Comprehensive mapping of interfacial mutations in the ATG101-ATG13 protein complex that affect protein stability and interaction: Implications in autophagy regulation

Autophagy, a highly orchestrated cellular process crucial for maintaining cellular homeostasis, involves the formation of autophagosomes, double-membraned structures that engulf and degrade cellular components. Central to this process are proteins such as ATG13 and ATG101, which play multifaceted roles beyond their involvement in ATG9/ATG9A trafficking and localization. Together, ATG13 and ATG101 serve as central scaffolding units, mediating a network of interactions among various autophagy initiation subcomplexes. The challenge lies in elucidating the biochemical and biophysical functions of individual proteins and complexes, as well as understanding their collaborative roles in autophagosome biogenesis and autophagy execution. In this context, we conducted an in-silico saturation mutagenesis analysis of interfacial residues within the ATG101-ATG13 complex to predict the impact of mutations on complex stability and interaction. After analyzing a total of 1102 interfacial mutations in protein complexes, we found that the majority of these changes reduced the binding affinity and destabilized the protein. These results provide insight into how mutations affect the stability and binding of autophagic components, which can effectively predict the functional effects of mutations on the function of protein complexes. This information may help researchers understand the complexities of the autophagy process and how it relates to neurodegenerative diseases.