Structural flexibility and shape similarity contribute to exclusive functions of certain ATG8 isoforms in the autophagy process

One of them relates to the curious interactions between certain ATG8 isoforms and its receptors/adaptors in plants during the autophagy process. These proteins ultimately regulate the initiation, expansion and maturation of the phagophore, which acts as a docking platform for numerous autophagy proteins. The bioinformatician analysis of the human, yeast and plant amino acid sequences allowed us to split them into groups and determine the head-liners taking the experimental data into account. We conducted a structure-based study aimed to identify some hidden reasons for the differences in selectivity of ATG8 isoforms. A series of molecular dynamics simulations were run in attempt to explain the ATG8s’ stage-dependent functionality. The canonic secondary structure organization and folding of all ATG8 proteins and therefore almost identical PPI interface areas make this investigation particularly important and interesting. Aware of the dual role of the ATG8 interacting motif (W/F/Y-X-X-X-L/I/V) in autophagosome biogenesis and the recruitment of an anchored selective autophagy receptor (SAR), we conducted a mobility domain analysis. To this end, sequence of amino acids associated with the LDS interface was localized and underwent an RMSD-based clustering analysis. The resulting ATG8-peptide complexes reflected significant binding preferences of different ATG8 isotypes.