Journal Article

A Strategy for Modulation of Enzymes in the Ubiquitin System

Vorobyov, Andrew, Ernst, Andreas, Durocher, Daniel, Juang, Yu-Chi, Vedadi, Masoud, Fan, Yihui, Zeqiraj, Elton, Raught, Brian, Sidhu, Sachdev S., Pelletier, Laurence, Tyers, Mike, Moffat, Jason, Garg, Pankaj, Yang, Jianhua, Alberts, Philipp, Persaud, Avinash, Tong, Jiefei, Chan, Pak-Kei, Sicheri, Frank, Beatty, Linda, Avvakumov, George, Allali-Hassani, Abdellah, Zhao, Yanling, Landry, Marie-Claude, Yeh, Christina, Rotin, Daniela, Karamboulas, Konstantina, Walker, John R., Neculai, Ana-Mirela, Neculai, Dante, Moran, Michael F., Dhe-Paganon, Sirano

2013

Overview

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 with 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. Last, 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.

• Publisher: American Association for the Advancement of Science,The American Association for the Advancement of Science
• Subject: Amino Acid Sequence / Antibodies / Bacteriophages / Combinatorial Chemistry Techniques / Conserved Sequence / Control / Crystal structure / Crystallography / Drug Design / Endopeptidases - chemistry / Endopeptidases - metabolism / Enzymatic activity / Enzyme substrates / Enzymes / HEK293 Cells / Humans / Immunoblotting / Libraries / Modulation / Molecular interactions / Molecular Sequence Data / Pathways / Protease Inhibitors - chemistry / Protease Inhibitors - isolation & purification / Protease Inhibitors - pharmacology / Protein Conformation / Protein Structure, Secondary / proteinases / Proteins / Regulators / Residues / Small Molecule Libraries / Strategy / ubiquitin / Ubiquitin - chemistry / Ubiquitin - genetics / Ubiquitin - metabolism / Ubiquitin Thiolesterase - chemistry / Ubiquitin Thiolesterase - metabolism / Ubiquitin-Conjugating Enzymes - chemistry / Ubiquitin-Conjugating Enzymes - metabolism / Ubiquitin-Protein Ligases - chemistry / Ubiquitin-Protein Ligases - metabolism / ubiquitination / Ubiquitination - drug effects / Ubiquitins / Uterine hemorrhage