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Ubiquitin Family Modifiers and the Proteasome: Reviews and Protocols (Methods

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. 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

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Ubiquitin Family Modifiers and the Proteasome: Reviews and Protocols (MethodsUbiquitin Family Modifiers and the Proteasome: Reviews and Protocols (Methods

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EAN: 9781493959051

UPC: 9781493959051

ISBN: 9781493959051

MPN: N/A

Item Length: 25.4 cm

Number of Pages: 666 Pages

Language: English

Publication Name: Ubiquitin Family Modifiers and the Proteasome: Reviews and Protocols

Publisher: Humana Press Inc.

Publication Year: 2016

Subject: Chemistry

Item Height: 254 mm

Item Weight: 1732 g

Type: Textbook

Author: Martin Scheffner, R. Jurgen Dohmen

Item Width: 178 mm

Format: Paperback

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