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Proximity Labeling

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Murat Sunbul

    1. Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany

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    You can also search for this editor in PubMed   Google Scholar

  2. Andres Jäschke

    1. Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2008)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. The EMARS Reaction for Proximity Labeling

    • Koichi Honke, Arisa Miyagawa-Yamaguchi, Norihiro Kotani
    Pages 1-12

  3. Proteomic Proximity Labeling to Reveal Interactions Between Biomolecules

    • Johanna Susan Rees
    Pages 13-28

  4. Establishing Cell Culture-Based Experimental Setups for Proximity Labeling Using Ascorbate Peroxidase (APEX)

    • David U. Mick
    Pages 29-39

  5. APEX Peroxidase-Catalyzed Proximity Labeling and Multiplexed Quantitative Proteomics

    • Marian Kalocsay
    Pages 41-55

  6. Identification of Lipid Droplet Proteomes by Proximity Labeling Proteomics Using APEX2

    • Kirill Bersuker, James A. Olzmann
    Pages 57-72

  7. Antibody-Driven Proximity Labeling in Fixed Tissues

    • Daniel Z. Bar, Francis S. Collins
    Pages 73-81

  8. BioID: A Method to Generate a History of Protein Associations

    • Danielle G. May, Kyle J. Roux
    Pages 83-95

  9. Direct Identification of Biotinylated Proteins from Proximity Labeling (Spot-BioID)

    • Song-Yi Lee, Jeong Kon Seo, Hyun-Woo Rhee
    Pages 97-105

  10. Identifying Synaptic Proteins by In Vivo BioID from Mouse Brain

    • Akiyoshi Uezu, Scott Soderling
    Pages 107-119

  11. A Proximity Ligation-Based Method to Detect RNA-DNA Association

    • Tyler K. Fenstermaker, Guizhi Sun, Alexander Mazo, Svetlana Petruk
    Pages 121-129

  12. Enzymatic Transfer of Photo-Cross-Linkers for RNA-Protein Photo-Cross-Linking at the mRNA 5′-Cap

    • Nils Muthmann, Fabian Muttach, Andrea Rentmeister
    Pages 131-146

  13. Proximity-Induced Bioorthogonal Chemistry Using Inverse Electron Demand Diels-Alder Reaction

    • Jasper S. Möhler, Philipp Werther, Richard Wombacher
    Pages 147-163

  14. Overcoming the Limitations of Sortase with Proximity-Based Sortase-Mediated Ligation (PBSL)

    • Hejia Henry Wang, Andrew Tsourkas
    Pages 165-177

  15. Proximity-Driven Site-Specific and Covalent Labeling of Proteins with a TexasRed Fluorophore Reacting (ReacTR) Peptide Tag

    • Murat Sunbul, Andres Jäschke
    Pages 179-190

  16. Affinity Conjugation for Rapid and Covalent Labeling of Proteins in Live Cells

    • Xi Chen, Fu Li, Yao-Wen Wu
    Pages 191-202

  17. Ligand-Directed N-Sulfonyl Pyridone Chemistry for Selective Native Protein Labeling and Imaging in Live Cell

    • Marie Masuda, Kazuya Matsuo, Itaru Hamachi
    Pages 203-224

  18. Back Matter

    Pages 225-231
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Keywords

About this book

This book provides detailed protocols and untold tips and tricks regarding the most well-known examples of proximity labeling methods, in which the protein of interest is genetically fused to or labeled with an enzyme that can generate short-lived reactive species to non-specifically label molecules within a certain radius of up to twenty nanometers. Beginning with peroxidase-based proximity labeling methods, the volume continues with BioID, proximity labeling methods that describe the proximity ligation assay to detect RNA-DNA interactions, UV cross-linking to demonstrate RNA-protein interactions, and how chemical and enzymatic reactivities can be improved upon DNA-DNA and protein-protein interactions, as well as “proximity-induced self-labeling,” where the radius of labeling is zero. Written for the highly successful Methods in Molecular Biology series, 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. 

Authoritative and practical, Proximity Labeling: Methods and Protocols serves as an ideal guide for researchers exploring the crucial roles that proximity-driven reactions play in biological systems.

Editors and Affiliations

  • Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany

    Murat Sunbul, Andres Jäschke

Bibliographic Information

  • Book Title: Proximity Labeling

  • Book Subtitle: Methods and Protocols

  • Editors: Murat Sunbul, Andres Jäschke

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9537-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9536-3Published: 25 May 2019

  • Softcover ISBN: 978-1-4939-9539-4Published: 14 August 2020

  • eBook ISBN: 978-1-4939-9537-0Published: 23 May 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 231

  • Number of Illustrations: 28 b/w illustrations, 46 illustrations in colour

  • Topics: Protein Science, Genetics and Genomics, Animal Biochemistry

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