PXD048452-1

PXD048452 is an original dataset announced via ProteomeXchange.

Title	Deciphering Diazirine Reaction Mechanism: through Irradiation Modulation for Residue-Specific Distance Restraints in Protein Photo-Crosslinking
Description	The diazirine photoreactive group has been widely used for photo-labeling and photo-cross-linking (PXL) of proteins. Yet, due to the mechanistic complexity of diazirine photo-reaction, site-specific and quantitative analysis of protein PXL data remains challenging. Herein, we have built an in-line photo-reaction monitoring system, capable of systematically varying optical power density and irradiation time. Using this system, we have determined the kinetic parameters of diazirine photo-reactions, and shown that an alkyl diazirine undergoes rearrangement upon irradiation to yield a diazo intermediate. A carbene intermediate is produced from the diazo intermediate upon further irradiation, whereas at a relatively small proportion, it is produced directly from the diazirine. Both diazo and carbene intermediates react with protein side-chains. Significantly, the diazo intermediate preferentially reacts with polar side-chains, exhibiting much higher specificity than the carbene intermediate. As the diazo and carbene intermediates are generated sequentially, modulating irradiation time and optical power density can achieve site- or space- selective PXL results through different mechanisms. Together, we have established a new approach for the kinetic mechanism of photo-reactions, and paved the way for quantitative analysis of PXLs to visualize protein structure and dynamics.
HostingRepository	PRIDE
AnnounceDate	2024-06-22
AnnouncementXML	Submission_2024-06-22_00:54:05.565.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	yida jiang
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-11 02:49:31	ID requested
⏵ 1	2024-06-22 00:54:05	announced

Dataset with its publication pending

submitter keyword: photo cross-linking, multiple reaction monitoring, optical power density, distance restraints, alkyl diazirine

Yida Jiang,
contact affiliation	1Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China. 2Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China. 3Center for Quantitative Biology, PKU-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
contact email	Tang_Chun@pku.edu.cn
lab head
yida jiang
contact affiliation	Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
contact email	jiangyida@pku.edu.cn
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD048452

PRIDE project URI

• PRIDE
  1. PXD048452
     1. Label: PRIDE project
     2. Name: Deciphering Diazirine Reaction Mechanism: through Irradiation Modulation for Residue-Specific Distance Restraints in Protein Photo-Crosslinking