Ubiquitin Family Modifiers and the Proteasome: Reviews and Protocols

ISBN-13: 9781493959051 / Angielski / Miękka / 2016 / 666 str.

R. Jurgen Dohmen; Martin Scheffner

Opis

This volume presents novel developments in UPS research and important methods related to recent advances in the field. The volume focuses on the enzymology and substrate identification of ubiquitin family modifiers, the recognition and chain formation of these modifiers, and more.

Spis treści

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 Phenotypes to Characterize Mutations Affecting Proteasome Function

            Benoît 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 Jörg Höhfeld

 

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 Hänzelmann, Antje Schäfer, Daniel Völler, 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

Blurb

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™ 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.