ArticleMolecular systems biology2023
Protein complexes in cells by AI-assisted structural proteomics.
Article in Molecular systems biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers, 2 of them syntheses that pooled it.
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.
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Who cites it
89 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Progress and trends on machine learning in proteomics during 1997-2024: a bibliometric analysis.Frontiers in medicine · 2025Pooled it
- Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry.Nature communications · 2023Pooled it
- The phenotypic landscape of the model firmicuteProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Structure and biochemistry reveal substrate-modulated ComEC nuclease activity during DNA processing.Nucleic acids research · 2026Article
- YpeB stability affects germination possibly through delaying SleB activity inJournal of bacteriology · 2026Article
- Integrative structural interactomics reveals protein organization and structure in a giant virus.Nature communications · 2026Article
- Regulation of iron ion homeostasis inmBio · 2026Review
- A cross-vertebrate brain protein interaction map identifies conserved neural and non-neural complexes.Cell reports · 2026Article
- A Bacillales-specific tubular scaffold essential for NADH dehydrogenase activity.Nature communications · 2026Article
- Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets.bioRxiv : the preprint server for biology · 2026Article
- Article
- AlphaFold-driven discovery of oxysterol-binding protein-related protein-phosphoinositide 3-, 4-, and 5-phosphatase interactions using new generation confidence scores.Protein science : a publication of the Protein Society · 2026Article
- Deciphering Membrane Protein Complexes in Plasmodium falciparum Gametocytes via Integrative Structural Systems Biology.Molecular & cellular proteomics : MCP · 2026Article
- Predicting the protein interaction landscape of a free-living bacterium with pooled-AlphaFold3.Molecular systems biology · 2026Article
- Shedding light on YfhS and YjlC: novel effectors of the NADH dehydrogenase activity of the electron transport chain inbioRxiv : the preprint server for biology · 2026Article
- Plant structural biology: Emerging technologies and future biological insights.The Plant journal : for cell and molecular biology · 2026Review
- Confidence scoring for deep learning-predicted antibody-antigen complexes: AntiConf as a precision-driven metric.Briefings in bioinformatics · 2026Article
- Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells.Molecular systems biology · 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
- Regulation of AP1 adaptor assembly by the bi-handed chaperone MEA1.Nature communications · 2026Article
29 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
Accurately modeling the structures of proteins and their complexes using artificial intelligence is revolutionizing molecular biology. Experimental data enable a candidate-based approach to systematically model novel protein assemblies. Here, we use a combination of in-cell crosslinking mass spectrometry and co-fractionation mass spectrometry (CoFrac-MS) to identify protein-protein interactions in the model Gram-positive bacterium Bacillus subtilis. We show that crosslinking interactions prior to cell lysis reveals protein interactions that are often lost upon cell lysis. We predict the structures of these protein interactions and others in the SubtiWiki database with AlphaFold-Multimer and, after controlling for the false-positive rate of the predictions, we propose novel structural models of 153 dimeric and 14 trimeric protein assemblies. Crosslinking MS data independently validates the AlphaFold predictions and scoring. We report and validate novel interactors of central cellular machineries that include the ribosome, RNA polymerase, and pyruvate dehydrogenase, assigning function to several uncharacterized proteins. Our approach uncovers protein-protein interactions inside intact cells, provides structural insight into their interaction interfaces, and is applicable to genetically intractable organisms, including pathogenic bacteria.
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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 Socratic graph.