PXD053500

PXD053500 is an original dataset announced via ProteomeXchange.

Title	Kinetic principles of chemical cross-link formation for protein-protein interactions
Description	Proteins play a central role in most biological processes within the cell and deciphering how they interact is key to understand their function. Cross-linking coupled to mass spectrometry is an essential tool for elucidating protein-protein interactions. Despite its importance, we still know surprisingly little about the principles that underlie the process of chemical cross-link formation itself and how it is influenced by different physicochemical factors. To understand the molecular details of cross-link formation, we have set-up a comprehensive kinetic model and carried out simulations of protein cross-linking on large protein complexes. We dissect the contribution on the cross-link yield of parameters such as amino acid reactivity, cross-linker concentration, and hydrolysis rate. Our model can compute cross-link formation based solely on the structure of a protein complex, thereby enabling realistic predictions for a diverse set of systems. We quantitatively show how cross-links and mono-links are in direct competition and how the hydrolysis rate and abundance of cross-linker and proteins directly influence their relative formation. We show how cross-links and mono-links exist in a “all-against-all” competition due to their simultaneous formation, resulting in a non-intuitive network of interdependence. We show that this interdependence is locally confined and mainly limited to direct neighbors or residues in direct vicinity. These results enable us to identify the optimal cross-linker concentration at which the maximal number of cross-links are formed. Taken together, our study establishes a comprehensive kinetic model to quantitatively describe cross-link formation for protein-protein interactions.
HostingRepository	PRIDE
AnnounceDate	2024-10-11
AnnouncementXML	Submission_2024-10-11_05:08:09.787.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Florian Stengel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-28 12:42:58	ID requested
⏵ 1	2024-10-11 05:08:10	announced

Dataset with its publication pending

submitter keyword: human S26 proteasome,Crosslinking mass spectrometry

Florian Stengel
contact affiliation	Prof. Dr. Florian Stengel University of Konstanz Department of Biology Universitätsstrasse 10, Box 642 78457 Konstanz (Germany)
contact email	florian.stengel@uni-konstanz.de
lab head
Florian Stengel
contact affiliation	Universität Konstanz
contact email	florian.stengel@uni-konstanz.de
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/2024/10/PXD053500

PRIDE project URI

• PRIDE
  1. PXD053500
     1. Label: PRIDE project
     2. Name: Kinetic principles of chemical cross-link formation for protein-protein interactions