Ubiquitin and Protein Degradation Part B 1st Edition by Raymond Deshaies ISBN 9780080884288 0080884288
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ISBN 10: 0080884288
ISBN 13: 9780080884288
Author: Raymond J. Deshaies
Ubiquitin and Protein Degradation, Part B covers 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.
Table of contents:
SECTION I. UBIQUITIN AND UBIQUITIN DERIVATIVES
Chapter 1: Chemical and genetic strategies for manipulating polyubiquitin chain structure
Chapter 2: Controlled synthesis of polyubiquitin chains
Chapter 3: Derivatization 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 identification
SECTION II. UBIQUITIN-BINDING DOMAINS
Chapter 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 ubiquitin-dependent protein sorting within the endocytic pathway in Saccharomyces cerevisiae
SECTION III. METHODS TO STUDY THE PROTEASOME
Chapter 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 Proteasomes
SECTION 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 degradation 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 pairs
SECTION 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 probes
SECTION VI. REAL TIME/NON-INVASIVE TECHNOLOGIES
Chapter 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 cells
SECTION VII. SMALL MOLECULE INHIBITORS
Chapter 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-substrate (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 APC
SECTION VIII. GENERALLY APPLICABLE TECHNOLOGIES
Chapter 50: The Split-Ubiquitin Sensor: Measuring interactions and conformations of proteins in vivo
Chapter 51: Heat-Inducible Degron and the making of conditional mutants
Chapter 52: Ectopic targeting of substrates to the ubiquitin pathway
Chapter 53: Chimeric Molecules to Target Proteins for Ubiquitination and Degradation
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