PXD025140

PXD025140 is an original dataset announced via ProteomeXchange.

Title	Labeling preferences of diazirines with protein biomolecules
Description	Diazirines 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.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:52:23.346.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christina Woo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; deaminated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-01 02:26:32	ID requested
1	2022-07-20 07:20:52	announced
⏵ 2	2023-11-14 08:52:23	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: SKNSH cells, diazirine, photoaffinity labeling,Proteomics, binding sites

Christina M. Woo
contact affiliation	Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
contact email	cwoo@chemistry.harvard.edu
lab head
Christina Woo
contact affiliation	Harvard University
contact email	cwoo@chemistry.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD025140
     1. Label: PRIDE project
     2. Name: Labeling preferences of diazirines with protein biomolecules