Characterizing the structural variability of HIV-2 protease upon the binding of diverse ligands using a structural alphabet approachThe HIV-2 protease (PR2) is an important target for designing new drugs against the HIV-2 infection. In this study, we explored the structural backbone variability of all available PR2 structures complexed with various inhibitors using a structural alphabet approach. 77% of PR2 positions are structurally variable, meaning they exhibit different local conformations in PR2 structures. This variability was observed all along the structure, particularly in the elbow and flap regions. A part of these backbone changes observed between the 18 PR2 are induced by intrinsic flexibility and ligand binding putatively induces others occurring in the binding pocket. These latter changes could be important for PR2 adaptation to diverse ligands and are accompanied by changes outside of the binding pocket. In addition, the study of the link between structural variability of the pocket and PR2-ligand interactions allowed us to localize pocket regions important for ligand binding and catalytic function, regions important for ligand recognition that adjust their backbone in response to ligand binding, and regions important for the pocket opening and closing that have large intrinsic flexibility.Finally, we suggested that differences in ligand effectiveness for PR2 could be partially explained by different backbone deformations induced by these ligands.To conclude, this study is the first characterization of the PR2 structural variability considering ligand diversity. It provides information about recognition of PR2 to various ligands and its mechanisms to adapt its local conformation to bound ligands that could help understanding the resistance of PR2 to its inhibitors, a major antiretroviral class.

HIV-2 protease (PR2) is a homodimer, which is an important target in the treatment of the HIV-2 infection. In this study, we developed an in silico protocol to analyze and characterize the asymmetry of the unbound PR2 structure using three levels of protein description by comparing the conformation, accessibility, and flexibility of each residue in the two PR2 chains. Our results showed that 65% of PR2 residues have at least one of the three studied asymmetries (structural, accessibility, or flexibility) with 10 positions presenting the three asymmetries in the same time. In addition, we noted that structural and flexibility asymmetries are linked indicating that the structural asymmetry of some positions result from their large flexibility. By comparing the structural asymmetry of the crystallographic and energetically minimized structures of the unbound PR2, we confirmed that the structural asymmetry of unbound PR2 is an intrinsic property of this protein with an important role for the PR2 deformation upon ligand binding. This analysis also allowed locating asymmetries corresponding to crystallization artefacts. This study provides insight that will help to better understand the structural deformations of PR2 and to identify key positions for ligand binding.