Intrinsic conformational dynamics of apo HIV-2 protease reveal two dynamical stages and multiple closed flap states

HIV-2 protease (PR2) is a homodimeric protein essential for viral maturation and represents a key therapeutic target. Structural studies of PR2 report a semi-open apo form and closed ligand-bound conformations. However, these static structural observations do not fully capture the intrinsic dynamics of PR2. Here, we use molecular dynamics simulations to investigate the conformational landscape sampled by the monoprotonated PR2 in the absence of ligand. The analysis of three independent trajectories reveals a reproducible two-stage dynamical behavior. An initial stage corresponds to a transition from semi-open conformations through transient opening, followed by a second phase characterized by flap closure leading to predominantly closed conformations. These results suggest that PR2 can both access open conformations and spontaneously reach closed states in the absence of ligand. Using complementary geometric descriptors, we show that PR2 closure involves a coordinated reorientation of the flap regions, in which flap B moves from a position in front of flap A to a position behind it, consistently preceding closure. During the late stage, PR2 samples multiple structurally distinct closed conformations, including extended, bent, and inward-bent states. Some of these conformations are consistent with those observed in ligand-bound systems, suggesting that they pre-exist in the apo enzyme. These results provide mechanistic insights into flap rearrangements in PR2. They are also consistent with a conformational selection mechanism in which ligand binding preferentially stabilizes conformations already sampled by the apo enzyme. This findings provide new insights into the intrinsic dynamics of apo PR2 and may assist future structure-based inhibitor design.