ArticleNature protocols2016
Deep interactome profiling of membrane proteins by co-interacting protein identification technology.
Article in Nature protocols, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Kv11.1 (hERG) Protein Interaction Networks Connect Endocytic Trafficking to Polygenic Influences on Cardiac Repolarization.Molecular & cellular proteomics : MCP · 2026Article
- Quantitative interactome mapping of skeletal muscle insulin resistance.Molecular systems biology · 2026Article
- O-Mannose Glycosylations Influence E-Cadherin Functional Interactions.Molecular & cellular proteomics : MCP · 2026Article
- Kv11.1 (hERG) Protein Interaction Networks Connect Endocytic Trafficking to Polygenic Influences on Cardiac Repolarization.bioRxiv : the preprint server for biology · 2026Article
- In vivo conformational space and defects of misfolded CFTR variants by covalent protein painting.Nature communications · 2025Article
- Structural host-virus interactome profiling of intact infected cells.Nature communications · 2025Article
- Proteostasis landscapes of cystic fibrosis variants reveal drug response vulnerability.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Proteostasis Landscapes of Cystic Fibrosis Variants Reveals Drug Response Vulnerability.bioRxiv : the preprint server for biology · 2025Article
- The MYO1B and MYO5B motor proteins and the sorting nexin SNX27 regulate apical targeting of membrane mucin MUC17 in enterocytes.The Biochemical journal · 2025Article
- BioID-Based Proximity Mapping of Transmembrane Proteins in Human Airway Cell Models.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Cystic Fibrosis Modulator Therapies: Bridging Insights from CF to other Membrane Protein Misfolding Diseases.Israel journal of chemistry · 2024Article
- Ribosomal frameshifting selectively modulates the assembly, function, and pharmacological rescue of a misfolded CFTR variant.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- DiPRO1 distinctly reprograms muscle and mesenchymal cancer cells.EMBO molecular medicine · 2024Article
- Ribosomal Frameshifting Selectively Modulates the Assembly, Function, and Pharmacological Rescue of a Misfolded CFTR Variant.bioRxiv : the preprint server for biology · 2024Article
- The proteostasis interactomes of trafficking-deficient variants of the voltage-gated potassium channel KThe Journal of biological chemistry · 2024Article
- A CPF-like phosphatase module links transcription termination to chromatin silencing.Molecular cell · 2024Article
- Initiation of B-type starch granules in wheat endosperm requires the plastidial α-glucan phosphorylase PHS1.The Plant cell · 2023Article
- EGFR-T790M Mutation-Derived Interactome Rerouted EGFR Translocation Contributing to Gefitinib Resistance in Non-Small Cell Lung Cancer.Molecular & cellular proteomics : MCP · 2023Article
- Nuclear translocation of an aminoacyl-tRNA synthetase may mediate a chronic "integrated stress response".Cell reports · 2023Article
- Elexacaftor/VX-445-mediated CFTR interactome remodeling reveals differential correction driven by mutation-specific translational dynamics.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Affinity purification coupled to mass spectrometry (AP-MS) is the method of choice for analyzing protein-protein interactions, but common protocols frequently recover only the most stable interactions and tend to result in low bait yield for membrane proteins. Here, we present a novel, deep interactome sequencing approach called CoPIT (co-interacting protein identification technology), which allows comprehensive identification and analysis of membrane protein interactomes and their dynamics. CoPIT integrates experimental and computational methods for a coimmunoprecipitation (Co-IP)-based workflow from sample preparation for mass spectrometric analysis to visualization of protein-protein interaction networks. The approach particularly improves the results for membrane protein interactomes, which have proven to be difficult to identify and analyze. CoPIT was used successfully to identify the interactome of the cystic fibrosis transmembrane conductance regulator (CFTR), demonstrating its validity and performance. The experimental step in this case achieved up to 100-fold-higher bait yield than previous methods by optimizing lysis, elution, sample clean-up and detection of interacting proteins by multidimensional protein identification technology (MudPIT). Here, we further provide evidence that CoPIT is applicable to other types of proteins as well, and that it can be successfully used as a general Co-IP method. The protocol describes all steps, ranging from considerations for experimental design, Co-IP, preparation of the sample for mass spectrometric analysis, and data analysis steps, to the final visualization of interaction networks. Although the experimental part can be performed in <3 d, data analysis may take up to a few weeks.
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