In silico Prediction and Analysis of Autophagy Related Gene-5 Interacting Proteins and their Physicochemical Features

Abstract

Autophagy related gene-5 (ATG5) acts as a marker for autophagosome formation and initiation of autophagy flux. For performing these functions, ATG5 may interacts with several proteins. Hence, this study aims to identify ATG5 interacting proteins and their regulatory features using in silico approaches. Briefly, Search Tool for the retrieval of interacting genes/proteins (STRING) database predicted thirty-four ATG5 interacting proteins. Physicochemical characterization of ATG5 interacting proteins were predicted using expert protein analysis system (ExPASY) Protparam. Out of thirty-four proteins, five were stable with acidic PI and hydrophilic in nature. The secondary structure and amino acid (aa) content were predicted by Self-Optimized Prediction Method from Alignment (SOPMA). ATG5 interacting proteins comprised with α-helix and random coils. In addition, ATG5 interacting proteins were rich in leucine and serine whereas cysteine and histidine were very few. Functional characterization by Secondary Structure Prediction of Membrane Proteins (SOSUI) database predicted five soluble signal peptides and two membrane proteins. Further, motifs of ATG5 interacting proteins were predicted by MOTIF search. Herein, motifs were predicted in prosite pattern, prosite profile and protein family database (pFAM) category. In this study, active sites of ATG5 interacting proteins were predicted by universal protein resource (UniProt) database showing glycyl thioester intermediate sites maximally. In conclusion, predicting different properties and binding sites may contribute a better understanding of ATG5 regulatory functions and protein-protein interactions that may give potential target for docking studies.