Conformational asymmetry of human immunodeficiency virus-1 protease flaps increases along the darunavir drug resistance pathway.

Under selective drug pressure, the structure and dynamics of HIV-1 protease (PR) evolve to confer resistance to the drug. Here, we report on the conformational changes in PR flaps for drug-resistance mutations using 19F nuclear magnetic resonance (NMR) spectroscopy. We prepared wild-type (wt) PR and its three mutant variants containing 4, 10, or 11 mutations, namely 4Mut, 10Mut, and 11Mut, that were previously found in a viral passage study against darunavir (DRV). The proteins were uniformly labeled with 15N and with 19F amino-acid specifically in the 5-indole positions of two conserved tryptophan residues, W6 and W42, which are located near the dimer interface and at the edge of the flap region of PR, respectively. In solution, 19F NMR spectra of these proteins in the inhibitor-free forms showed a downfield shift of the W42 resonance as the number of mutations increased. In the DRV-bound form, the W42 resonance again shifted with increasing number of mutations and, importantly, split into two peaks, reflecting different local electronic environments of the two flaps of the dimer. Solid-state 19F magic angle spinning (MAS) NMR spectra of wt-PR and 10Mut also exhibited two W42 resonances in DRV-bound crystalline forms. These observations indicate that drug-resistance mutations increase the asymmetry between the two flaps in the PR-inhibitor interaction in the inhibitor-bound forms.