Deciphering protein ubiquitination with chemical biology tools

Ubiquitination as a reversible post-translational modification is essential to a broad range of cellular processes in humans. In addition to its function in proteasome-mediated protein degradation, ubiquitination is crucial for many non-proteolytic cellular processes. These cellular processes are regulated by a diverse array of polyubiquitin chains of different linkages and topologies, including recently discovered branched polyubiquitin chains. Deubiquitinases (DUBs) modulate the ubiquitin chain linkage and structure and are considered promising new targets for therapeutic intervention. The goals of our work are to investigate the recognition and cleavage of atypical polyubiquitin chains and ubiquitinated proteins by DUBs; identify and characterize reader proteins of branched ubiquitin chains and understand the roles of branched ubiquitin chains in mitophagy and receptor endocytosis. These projects are interconnected and complementary to each other, building on our success in chemical protein ubiquitination and DUB probe construction using semisynthetic approaches. The new chemical biology tools developed, particularly novel activity-based DUB probes, will serve to unveil new biological targets and functions in the ubiquitin system and provide new ways of identifying the reader and eraser proteins of ubiquitin signals. The mechanistic and structural insights obtained will in turn propel drug discovery efforts exploiting the ubiquitin system and lead to new opportunities and means for treating human diseases including neurodegeneration and cancer.