Ubiquitin family modifiers and the proteasome : reviews and protocols
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Bibliographic Information
Ubiquitin family modifiers and the proteasome : reviews and protocols
（Methods in molecular biology / John M. Walker, series editor, 832）（Springer protocols）
Humana Press, c2012
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Description and Table of Contents
Description
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
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