Intrinsic Conformational Dynamics of Apo HIV-2 Protease Reveal Two Dynamical Phases and Multiple Closed Flap States

HIV-2 protease (PR2) is essential for viral maturation, making it a key therapeutic target. Experimental structures show a semi-open apo state and a closed ligand-bound state, but the intrinsic dynamics of apo PR2 remain incompletely characterized, despite their central role in enzymatic function, inhibitor recognition, and drug resistance. Here, molecular dynamics simulations combined with structural and dynamical analyses are used to investigate the conformational landscape of PR2 in the absence of ligands. Analysis of three independent trajectories reveals that PR2 undergoes a reproducible two-phase dynamical behavior. An initial dynamic phase is characterized by enhanced flexibility and extensive cooperative motions, followed by a stabilization phase associated with reduced mobility. This progression reflects PR2’s shift from semi-open ensembles through transient openings toward predominantly closed conformations. To structurally dissect these conformational transitions, we developed complementary geometric metrics that separately quantify flap–flap rearrangements and residue movements relative to the active site. The detailed analysis of flap conformations demonstrates that full flap opening enables a reorientation step in which flap B moves in front of flap A, a prerequisite for subsequent closure. During the stabilization phase, PR2 predominantly samples three distinct closed conformations—extended, bent, and inward-bent. These conformational states differ in both inter-flap distance and local flap geometry. These results establish a detailed reference description of the intrinsic conformational landscape and flap dynamics of apo PR2. By defining this intrinsic reference, these findings may help elucidate how ligand binding, inhibitor specificity, and resistance-associated mutations could modulate the conformational landscape of PR2.