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Ubiquitin Family Modifiers and the Proteasome R. Jurgen Dohmen

Ubiquitin Family Modifiers and the Proteasome By R. Jurgen Dohmen

Ubiquitin Family Modifiers and the Proteasome by R. Jurgen Dohmen


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Ubiquitin Family Modifiers and the Proteasome Summary

Ubiquitin Family Modifiers and the Proteasome: Reviews and Protocols by R. Jurgen Dohmen

The ubiquitin-proteasome system (UPS) and ubiquitin-related modifiers are not only involved in cellular protein quality control but also in the regulation of many fundamental cellular processes/pathways as well as in their disease-relevant aberrations. Ubiquitin Family Modifiers and Proteasome: Reviews and Protocols presents both novel developments in UPS research and important methods related to the main recent advances in the field of ubiquitin family modifiers. Divided into five convenient sections, this volume focuses on the enzymology and substrate identification of ubiquitin family modifiers, the recognition and chain formation of these modifiers, the analysis of proteasome biogenesis and function, protein quality control, and finally the use of small molecules and strategies to study or manipulate the function of the UPS and of ubiquitin family modifiers, respectively. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, Ubiquitin Family Modifiers and Proteasome: Reviews and Protocols will be of great use to investigators and students engaged in both basic and applied research in life sciences.

Table of Contents

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. Jurgen 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, Monica Torres-Ramos, Valerie Lang, and Manuel S. Rodriguez

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 Phenotypes to Characterize Mutations Affecting Proteasome Function

Benoit Le Tallec and Anne Peyroche

26. Analysing Properties of Proteasome Inhibitors using Kkinetic and X-Ray Crystallographic Studies

Nerea Gallastegui and Michael Groll

27. Immunoproteasome-Specific Inhibitors and Their Application

Michael Basler and Marcus Groettrup

28. Binding of Ubiquitin Conjugates to Proteasomes as Visualized with Native Gels

Susanne Elsasser, Yuan Shi, and Daniel Finley

29. Affinity Purification of Mmammalian 26S Proteasomes Using an Ubiquitin-Like Domain

Henrike C. Besche and Alfred L. Goldberg

30. Using siRNA Techniques to Dissect Proteasome Assembly Pathways in Mammalian Cells

Takeumi Kaneko and Shigeo Murata

31. Reconstitution of PA700, the 19S Regulatory Particle, from Purified Precursor Complexes

George N. DeMartino

Part IV. Protein Quality Control

32. Cellular Responses to Misfolded Proteins and Protein Aggregates

Scott A. Houck, Sangita Singh, and Douglas M. Cyr

33. Live-Cell Imaging of Ubiquitin-Proteasome System Function

Mark S. Hipp, Kirill Bersuker, and Ron R. Kopito

34. Analysis of Chaperone-assisted Ubiquitylation

Michael Dreiseidler, Niko Dick, and Joerg Hoehfeld

35. Use of CPY* and its Derivatives to Study Protein Quality Control in Various Cell Compartments

Alexandra Stolz and Dieter H. Wolf

36. Assays to Measure ER-Associated Degradation in Yeast

Joseph R. Tran and Jeffrey L. Brodsky

37. SDS-PAGE Techniques to Study Ubiquitin-Like Conjugation Systems in Yeast Autophagy

Hitoshi Nakatogawa and Yoshinori Ohsumi

38. Analysis of Ubiquitin-Dependent Proteolysis in C. elegans

Alexandra Segref and Thorsten Hoppe

Part V. Cellular and Chemical Strategies to Study and Manipulate UbF Related Processes

39. Structural Insights into Functional Modes of Proteins Involved in Ubiquitin Family Pathways

Petra Hanzelmann, Antje Schafer, Daniel Voeller, and Hermann Schindelin

40. Identification and Application of NEDD8 E1 Inhibitors

Frank J. Bruzzese, Michael A. Milhollen, James M. Gavin, Helen R. Josephine, and James E. Brownell

41. Formation of Ubiquitin Dimers via Azide Alkyne Click Reaction

Silvia Eger, Martin Scheffner, Andreas Marx, and Marina Rubini

42. Synthesis of Atypical Diubiquitin Chains

Farid El Oualid, Dharjath S. Hameed, Dris El Atmioui, Henk Hilkmann, and Huib Ovaa

43. TIPI - TEV Protease-Mediated Induction of Protein Instability

Christof Taxis and Michael Knop

44. PROTAC-Induced Proteolytic Targeting

Kimberly Cornish Carmony and Kyung-Bo Kim

Additional information

NLS9781493959051
9781493959051
1493959050
Ubiquitin Family Modifiers and the Proteasome: Reviews and Protocols by R. Jurgen Dohmen
New
Paperback
Humana Press Inc.
2016-08-23
666
N/A
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