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The Ubiquitin Proteasome System

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Thibault Mayor

    1. Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Gary Kleiger

    1. Department of Chemistry and Biochemistry, University of Nevada Las Vegas, Las Vegas, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1844)

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Table of contents (25 protocols)

  1. Front Matter

    Pages i-xv
    Download chapter PDF

  2. Methods to Uncover the Mechanisms of Action for Enzymes that Assemble or Disassemble Poly-Ubiquitin Chains

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Characterization of RING-Between-RING E3 Ubiquitin Transfer Mechanisms

      • Katherine H. Reiter, Rachel E. Klevit
      Pages 3-17

    3. Single-Turnover RING/U-Box E3-Mediated Lysine Discharge Assays

      • Lori Buetow, Mads Gabrielsen, Danny T. Huang
      Pages 19-31

    4. Methods for NAD-Dependent Ubiquitination Catalyzed by Legionella pneumophila Effector Proteins

      • Jiazhang Qiu, Zhao-Qing Luo
      Pages 33-38

    5. Using In Vitro Ubiquitylation Assays to Estimate the Affinities of Ubiquitin-Conjugating Enzymes for Their Ubiquitin Ligase Partners

      • Spencer Hill, Connor Hill, Gary Kleiger
      Pages 39-58

    6. Competition Assay for Measuring Deubiquitinating Enzyme Substrate Affinity

      • Michael T. Morgan, Cynthia Wolberger
      Pages 59-70

  3. Tools to Study Ubiquitylation

    1. Front Matter

      Pages 71-71
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    2. Enzymatic Assembly of Ubiquitin Chains

      • Martin A. Michel, David Komander, Paul R. Elliott
      Pages 73-84

    3. Ubiquitin-Activated Interaction Traps (UBAITs): Tools for Capturing Protein-Protein Interactions

      • Hazel F. O’Connor, Caleb D. Swaim, Larissa A. Canadeo, Jon M. Huibregtse
      Pages 85-100

    4. Generating Intracellular Modulators of E3 Ligases and Deubiquitinases from Phage-Displayed Ubiquitin Variant Libraries

      • Wei Zhang, Sachdev S. Sidhu
      Pages 101-119

    5. Integrated Proteogenomic Approach for Identifying Degradation Motifs in Eukaryotic Cells

      • Yifat Geffen, Alon Appleboim, Richard G. Gardner, Tommer Ravid
      Pages 121-136

    6. A Method to Monitor Protein Turnover by Flow Cytometry and to Screen for Factors that Control Degradation by Fluorescence-Activated Cell Sorting

      • Sophie A. Comyn, Thibault Mayor
      Pages 137-153

    7. E. coli-Based Selection and Expression Systems for Discovery, Characterization, and Purification of Ubiquitylated Proteins

      • Olga Levin-Kravets, Tal Keren-Kaplan, Ilan Attali, Itai Sharon, Neta Tanner, Dar Shapira et al.
      Pages 155-166

  4. Structural Approaches as Applied to Enzymes that Participate in the Ubiquitin Proteasome System

    1. Front Matter

      Pages 167-167
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    2. Strategies to Trap Enzyme-Substrate Complexes that Mimic Michaelis Intermediates During E3-Mediated Ubiquitin-Like Protein Ligation

      • Frederick C. Streich Jr., Christopher D. Lima
      Pages 169-196

    3. Small-Angle X-Ray Scattering for the Study of Proteins in the Ubiquitin Pathway

      • Jean-François Trempe, Kalle Gehring
      Pages 197-208

    4. Methods for Preparing Cryo-EM Grids of Large Macromolecular Complexes

      • Leifu Chang, David Barford
      Pages 209-215

  5. Methods to Study 26S Proteasome Function

    1. Front Matter

      Pages 217-217
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    2. Recombinant Expression, Unnatural Amino Acid Incorporation, and Site-Specific Labeling of 26S Proteasomal Subcomplexes

      • Jared A. M. Bard, Andreas Martin
      Pages 219-236
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Keywords

About this book

“This volume explores numerous techniques used to study the ubiquitin proteasome system. The chapters in this book are organized into five parts and cover topics such as determining the mechanisms of action for E2s, E3s, and DUB enzymes; the latest advances to study the formation of poly-ubiquitin chains as well as their linkage types; the binding partners of proteins in the UPS; methods for structure determination by x-ray crystallography, cryo electron microscopy and SAXS; screening assays to select for degrons or modulators of E3s and DUBs; proteomics approaches in the ubiquitin field and methods to study 26S proteasome function. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.


Thorough and authoritative, The UbiquitinProteasome System: Methods and Protocols is a valuable resource for both experienced and novice scientists who are interested in expanding their knowledge in this field.


Editors and Affiliations

  • Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada

    Thibault Mayor

  • Department of Chemistry and Biochemistry, University of Nevada Las Vegas, Las Vegas, USA

    Gary Kleiger

Bibliographic Information

  • Book Title: The Ubiquitin Proteasome System

  • Book Subtitle: Methods and Protocols

  • Editors: Thibault Mayor, Gary Kleiger

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-8706-1

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2018

  • Hardcover ISBN: 978-1-4939-8705-4Published: 22 September 2018

  • Softcover ISBN: 978-1-4939-9371-0Published: 10 December 2019

  • eBook ISBN: 978-1-4939-8706-1Published: 21 September 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XV, 413

  • Number of Illustrations: 29 b/w illustrations, 39 illustrations in colour

  • Topics: Protein Science

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