Flap flexibility amongst plasmepsins I, II, III, IV, and V: Sequence, structural, and molecular dynamics analyses

Abstract

Herein, for the first time, we comparatively report the opening and closing of apo plasmepsin I - V. Plasmepsins belong the aspartic protease family of enzymes, and are expressed during the various stages of the P. falciparum lifecycle, the species responsible for the most lethal and virulent malaria to infect humans. Plasmepsin I, II, IV and HAP degrade hemoglobin from infected red blood cells, whereas plasmepsin V transport proteins crucial to the survival of the malaria parasite across the endoplasmic reticulum. Flap-structures covering the active site of aspartic proteases (such as HIV protease) are crucial to the conformational flexibility and dynamics of the protein, and ultimately control the binding landscape. The flap-structure in plasmepsins is made up of a flip tip in the N-terminal lying perpendicular to the active site, adjacent to the flexible loop region in the C-terminal. Using molecular dynamics, we propose three parameters to better describe the opening and closing of the flap-structure in apo plasmepsins. Namely, the distance, d1, between the flap tip and the flexible region; the dihedral angle, ϕ, to account for the twisting motion; and the TriCα angle, θ1. Simulations have shown that as the flap-structure twists, the flap and flexible region move apart opening the active site, or move toward each other closing the active site. The data from our study indicate that of all the plasmepsins investigated in the present study, Plm IV and V display the highest conformational flexibility and are more dynamic structures versus Plm I, II, and HAP.

Egress and invasion machinery of malaria: an in-depth look into the structural and functional features of the flap dynamics of plasmepsin IX and X

“…It was interesting to note that the average values of uctuation observed in the key residues of Plm IX and X (Table 2) follow a similar trend to those observed for Plm's I-V, displaying slightly greater exibility in the aspartic residues, ap tip and hinge region as opposed to other Plm family members. 42 Plm IX and X displayed greater exibility particularly in Asp 2 and the hinge residue as opposed to Asp 1 and the ap tip, which coincides with the similar observation made in Plm I-V. The increased exibility interjected by Asp 2 and the hinge residue may be linked to the "twisting" characteristic of the opening and closing of the active site to enhance and stabilize ligand binding.…”

Flap Dynamics in Aspartic Proteases: A Computational Perspective

“…Later, McGillewie et al . extended the study performed by Karubiu et al . and compared conformational flexibility and flap dynamics across Plm I, II, IV, V and HAP.…”

“…Plasmepsins are generally activated at a certain pH, specifically in acidic condition where one Asp is protonated and the other is still in the form of a carboxylate anion. The catalytic Asp residues involve in a push and pull mechanism where one Asp pulls the proton from a water molecule and the other pushes the proton onto the substrate (Figure ) . This chemical exchange (proton) via a water molecule facilitates the breakage of energetically labile bonds like Phe33‐Leu34 in haemoglobin.…”

Aspartyl Proteinases of Eukaryotic Microbial Pathogens: From Eating to Heating

“…The N-terminal domain contains a “flap” β-hairpin that overhangs the active site. By virtue of its high flexibility, the flap controls access to the active site [2,3]. AP evolution from a common ancestor is exemplified by similar structures and sequence similarities, with predominantly conserved regions containing the catalytic aspartic residues.…”