Introduction

1. Three Decades of Studies to Understand the Functions of the Ubiquitin Family

Alexander Varshavsky

Part I. Enzymology and Substrates of Ubiquitin Family Modifiers

2. Structure and Evolution of Ubiquitin and Ubiquitin-Related Domains

A. Maxwell Burroughs, Lakshminarayan M. Iyer, and L. Aravind

3. Deciphering Tissue-Specific Ubiquitylation by Mass Spectrometry

Ugo Mayor and Junmin Pen

4. Analysis of Cellular SUMO and SUMO-Ubiquitin Hybrid Conjugates

Marion Schnellhardt, Kristina Uzunova, Veronica N. Bade, Anke Krause, Stefan R. Weisshaar, Gerrit J. K. Praefcke, and R. Jürgen Dohmen

5. Recombinant Reconstitution of Sumoylation Reactions In vitro

Annette Flotho, Andreas Werner, Tobias Winter, Andrea S. Frank, Heidi Ehret, and Frauke Melchior

6. Reconstitution of SUMO-Dependent Ubiquitylation In vitro

Kirstin Keusekotten and Gerrit J. K. Praefcke

7. Detection and Analysis of FAT10 Modification

Annette Aichem and Marcus Groettrup

8. Isolation of NEDDylated Proteins in Human Cells

Orsolya Leidecker and Dimitris P. Xirodimas

9. The ISG15 Conjugation System

Larissa A. Durfee and Jon M. Huibregtse

10. Pupylation: Proteasomal Targeting by a Protein Modifier in Bacteria

Kristin E. Burns and K. Heran Darwin

Part II. Recognition and Chain Formation of UbF Modifiers

11. Role of UbF Family Modifiers and their Binding Proteins in Cell Signaling

Sjoerd J. L. van Wijk, Magda Bienko, and Ivan Dikic

12. Isolation of Ubiquitylated Proteins using Tandem Ubiquitin-Binding Entities (TUBEs)

Fabienne Aillet, Fernando Lopitz-Otsoa, Roland Hjerpe, Mónica Torres-Ramos, Valérie Lang, and Manuel S. Rodríguez

13. Using Linkage-Specific Monoclonal Antibodies to Analyze Cellular Ubiquitination

Kim Newton, Marissa L. Matsumoto, Ronald E. Ferrando, Katherine E. Wickliffe, Michael Rape, Robert F. Kelley, and Vishva M. Dixit

14. Measuring Rates of Ubiquitin Chain Formation as a Functional Readout of Ligase Activity

Virginia P. Ronchi and Arthur L. Haas

15. Synthesis and Analysis of K11-Linked Ubiquitin Chains

Anja Bremm and David Komander

16. Synthesis and Analysis of Linear Ubiquitin Chains

Kazuhiro Iwai

17. Detection and Quantitation of SUMO Chains by Mass Spectrometry

Ivan Matic and Ron T. Hay

18. Bioinformatical Detection of Recognition Factors for Ubiquitin and SUMO

Benjamin Vogt and Kay Hofmann

19. Surface Plasmon Resonance to Measure Interactions of UbFs with Their Binding Partners

Julian Stingele, Uwe W. Roder, and Shahri Raasi

20. Identifying and Studying Ubiquitin Receptors by NMR

Xiang Chen and Kylie J. Walters

21. Exploring the Role of p97 and its UBX-Domain Cofactors Through Identification of Their Interacting Proteins

Gabriela Alexandru

Part III. Proteasome Biogenesis, Regulation and Function

22. Assembly and Function of the Proteasome

Yasushi Saeki and Keiji Tanaka

23. Using Native Gel Electrophoresis and Phosphofluoroimaging to Analyse GFP-tagged Proteasomes

Cordula Enenkel

24. Disulfide Engineering to Map Subunit Interactions in the Proteasome and Other Macromolecular Complexes

Mark Hochstrasser and Minoru Funakoshi

25. Using DNA Damage Sensitivity Phenoty