Mol Inform 2025, 44 (7), e202500025
DOI: 10.1002/minf.70004
Despite the abundance of systematically collected experimental data and facts, the multistep process of autophagy still contains many dark spots. One concerns the background selectivity of interactions between certain autophagy-related protein (ATG8) isoforms and their receptors/adaptors in plants during the autophagy process. By regulating phagophore initiation, expansion, and maturation, these proteins control the assembly of numerous autophagy proteins at this key docking platform. Bioinformatics analysis of human, yeast, and plant ATG8 amino acid sequences allow us to build a sequence tree of plant ATG8s, divided in three groups. We perform a structural study aimed at revealing some of the underlying reasons for the differences in the selectivity of ATG8 isoforms. A series of molecular dynamics (MD) simulations are performed to explain the stage-dependent functionality of ATG8. The conserved secondary structure and folding across all ATG8 proteins, resulting in nearly identical protein–protein interaction interfaces, makes this study particularly important and interesting. Recognizing the dual role of the LC3 interacting region (LIR) in autophagosome biogenesis and recruitment of the anchored selective autophagy receptor (SAR), we perform a mobility domain analysis. To this end, the amino acid sequence associated with the LIR docking site (LDS) interface is localized and subjected to root mean square deviation (RMSD)-based clustering analysis. Starting from Atg8-targeted protein-peptide docking, we attempt to identify conformational changes in the contact region of the corresponding adaptors and receptors involved in the common biogenesis events in autophagy. For the molecular dynamics, we select three representatives, sharing common patterns with other members of the groups. The resulting ATG8-peptide complexes display a significant preference for binding specific partners by different ATG8 isotypes.