Figure 1. Top and side views of the three important conformations of HIV-1 protease. (a) The ‘closed’ form is observed in crystal structures with ligands bound [structure with protein databank (PDB) code 1HVR is shown]. (b) The flaps of the free protease assume a ‘semi-open’ conformation in crystal structures (PDB 1HHP is shown). The three top views (a–c) highlight the change in flap handedness between closed and semi-open structures. Proposed allosteric inhibition sites are labeled as (i) and (ii). (c) The fully ‘open’ form in which the active site becomes accessible to substrate or inhibitors was not observed in crystal structures but was implied from NMR experiments. The structure shown is from molecular dynamics simulations [35].

Figure 2. Snapshots from molecular dynamics simulations of inhibitor-bound and free protease, and from simulations following the manual docking of the inhibitor into the binding site. The ‘closed’ conformation (a) is represented by an ensemble of closed structures with high similarity (f). By contrast, the ‘semi-open’ conformation (b) represents a much more flexible ensemble (g) with larger fluctuations of the flaps. These eventually lead to full opening of flaps (c,d); the ‘open’ form is transient and returns to the semi-open conformation (e). When the inhibitor is manually placed into a binding site (h), it induces an asymmetric flap closure with initial closing of one of the flaps (i), finally converting to the fully closed form (j) with flaps pulled into the binding site and flap handedness appropriate for the closed state.

Figure 3. Schematic representation of simulated transitions between the three protease forms. The ‘closed’ flap conformation converts to the ‘semi-open’ one upon removal of ligand. Ligand induces the closure of the ‘open’ form. Free protease exists primarily in the semi-open form but transiently changes to the fully open form and, occasionally, even to the closed form that is only weakly populated in the absence of a ligand.