PXD035521

PXD035521 is an original dataset announced via ProteomeXchange.

Title	Protein complexes in cells by AI-assisted structural proteomics (Proteomics)
Description	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.
HostingRepository	jPOST
AnnounceDate	2023-02-16
AnnouncementXML	Submission_2023-08-29_14:45:52.618.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Forbrig
SpeciesList	scientific name: Bacillus subtilis subsp. subtilis str. 168; NCBI TaxID: 224308;
ModificationList	unknown modification; L-methionine sulfoxide; alpha-amino acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-22 16:37:57	ID requested
1	2023-02-16 01:57:49	announced
⏵ 2	2023-08-29 14:45:53	announced	2023-08-30: Updated PubMed.

O'Reilly FJ, Graziadei A, Forbrig C, Bremenkamp R, Charles K, Lenz S, Elfmann C, Fischer L, St, ü, lke J, Rappsilber J, Protein complexes in cells by AI-assisted structural proteomics. Mol Syst Biol, 19(4):e11544(2023) [pubmed]

submitter keyword: Bacillus subtilis, Label-free-quantifiction, protein-protein interaction

Juri Rappsilber
lab head
Christian Forbrig
contact affiliation	Technische Universität Berlin, Institute of Biotechnology, Bioanalytics, 13355 Berlin, Germany
dataset submitter

jPOST dataset URI

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