Exploration of the effects of sequence variations between HIV-1 and HIV-2 proteases on their three-dimensional structures

Abstract

HIV protease inhibitors (PIs) approved by the FDA (US Food and Drug Administration) are a major class of antiretroviral. HIV-2 protease (PR2) is naturally resistant to most of them as PIs were designed for HIV-1 protease (PR1). In this study, we explored the impact of amino-acid substitutions between PR1 and PR2 on the structure of protease (PR) by comparing the structural variability of 13 PR regions using 24 PR1 and PR2 structures complexed with diverse ligands. Our analyses confirmed structural rigidity of the catalytic region and highlighted the important role of three regions in the conservation of the catalytic region conformation. Surprisingly, we showed that the flap region, corresponding to a flexible region, exhibits similar conformations in PR1 and PR2. Furthermore, we identified regions exhibiting different conformations in PR1 and PR2, which could be explained by the intrinsic flexibility of these regions, by crystal packing, or by PR1 and PR2 substitutions. Some substitutions induce structural changes in the R2 and R4 regions that could have an impact on the properties of the PI-binding site and could thus modify PI binding mode. Substitutions involved in structural changes in the elbow region could alter the flexibility of the PR2 flap regions relative to PR1, and thus play a role in the transition from the semi-open form to the closed form, and have an impact on ligand binding. These results improve the understanding of the impact of sequence variations between PR1 and PR2 on the natural resistance of HIV-2 to commercially available PIs.

Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease

“…One possible explanation for the observed structural asymmetry that we did not consider in this study is the error or packing in the crystallographic structure. We previously showed that 24 positions were involved in crystal packing in the PR2 structure complexed with DRV (PDB code 3EBZ) [37]. In addition, we previously highlighted some structural asymmetry linked to crystal packing in unbound PR2, for example, at positions 3 and 18 [33].…”

“…To explore the structural effects of the studied drug resistance mutations, we compared the structural asymmetry in the three 3EBZ mini structures and the 150 modeled mutant structures using an approach based on a structural alphabet [31]. [32,37,38]. Each PR2 region is colored as follows: the Nter and Cter regions in grey, the R1 region in dark blue, the fulcrum region in green, the catalytic region in purple, the R2 region in orange, the elbow region in blue, the flap region in magenta, the cantilever region in yellow, the R3 region in pink, the wall region in cyan, the R4 region in brown, and the α-helix region in red.…”

“…We determined the structural symmetric and asymmetric positions in the three 3EBZ mini structures and their location in the 13 PR2 regions defined in [32,37,38] (Additional file 2: Figure S2). Half of the positions (53% of positions) were detected as symmetric (i.e., showing similar local conformations in the two chains in the three 3EBZ mini structures).…”

Exploration of the Structural Asymmetry Induced by the Intrinsic Flexibility of HIV-2 Protease

“…To do so, we computed the RMSD of the 13 structural and functional regions between their two chains (RMSD reg AB ). This criterion has been previously used to compare the local conformations of PR1 and PR2 [28]. Our results showed that the global asymmetry of PR2 is not explained by deformations of only one region, but it is linked to the deformation of several regions.…”

“…Figure 1. The 3D structure of PR2 colored according to the 13 regions: the nter region (1-4) is colored in forest green, the r1 region (5)(6)(7)(8)(9) in blue, the fulcrum region (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23) in green, the catalytic-site region (24)(25)(26)(27)(28)(29)(30) in purple, the r2 region (31)(32)(33)(34)(35)(36) in marine blue, the elbow region (37)(38)(39)(40)(41)(42) in magenta, the flap region (43)(44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54)(55)...…”