Proximity Labeling: Methods and Protocols

Description

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. Front Matter ....Pages i-x The EMARS Reaction for Proximity Labeling (Koichi Honke, Arisa Miyagawa-Yamaguchi, Norihiro Kotani)....Pages 1-12 Proteomic Proximity Labeling to Reveal Interactions Between Biomolecules (Johanna Susan Rees)....Pages 13-28 Establishing Cell Culture-Based Experimental Setups for Proximity Labeling Using Ascorbate Peroxidase (APEX) (David U. Mick)....Pages 29-39 APEX Peroxidase-Catalyzed Proximity Labeling and Multiplexed Quantitative Proteomics (Marian Kalocsay)....Pages 41-55 Identification of Lipid Droplet Proteomes by Proximity Labeling Proteomics Using APEX2 (Kirill Bersuker, James A. Olzmann)....Pages 57-72 Antibody-Driven Proximity Labeling in Fixed Tissues (Daniel Z. Bar, Francis S. Collins)....Pages 73-81 BioID: A Method to Generate a History of Protein Associations (Danielle G. May, Kyle J. Roux)....Pages 83-95 Direct Identification of Biotinylated Proteins from Proximity Labeling (Spot-BioID) (Song-Yi Lee, Jeong Kon Seo, Hyun-Woo Rhee)....Pages 97-105 Identifying Synaptic Proteins by In Vivo BioID from Mouse Brain (Akiyoshi Uezu, Scott Soderling)....Pages 107-119 A Proximity Ligation-Based Method to Detect RNA-DNA Association (Tyler K. Fenstermaker, Guizhi Sun, Alexander Mazo, Svetlana Petruk)....Pages 121-129 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 Proximity-Induced Bioorthogonal Chemistry Using Inverse Electron Demand Diels-Alder Reaction (Jasper S. Möhler, Philipp Werther, Richard Wombacher)....Pages 147-163 Overcoming the Limitations of Sortase with Proximity-Based Sortase-Mediated Ligation (PBSL) (Hejia Henry Wang, Andrew Tsourkas)....Pages 165-177 Proximity-Driven Site-Specific and Covalent Labeling of Proteins with a TexasRed Fluorophore Reacting (ReacTR) Peptide Tag (Murat Sunbul, Andres Jäschke)....Pages 179-190 Affinity Conjugation for Rapid and Covalent Labeling of Proteins in Live Cells (Xi Chen, Fu Li, Yao-Wen Wu)....Pages 191-202 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 Back Matter ....Pages 225-231