Ubiquitin and Protein Degradation, Part B

Edited by

  • Raymond Deshaies, Howard Hughes Medical Institute, Caltech, Pasadena, CA, USA

Ubiquitin and Protein Degradation, Part B will cover chemical biology, ubiquitin derivatives and ubiquitin-like proteins, deubiquitinating enzymes, proteomics as well as techniques to monitor protein degradation. The chapters are highly methodological and focus on application of techniques.
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Biochemists, biophysicists, cell biologists, molecular biologists, geneticists, developmental biologists


Book information

  • Published: October 2005
  • ISBN: 978-0-12-182804-2


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Table of Contents

SECTION I. UBIQUITIN AND UBIQUITIN DERIVATIVESChapter 1. Chemical and genetic strategies for manipulating polyubiquitin chain structure; Chapter 2. Controlled synthesis of polyubiquitin chains; Chapter 3. Derivitization of the C-terminus of ubiquitin and ubiquitin-like proteins using Intein chemistry: Methods & Uses; Chapter 4. Preparation, characterization, and use of tagged ubiquitin; Chapter 5. Knocking out ubiquitin proteasome system function in vivo and in vitro with genetically-encodable tandem ubiquitin; Chapter 6. Production of anti-polyubiquitin antibodies and their use for characterization and isolation of polyubiquitinated proteins; Chapter 7. Application of Ubiquitin Immunohistochemistry to Diagnosis of Disease; Chapter 8. Mechanism-based proteomics tools based on ubiquitin and ubiquitin-like proteins: crystallography, activity profiling and protease identificationSECTION II. UBIQUITIN-BINDING DOMAINSChapter 9. Identification and characterization of modular domains that bind ubiquitin; Chapter 10. Analysis of Ubiquitin chain-binding proteins by two-hybrid methods; Chapter 11. Quantifying protein-protein interactions in the ubiquitin pathway by surface plasmon resonance; Chapter 12. Using NMR spectroscopy to monitor ubiquitin chain conformation and interactions with ubiquitin-binding domains; Chapter 13. Analysis of ubquitin-dependent protein sorting within the endocytic pathway in Saccharomyces cerevisiaeSECTION III. METHODS TO STUDY THE PROTEASOMEChapter 14. Preparation of ubiquitinated substrates by the PY motif-insertion method for monitoring 26S proteasome activity; Chapter 15. Large- and Small-scale Purification of Mammalian 26S ProteasomesSECTION IV. IDENTIFICATION AND CHARACTERIZATION OF SUBSTRATES AND UBIQUITIN LIGASES Chapter 16. Is my protein ubiquitinated?; Chapter 17. Experimental tests to definitively determine ubiquitination of a substrate; Chapter 18. Identification of ubiquitination sites and determination of ubiquitin-chain architectures by mass spec; Chapter 19. Mapping of ubiquitination sites on target proteins; Chapter 20. Identification of substrates for F-box proteins; Chapter 21. Fusion -based strategies to identify genes involved in degradations of a specific substrate; Chapter 22. Bisubstrate kinetic analysis of an E3-ligase dependent ubiquitylation reaction; Chapter 23. Screening of Tissue Microarrays for Ubiquitin Proteasome System Components in Tumors; Chapter 24. Structure-based approaches to create new E2-E3 enzyme pairsSECTION V. GENOME- AND PROTEOME-WIDE APPROACHES TO IDENTIFY SUBSTRATES AND ENZYMES Chapter 25. Proteomic analysis of ubiquitin conjugates in yeast; Chapter 26. Two-Step Affinity Purification of Multiubiquitylated Proteins from Saccharomyces cerevisiae; Chapter 27. Identification of SUMO-Protein Conjugates; Chapter 28. Identification of Ubiquitin Ligase Substrates by in Vitro Expression Cloning; Chapter 29. In vitro screening for substrates of the N-end rule-dependent ubiquitylation; Chapter 30. Genome-wide surveys for phosphorylation–dependent substrates of SCF ubiquitin ligases; Chapter 31. Yeast genomics in the elucidation of endoplasmic reticulum (ER) quality control and associated protein degradation (ERQD); Chapter 32. Mechanism-based proteomics tools based on ubiquitin and ubiquitin-like proteins: Synthesis of active site directed probesSECTION VI. REAL TIME/NON-INVASIVE TECHNOLOGIESChapter 33. Application and analysis of the GFPu family of ubiquitin-proteasome system reporters; Chapter 34. Monitoring of Ubiquitin-Dependent Proteolysis with Green Fluorescent Protein Substrates; Chapter 35. Monitoring proteasome activity in cellulo and in living animals by bioluminescent imaging: technical considerations for design and use of genetically-encoded reporters; Chapter 36. Bioluminescent imaging of ubiquitin ligase activity: measuring Cdk2 activity through changes in p27 turnover; Chapter 37. Monitoring the distribution and dynamics of proteasomes in living cellsSECTION VII. SMALL MOLECULE INHIBITORSChapter 38. Identifying Small Molecules Inhibitors of the Ubiquitin-Proteasome Pathway in Xenopus Extracts; Chapter 39. Development and characterization of proteasome inhibitors; Chapter 40. Screening for selective small molecule inhibitors of the proteasome using activity based probes; Chapter 41. Development of E3-substract (MDM2-p53) binding inhibitors: structural aspects; Chapter 42. Druggability of SCF Ubiquitin Ligase Protein Interfaces; Chapter 43. Overview on approaches for screening for ubiquitin ligase inhibitors; Chapter 44. A homogeneous FRET assay system for multi-ubiquitin chain assembly and disassembly; Chapter 45. Assays for High-throughput screening of E2 and E3 ubiquitin ligases; Chapter 46. Quantitative Assays for MDM2 Ubiquitin Ligase Activity and Other Ubiquitin-Utilizing Enzymes in Inhibitor Discovery; Chapter 47. High-throughput screening for inhibitors of the Skp2-Cks1 interaction; Chapter 48. In vitro SCFb-Trcp1-Mediated IkBa Ubiquitination Assay for High Throughput Screen; Chapter 49. High throughput screening for inhibitors of the E3 ubiquitin ligase APCSECTION VIII. GENERALLY APPLICABLE TECHNOLOGIESChapter 50. The Split-Ubiquitin Sensor: Measuring interactions and conformations of proteins in vivo; Chapter 51. Heat-Inducible Degron and the making of codintional mutants; Chapter 52. Ectopic targeting of substrates to the ubiquitin pathway; Chapter 53. Chimeric Molecules to Target Proteins for Ubiquitination and Degradation