PROJECT SUMMARY Ubiquitin (Ub) is a principal post-translational modifier crucial to eukaryotic biology. The Ub system relays an intricate control over cellular processes through its attachment and detachment on substrate protein, giving rise to a “ubiquitin code”. Deregulation in this code has severe consequences, primarily in disease pathogenesis. In contrast to other post-translational modifications being singular, ubiquitination comes in many different flavors. Subsequent attachment of the C-terminus of one Ub moiety onto a substrate lysine residue or one of eight amines (Met1, Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, Lys63) of another Ub moiety gives rise to distinct Ub linkages that are recognized by the decoders or readers of the “ubiquitin code”. These Ub receptors facilitate important functions such as inflammatory response and DNA damage repair. Research over the past few decades has provided critical insight into the writers that establish and erasers that remove the “ubiquitin code”, yet our understanding of these Ub-receptors and Ub-interacting proteins is limited in comparison. This proposal describes the use of Ub-based probes for profiling UBDs and Ub-dependent protein-protein interactions using expanded protein chemistry. In two aims, we leverage genetic code expansion and liquid chromatography-tandem mass spectrometry to address the goal of this project: to develop a means to identify and structurally characterize Ub-dependent protein-protein interactions. Aim 1. Identify transiently interacting UBDs of eukaryotic origin using photoaffinity biotinylated Ub probes and structurally characterize promising candidates using chemo-selective ligation and X-ray crystallography. Aim 2. Develop a means to perform chemical (poly)ubiquitination using the traceless Staudinger ligation for access to homogenous (poly)Ub probes and (poly)ubiquitinated substrate protein. This will be applied to the atypical Lys29 ubiquitination of the 26S proteasome receptor Rpn13, a regulatory effect of the E3 ligase UBE3C. These approaches in Ub chemical biology will allow us to study Ub-dependent protein-protein interactions and their biophysical counterpart by reconstituting the elements needed to chemically trap noncovalent interactions, a feature currently limiting the study of the Ub system. Taken together, we seek to describe how these Ub-based interactions biochemically attenuate function and corroborate these findings using structural evidence.