ArticleMolecular & cellular proteomics : MCP2009
Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry.
Article in Molecular & cellular proteomics : MCP, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
- Developing a new cleavable crosslinker reagent for in-cell crosslinking.Communications chemistry · 2025Article
- Strategies for Acid and Amine Cross-linking and Labeling for Protein Structural Characterization Using Mass Spectrometry.Analytical chemistry · 2025Article
- Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provide New Insight into Protein Conformational Plasticity within Organelles, Cells, and Tissues.Journal of proteome research · 2025Article
- Cross-Linking Mass Spectrometry to Capture Protein Network Dynamics of Cell Membranome.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS.Journal of proteome research · 2023Article
- Membrane Protein Binding Interactions Studied in Live Cells via Diethylpyrocarbonate Covalent Labeling Mass Spectrometry.Analytical chemistry · 2023Article
- Cross-linking mass spectrometry for mapping protein complex topologies in situ.Essays in biochemistry · 2023Article
- Improved Peptide Backbone Fragmentation Is the Primary Advantage of MS-Cleavable Crosslinkers.Analytical chemistry · 2022Article
- Improved Interpretation of Protein Conformational Differences and Ligand Occupancy in Large-Scale Cross-Link Data.Journal of proteome research · 2022Article
- In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.Chemical reviews · 2022Review
- Targeted Cross-Linking Mass Spectrometry on Single-Step Affinity Purified Molecular Complexes in the Yeast Saccharomyces cerevisiae.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Crosslinking mass spectrometry: A link between structural biology and systems biology.Protein science : a publication of the Protein Society · 2021Review
- Leveraging the Entirety of the Protein Data Bank to Enable Improved Structure Prediction Based on Cross-Link Data.Journal of proteome research · 2021Article
- Quantitative Cross-Linking of Proteins and Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications.Chemical reviews · 2020Review
- PhoX: An IMAC-Enrichable Cross-Linking Reagent.ACS central science · 2019Article
- Identification of Cross-linked Peptides Using Isotopomeric Cross-linkers.Journal of the American Society for Mass Spectrometry · 2019Article
- Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies.Journal of proteome research · 2019Article
- Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks.Bioinformatics (Oxford, England) · 2019Article
- The in vivo specificity of synaptic Gβ and Gγ subunits to the αScientific reports · 2019Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
We present results from a novel strategy that enables concurrent identification of protein-protein interactions and topologies in living cells without specific antibodies or genetic manipulations for immuno-/affinity purifications. The strategy consists of (i) a chemical cross-linking reaction: intact cell labeling with a novel class of chemical cross-linkers, protein interaction reporters (PIRs); (ii) two-stage mass spectrometric analysis: stage 1 identification of PIR-labeled proteins and construction of a restricted database by two-dimensional LC/MSMS and stage 2 analysis of PIR-labeled peptides by multiplexed LC/FTICR-MS; and (iii) data analysis: identification of cross-linked peptides and proteins of origin using accurate mass and other constraints. The primary advantage of the PIR approach and distinction from current technology is that protein interactions together with topologies are detected in native biological systems by stabilizing protein complexes with new covalent bonds while the proteins are present in the original cellular environment. Thus, weak or transient interactions or interactions that require properly folded, localized, or membrane-bound proteins can be labeled and identified through the PIR approach. This strategy was applied to Shewanella oneidensis bacterial cells, and initial studies resulted in identification of a set of protein-protein interactions and their contact/binding regions. Furthermore most identified interactions involved membrane proteins, suggesting that the PIR approach is particularly suited for studies of membrane protein-protein interactions, an area under-represented with current widely used approaches.
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