Dataset Information

Protein complexes in cells by AI-assisted structural proteomics (Proteomics)

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.

ORGANISM(S): Bacillus Subtilis Subsp. Subtilis Str. 168

SUBMITTER: Juri Rappsilber

PROVIDER: PXD035521 | JPOST Repository | Thu Feb 16 00:00:00 GMT 2023

REPOSITORIES: jPOST

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Dataset's files

Source:

			Action	DRS
	B220518_08_HF_CF_IN_130_BSCL5_linear_old_rep1.raw	Raw
	B220518_09_HF_CF_IN_130_BSCL5_linear_old_rep2.raw	Raw
	B220518_10_HF_CF_IN_130_BSCL5_linear_old_rep3.raw	Raw
	Bacillus-subtilis_168.fasta.fasta	Fasta
	allSpectra.HCD.FTMS.iso_0.apl	Other

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Publications

Protein complexes in cells by AI-assisted structural proteomics.

O'Reilly Francis J FJ Graziadei Andrea A Forbrig Christian C Bremenkamp Rica R Charles Kristine K Lenz Swantje S Elfmann Christoph C Fischer Lutz L Stülke Jörg J Rappsilber Juri J

Molecular systems biology 20230223 4

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 t ...[more]

PMID: 36815589

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