Main description:

This book aims to advance the understanding of deubiquitinases (DUBs) and DUB-like enzymes. Chapters detail methods used to identify, classify,and biochemically characterize DUBs along with approaches that enable both the determination and alteration of DUB biological function.. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

Authoritative and cutting-edge, Deubiquitinases: Methods and Protocols aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.

Contents:

1. Characterization of Deubiquitinase Catalytic State Using a Structure-Based Approach

Zhengrui Zhang and Chittaranjan Das

2. Synthetic Diubiquitin Fluorogenic Substrates to Study DUBs

Max S. Kloet and Gerbrand J. van der Heden van Noort

3. Fluorometric Characterization of DUB Activity: From Single Enzyme Reactions to Live Intact Cell

Alireza Rahnama and Adam T. Melvin

4. Using Activity-Based Proteomics for the Quantification of Deubiquitinases in Animal Tissue

Bindu Nanduri, Leslie A Shack, John Santelices, and Mariola J Edelmann

5. Design and Synthesis of Ubiquitin-Based Chemical tools with Unnatural Amino Acids for Selective Detection of Deubiquitinases

Wioletta Rut, Mikolaj Zmudzinski, and Marcin Drag

6. High Throughput Assay for Characterizing Rpn11 Deubiquitinase Activity

Gang Xie, Ken C Dong, Evan J Worden, and Andreas Martin

7. Activity-Based Protein Profiling (ABPP) for Cellular Deubiquitinase (DUB) and Inhibitor Profiling at Deep and High-Throughput Levels

Hannah B. L. Jones, Raphael Heilig, Benedikt M. Kessler, and Adan Pinto-Fernandez

8. High-Throughput MALDI-TOF Mass-Spectrometry-based Deubiquitylating Enzyme Assay for Drug Discovery

Virginia De Cesare and Paul Davies

9. Bioinformatical Approaches to The Discovery and Classification of Novel Deubiquitinases

Thomas Hermanns and Kay Hofmann

10. Application of Archaea in Deubiquitinase-Like Enzyme Discovery and Activity Assay

Nathaniel Hepowit and Julie A. Maupin-Furlow

11. Characterization of the Ubiquitin and ISG15 Deconjugase Activity of SARS-CoV-1 and 2 Papain-like Protease

Digant Nayak, Priscila dos Santos Bury, Marcin Drag, Alfred N. Nijkerk, Farid El Oualid, and Shaun K. Olsen

12. Next-generation Phage Display to Identify Peptide Ligands of Deubiquitinases

Anastasios Spiliotopoulos, Sigrun K. Maurer, Maria T. Tsoumpeli, Juan A. F. Bonfante, Jonathan P. Owen, Kevin C. Gough, and Ingrid Dreveny

13. Identification of Deubiquitinase Substrates in Xenopus Egg Extract

Valentina Rossio, Joao A. Paulo, and Randall W. King

14. Identification of Deubiquitinase Substrates in Saccharomyces cerevisiae by Systematic Overexpression

Heather E. Arsenault and Jennifer A. Benanti

15. Real-time Deubiquitination Assays using a Free-Ubiquitin Sensor

Yun-Seok Choi and Robert E. Cohen

16. A Method to Monitor Activity of SARS-CoV-2 Nsp3 from Cells

Christopher Rainville, David E. Sterner, and Kumar Suresh

17. Use of Deubiquitinase Fusion Proteins to Characterize Endocytic Trafficking in Yeast

Nathaniel L. Hepowit, Aeva S. Denise, and Jason A. MacGurn