutations in its protease and the protease substrate – the Group-specific antigen (Gag) polyprotein – work together to confer drug resistance against protease inhibitors and compensate the effects of the mutations on viral fitness. Some Gag mutations have been reported to restore Gag-protease binding, yet most Gag-protease correlated mutations occur outside of the Gag cleavage site. To rationalize this, we report multiscale modelling approaches to investigate various sequentially cleaved Gag products in the context of clinically relevant mutations that occur outside of the cleavage sites. Simulations of the complete oligomeric structure of the largest Gag proteolytic product in its viral membrane-bound state revealed how non-cleavage site mutations can directly interact with cleavage site residues to affect their local environment, facilitated by conformational changes upon lipid interaction. Mutations in the matrix domain led to the enrichment of phosphatidylinositol bisphosphate (PIP2) lipids – whose association is essential for Gag targeting and assembly on the plasma membrane – facilitated by creation of novel PIP2 binding sites. Additional studies of the mature CA hexamer suggest that some mutations can modulate recruitment of cyclophilin A (CypA) into the mature virion, as well as stabilise the oligomerisation of the viral core. Collectively, our results reveal that non-cleavage site mutations have far-reaching implications outside of Gag proteolysis, with important consequences for drugging Gag maturation intermediates and tackling protease inhibitor resistance.
Competing Interest Statement
The authors have declared no competing interest.