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

Ashalatha Sreshty Mamidi,Namita Surolia,Ananya Ray

doi:10.3389/fbioe.2019.00240

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.

Highlights

Autophagy is a catabolic process in which lysosomal hydrolases clear damaged sub cellular organelles and cytoplasmic constituents
This work is a comprehensive study toward identifying the interactions between autophagy interacting motifs (AIM)/LC3 interacting region (LIR) motifs of Pf Sec62 and Pf Atg8 to decipher existence of Sec62 mediated recovER-phagy in P. falciparum
Four peptide AIM sequences of Pf Sec62 were chosen from Pf Sec62 C-terminal and subjected to similaritybased peptide-protein docking calculations followed by energy optimization

Summary

Introduction

Autophagy is a catabolic process in which lysosomal hydrolases clear damaged sub cellular organelles and cytoplasmic constituents. In addition to macroautophagy/non-selective autophagy, which is generally induced by starvation, several autophagic processes selectively target particular organelles to lysosomes, such as peroxisomes, parts of nucleus, lipid droplets and endoplasmic reticulum and this is termed as selective autophagy (Stolz et al, 2014). Both selective and chaperone mediated autophagy mediates the delivery of cytoplasmic cargo via autophagosomes to the vacuole for degradation. These short peptide motifs called Atg8-interacting motifs/LC3 interacting regions (AIM in yeast/LIRs in humans) are represented by a short consensus sequence [W/F/Y]xx[L/I/V], where “x” can be any amino acid and the core motif can be flanked at their N or C terminus by Ser, Thr and/or an acidic amino acid such as Glu and/or Asp (Birgisdottir et al, 2013; Hurley and Schulman, 2014; Rogov et al, 2014)

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