As part of a collaboration with extramural researchers we helped establish Rpn13 as a proteasome ubiquitin receptor. We solved its structure complexed with ubiquitin by NMR and more recently, have evaluated Rpn13 specificity for ubiquitin chains of different linkage type. A similar analysis was also done on Rpn10/S5a, the proteasome's other established ubiquitin receptor. This work is being extended to evaluate the specific roles of Rpn10 and Rpn13 in ubiquitin signaling for proteolysis, both by biophysical methods and cell biology techniques. In addition, we are determining how Rpn13 is docked into proteasome by solving its structure with its proteasome binding partner by NMR. Our collaborator, Richard Roden from Johns Hopkins University, has found bis-benzylidine piperidone derivatives that restrict growth of multiple myeloma and ovarian cancer xenografts by targeting Rpn13. We determined the target site of these molecules to be at a specific cysteine of the Rpn13 ubiquitin-binding domain. We are further characterizing the mechanism of action of these and other small molecules that target Rpn13, as well as distinct cellular activities of Rpn13. As part of this effort, we are solving the structure of Rpn13 with small molecule inhibitors as well as determining the in vivo mechanism of action of the bis-benzylidine piperidone derivative that targets Rpn13. Finally, we have identified another binding site for ubiquitin in proteasome and we are using NMR to solve the structure of this component and its complex with ubiquitin chains. We are collaborating with Dan Finley at Harvard Medical School to determine the functional significance of this new binding site for ubiquitinated substrates in proteasome. This project is providing fundamental information on how proteasome recognizes ubiquitinated substrates.
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