ArticleeLife2016
Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states.
Article in eLife, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
61 citing papers in PubMed, 139 citations in OpenAlex.
- To cleave or not to cleave: a systemic evaluation of DSS versus DSSO for cross-linking mass spectrometry analysis.Molecular systems biology · 2026Article
- Hierarchical Contrastive Learning for Protein-Protein Interaction Prediction Across Organisms.International journal of molecular sciences · 2026Article
- The multidimensional significance of virus-host protein interactions and their implications in the antiviral defense of plants.Stress biology · 2026Review
- Intrinsic N-Terminal Reactivity and Improved Analysis of DSSO-Carbamate and Carbamate-Based Cross-Linkers.Analytical chemistry · 2026Article
- Optimized In-Solution and Gas-Phase Chemistry Enables High-Efficiency Interactome Mapping by DSBSO-Based Cross-Linking Mass Spectrometry.Angewandte Chemie (International ed. in English) · 2026Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- A practical guide to sample preparation for immunoprecipitation coupled with mass spectrometry analysis ofmicroPublication biology · 2026Article
- Enrichable cross-linkers for mapping direct protein interactions.Genome biology · 2025Article
- Developing a new cleavable crosslinker reagent for in-cell crosslinking.Communications chemistry · 2025Article
- Analysis ofComputational and structural biotechnology journal · 2024Article
- Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells.Nature communications · 2024Article
- Characterize direct protein interactions with enrichable, cleavable and latent bioreactive unnatural amino acids.Nature communications · 2024Article
- Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology.JACS Au · 2024Review
- Higher-Order Structural Organization of the Mitochondrial Proteome Charted by In Situ Cross-Linking Mass Spectrometry.Molecular & cellular proteomics : MCP · 2023Article
- Cross-linking mass spectrometry for mapping protein complex topologies in situ.Essays in biochemistry · 2023Article
- In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.Chemical reviews · 2022Review
- Two-Dimensional Fractionation Method for Proteome-Wide Cross-Linking Mass Spectrometry Analysis.Analytical chemistry · 2022Article
- Developing a Targeted Quantitative Strategy for Sulfoxide-Containing MS-Cleavable Cross-Linked Peptides to Probe Conformational Dynamics of Protein Complexes.Analytical chemistry · 2022Article
- Enhanced protein-protein interaction network construction promoted byFrontiers in chemistry · 2022Article
- 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
1 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
21 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To improve chemical cross-linking of proteins coupled with mass spectrometry (CXMS), we developed a lysine-targeted enrichable cross-linker containing a biotin tag for affinity purification, a chemical cleavage site to separate cross-linked peptides away from biotin after enrichment, and a spacer arm that can be labeled with stable isotopes for quantitation. By locating the flexible proteins on the surface of 70S ribosome, we show that this trifunctional cross-linker is effective at attaining structural information not easily attainable by crystallography and electron microscopy. From a crude Rrp46 immunoprecipitate, it helped identify two direct binding partners of Rrp46 and 15 protein-protein interactions (PPIs) among the co-immunoprecipitated exosome subunits. Applying it to E. coli and C. elegans lysates, we identified 3130 and 893 inter-linked lysine pairs, representing 677 and 121 PPIs. Using a quantitative CXMS workflow we demonstrate that it can reveal changes in the reactivity of lysine residues due to protein-nucleic acid interaction.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.