In-Culture Cross-Linking of Bacterial Cells Reveals Large-Scale Dynamic Protein-Protein Interactions at the Peptide Level.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28516784", "kind": "science-record", "revision": 4, "content_hash": "sha256:e096435b2c9b336e78bd3999cf5805f8c54c2893728dde6d561cbd0b0012c5c6", "created_at": "2026-11-01T15:40:25Z", "updated_at": "2026-11-01T21:20:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "In-Culture Cross-Linking of Bacterial Cells Reveals Large-Scale Dynamic Protein-Protein Interactions at the Peptide Level.", "doi": "10.1021/acs.jproteome.7b00068", "pmid": "28516784", "authors": ["Luitzen de Jong", "Edward A de Koning", "Winfried Roseboom", "Hansuk Buncherd", "Martin J Wanner", "Irena Dapic", "Petra J Jansen", "Jan H van Maarseveen", "Garry L Corthals", "Peter J Lewis", "Leendert W Hamoen", "Chris G de Koster"], "journal": "Journal of proteome research", "year": 2017, "abstract": "Identification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram-positive model bacterium Bacillus subtilis as an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species, Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG. We were able to identify 82 unique interprotein cross-linked peptides with <1% false discovery rate by mass spectrometry and genome-wide database searching. Nearly 60% of the interprotein cross-links occur in assemblies involved in transcription and translation. Several of these interactions are new, and we identified a binding site between the δ and β' subunit of RNA polymerase close to the downstream DNA channel, providing a clue into how δ might regulate promoter selectivity and promote RNA polymerase recycling. Our methodology opens new avenues to investigate the functional dynamic organization of complex protein assemblies involved in bacterial growth. Data are available via ProteomeXchange with identifier PXD006287.", "claims": [{"id": "claim-method", "statement": "Validation and FDR determination is facilitated by a software tool called Yeun Yan. Importantly, no decoy peptides fulfilled these criteria, indicating a low FDR.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28516784", "locator": "sections[22] \"Cross-Link Mapping and Validation\" paragraph 2", "quote": "Validation and FDR determination is facilitated by a software tool called Yeun Yan."}, {"asset": "source:pmid:28516784", "locator": "sections[29] \"Mass Spectrometric Analysis Reveals a Large Number of Cross-Linked Peptides at a Low False Discovery Rate\" paragraph 4", "quote": "Importantly, no decoy peptides fulfilled these criteria, indicating a low FDR."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD006287.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28516784", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD006287."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:28516784"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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