Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems

Abstract

The flexibility of a {beta} hairpin structure known as the flap plays a key role in catalytic activity and substrate intake in pepsin-like aspartic proteases. Most of these enzymes share structural and sequential similarity. In the apo form of the proteases, a conserved tyrosine residue in the flap region is in dynamic equilibrium between the normal and flipped states through rotation of the{chi} 1 and{chi} 2 angles. In this study, we have used apo Plm-II and BACE-1 as model systems. Independent MD simulations of Plm-II and BACE-1 remained stuck either in the normal or flipped state. Metadynamics simulations using side-chain torsion angles ({chi}1 and{chi} 2 of tyrosine) as collective variables sampled the transition between the normal and flipped states. Qualitatively, the two states were predicted to be equally populated. The normal and flipped states were stabilised by H-bond interactions to a tryptophan residue and to the catalytic aspartate, respectively. Further, mutation of tyrosine to an amino-acid with smaller side-chain, such as alanine, reduced the flexibility of the flap and resulted in a flap collapse (flap loses flexibility and remains stuck in a particular state). This is in accordance with previous experimental studies, which showed that mutation to alanine resulted in loss of activity in pepsin-like aspartic proteases. Our results suggest that the rotation of the tyrosine side-chain is the key movement that governs flap dynamics and opening of the binding pocket in most pepsin-like aspartic proteases.