Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems.

Soumendranath Bhakat,Pär Söderhjelm

doi:10.1021/acs.jcim.1c00840

Abstract

The flexibility of β 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 this study, we have used apo Plm-II and BACE-1 as model systems. In the apo form of the proteases, a conserved tyrosine residue in the flap region remains in a dynamic equilibrium between the normal and flipped states through rotation of the χ1 and χ2 angles. 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 (χ1 and χ2 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 stabilized 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 ring flipping associated with the tyrosine side-chain is the key order parameter that governs flap dynamics and opening of the binding pocket in most pepsin-like aspartic proteases.

Highlights

Aspartic proteases play an important role in the life cycle of different pathogens and act as a promising target in structure-based drug discovery
Our results suggest that the ring flipping associated with the tyrosine side-chain is the key order parameter that governs flap dynamics and opening of the binding pocket in most pepsin-like aspartic proteases
MD simulations of apo Plm-II and BACE-1 showed that the hydroxyl group of this residue was interchangeably involved in several hydrogen-bond interactions and that slow conformational dynamics occurred around this residue, on a time scale of at least hundreds of nanoseconds

Summary

Introduction

Aspartic proteases play an important role in the life cycle of different pathogens and act as a promising target in structure-based drug discovery. The flap is a highly flexible part that plays a critical role in the ligand binding by displaying a scissor-like motion necessary for ligand uptake (Figure 1). The conformational flexibility of aspartic proteases and the role of the flap in ligand binding have been studied in several systems, e.g., HIV proteases,[2,3] cathepsin-D,4 and BACE1.5−7 Pepsin-like aspartic proteases[8] are a subset of aspartic proteases which has a conserved flap and coil region (Figure 1). Tyrosine (Tyr) is a conserved residue present in the flap of most of the pepsin-like aspartic proteases, e.g., plasmepsin I, II, IV; human cathepsin-D; cathepsin-E; BACE-1; and BACE-2. It is believed that the rotation of the Tyr side-chain plays an important role in the flap dynamics of these enzymes

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Results

Discussion

Conclusion