Structural Analysis of PfSec62-Autophagy Interacting Motifs (AIM) and PfAtg8 Interactions for Its Implications in RecovER-phagy in Plasmodium falciparum

Abstract

Autophagy is a degradative pathway associated with many pathological and physiological processes crucial for cell survival. During ER stress, while selective autophagy occurs via ER-phagy, the re-establishment of physiologic ER homeostasis upon resolution of a transient ER stress is mediated by recovER-phagy. Recent studies demonstrated that recovER-phagy is governed via association of Sec62 as an ER-resident autophagy receptor through its autophagy interacting motifs (AIM)/LC3-interacting region (LIR) toAtg8/LC3. Atg8 is an autophagy protein, which is central to autophagosome formation and maturation. Plasmodium falciparum Atg8 (PfAtg8) has both autophagic and non-autophagic functions critical for parasite survival. Since Plasmodium also has Sec62 in the ER membrane and is prone to ER stress due to drastic transformation during their complex intraerythrocytic cycle; hence, we initiated the studies to check whether recovER-phagy occurs in the parasite. To achieve this, a comprehensive study based on the computational approaches was carried out. This study embarks upon identification of AIM sequences in PfSec62 by carrying out peptide-protein docking simulations and comparing the interactions of these AIMs with PfAtg8, based on the molecular dynamic simulations. Detailed analysis is based on electrostatic surface complementarity, peptide-protein interaction strength, mapping of non-covalent bond interactions and rupture force calculated from steered MD simulations. Potential mean forces and unbinding free energies (ΔGdissociation) using Jarzynski's equality were also computed for the AIM/LIR motif complexes with PfAtg8/HsLC3 autophagy proteins to understand their dissociation free energy profiles and thereby their binding affinities and stability of the peptide-protein complexes. Through this study, we predict Sec62 mediated recovER-phagy in Plasmodium falciparum, which might open new avenues to explore novel drug targets for antimalarial drug discovery.

Autophagy Underlies the Proteostasis Mechanisms of Artemisinin Resistance in P. falciparum Malaria

“…Autophagy is known to counterbalance UPR-mediated ER stress in yeast and higher organisms through sequestration and subsequent degradation of excess ER-containing toxic protein aggregates ( 47 , 49 , 50 ). Our recent studies demonstrated that Pf Sec62 is an ER-resident autophagy receptor ( 51 ), implicating recovER-phagy as needed to reestablish ER homeostasis upon resolution of ER stress in the parasite. Since there has been no experimental demonstration showing involvement of parasite autophagy upon induction of ER stress, we investigated this topic by incubating young trophozoites with DHA (700 nM, 1.5 h) and analyzed for the presence of autophagosome-like structures.…”

A Potent Kalihinol Analogue Disrupts Apicoplast Function and Vesicular Trafficking inP. falciparumMalaria

“…3E). Specifically, three proteins known to be involved in the endoplasmic reticulum (ER) COPII trafficking systems Sec62 (PF3D7_1438100), syntaxin (PF3D7_1104100), a member of the Qa-SNARE family, and a conserved protein recently annotated as a putative translocation protein SEC66 (PF3D7_0204200) were found to be significantly enriched in the pull-down experiments from the MED6-189-treated but not the vehicle control samples (41)(42)(43)(44)(45).…”

The role of electrostatic potential in the translocation of triangulene across membranes

“…The electrostatic potential of triangulene are calculated by Adaptive Poisson-Boltzmann Solver (APBS). [30][31][32] The triangulene are placed on a plane parallel to the x-y plane, about 3 nm from the center of the POPC membrane. The side length of triangulene is 0.925 nm.…”