ASSESSMENT OF APPROACHES TO STUDY UBIQUITIN BINDING INTERFACES

The process of ubiquitination is an important regulatory process that helps modulate eukaryotic signaling inside the cell. This process is described as the formation of an isopeptide linkage between the C-terminal residue of ubiquitin to the lysine residue of a target protein, a process catalyzed by the E1, E2, and E3 enzyme cascade. As mentioned, this process has only been observed in eukaryotes, although recently, prokaryotic pathogens have been shown to possess enzymes that affect the ubiquitination pathway in their hosts. While some of these enzymes have well known mechanisms, there are still many that are unknown and are novel when compared to other well documented enzymes. The studies conducted in this Thesis involve biochemical, structural, and bioinformatic studies involving both prokaryotic and eukaryotic enzymes as an approach to develop methodologies that help study processes involving ubiquitin. Among the insights provided in this document, the importance of a unique insertion found in the Legionella effector MavC, that is important for substrate recognition. The use of disulfide bridge formation to obtain Ub-DUB complexes through the design of a simple cysteine mutation on Ub. Finally, utilizing AlphaFold, in combination with other bioinformatic processes, to help study large, protein family data sets, like the USP family DUBs that is studied in this Thesis. Altogether, these findings show that through a combination of multiple techniques, we can have a more streamlined way of studying these new, exciting protein pathways.