Ubiquitin family modifiers and the proteasome : reviews and protocols

著者

• Dohmen, R. Jurgen
• Scheffner, Martin

書誌事項

Ubiquitin family modifiers and the proteasome : reviews and protocols

edited by R. Jurgen Dohmen, Martin Scheffner

（Methods in molecular biology / John M. Walker, series editor, 832）（Springer protocols）

Humana Press, c2012

内容説明・目次

内容説明

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.

目次

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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詳細情報

• NII書誌ID(NCID): BB08603816
• ISBN:
  • 9781617794735
• 出版国コード: us
• タイトル言語コード: eng
• 本文言語コード: eng
• 出版地: New York
• ページ数/冊数: xvi, 666 p.
• 大きさ: 26 cm
• 親書誌ID:
  • BA10794673
  • BA88873632