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PXD025140-1

PXD025140 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleLabeling preferences of diazirines with protein biomolecules
DescriptionDiazirines are widely used in photoaffinity labeling (PAL) to trap non-covalent interactions with biomolecules. However, design and interpretation of PAL experiments is challenging without a molecular understanding of the reactivity of diazirines with protein biomolecules. Here, we report a systematic evaluation of the labeling preferences of alkyl and aryl diazirines with individual amino acids, single proteins, and in the whole cell proteome. We find that alkyl diazirines exhibit preferential labeling of acidic amino acids in a pH-dependent manner that is characteristic of a reactive alkyl diazo intermediate, while aryl-fluorodiazirines labeling patterns reflect reaction primarily through a carbene intermediate. From a survey of 32 alkyl diazirine probes, we use this reactivity profile to rationalize why alkyl diazirine probes preferentially enrich highly acidic proteins or those embedded in membranes and why probes with a net positive-charge tend to produce higher labeling yields in cells and in vitro. These results indicate that alkyl diazirines are an especially effective chemistry for surveying the membrane proteome, and will facilitate design and interpretation of biomolecular labeling experiments with diazirines.
HostingRepositoryPRIDE
AnnounceDate2022-07-20
AnnouncementXMLSubmission_2022-07-20_07:20:51.679.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterChristina Woo
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; deaminated residue; deamidated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-04-01 02:26:32ID requested
12022-07-20 07:20:52announced
22023-11-14 08:52:23announced2023-11-14: Updated project metadata.
Publication List
10.1021/JACS.1C02509;
Keyword List
submitter keyword: Proteomics, SKNSH cells, diazirine, photoaffinity labeling, binding sites
Contact List
Christina M. Woo
contact affiliationDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
contact emailcwoo@chemistry.harvard.edu
lab head
Christina Woo
contact affiliationHarvard University
contact emailcwoo@chemistry.harvard.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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