A proteome-wide screen elaborates binding determinants of
the core autophagy protein LC3B
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kosmatka-kosmatka-phd-bio-2025-thesis .pdf
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Author(s)
Kosmatka, Jennifer E.
Advisor(s)
Keating, Amy E.
Davis, Joseph H.
Date Issued
February 2026
Publisher
Massachusetts Institute of Technology
Abstract
Cells adapt to changing environments by remodeling their proteome, often through degradation of damaged, misfolded, or otherwise unneeded proteins. In eukaryotes, protein degradation is controlled by two pathways - the ubiquitin–proteasome system and the autophagy–lysosome pathway. Within the latter, Atg8 proteins recognize poorly characterized short linear motifs embedded in disordered protein regions to regulate autophagy by directing substrates for lysosomal degradation. To better understand the determinants of ATG8 substrate selection, I performed a high-throughput screen of a human proteome-derived library to identify candidate client proteins and map the sequence binding landscape of the human Atg8 paralog LC3B. Doing so, I identified an expanded LC3B-binding motif that binds the core motif docking site (LDS) and demonstrated how the presence of acidic residues flanking the core motif influence binding. Predictive models trained on this data are on par with existing scoring methods and incorporate additional expanded motifs. Furthermore, attempts to isolate peptides that bind outside the core binding pocket revealed that commonly used LDS knockout mutations do not completely abrogate binding and should be applied with caution. Collectively, these results refine our understanding of LC3B substrate-selection and the influence of binding site architecture on this process. Such insights lay a foundation for the rational design of autophagy-targeting therapeutics and provide a framework for understanding how post-translational modifications, differences between paralogs, and disease-associated mutations play a role in autophagy regulation.
MIT Department
Massachusetts Institute of Technology. Department of Biology
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