A Strategy for Modulation of Enzymes in the Ubiquitin System

Andreas Ernst1, George Avvakumov2, Jiefei Tong3, Yihui Fan4, Yanling Zhao4, Philipp Alberts3, Avinash Persaud3,5,John R. Walker2, Ana-Mirela Neculai1, Dante Neculai2, Andrew Vorobyov1, Pankaj Garg1, Linda Beatty1,Pak-Kei Chan6, Yu-Chi Juang7, Marie-Claude Landry7, Christina Yeh7,8, Elton Zeqiraj7, Konstantina Karamboulas1,Abdellah Allali-Hassani2, Masoud Vedadi2, Mike Tyers6,7, Jason Moffat1,8,9,10, Frank Sicheri7,Laurence Pelletier7, Daniel Durocher7, Brian Raught10, Daniela Rotin3,5, Jianhua Yang4, Michael F. Moran3,8,9,Sirano Dhe-Paganon2,11, Sachdev S. Sidhu1,8,9,10,*

The ubiquitin system regulates virtually all aspects of cellular function. We report a method to target the myriad enzymes that govern ubiquitination of protein substrates. We used massively diverse combinatorial libraries of ubiquitin variants to develop inhibitors of four deubiquitinases (DUBs) and analyzed the DUB-inhibitor complexes by crystallography. We extended the selection strategy to the ubiquitin conjugating (E2) and ubiquitin ligase (E3) enzymes, and found that ubiquitin variants can also enhance enzyme activity. Finally, we showed that ubiquitin variants can bind selectively to ubiquitin-binding domains. Ubiquitin variants exhibit selective function in cells and thus enable orthogonal modulation of specific enzymatic steps in the ubiquitin system.

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