PXD027743

PXD027743 is an original dataset announced via ProteomeXchange.

Title	Quantitative fragmentomics to map affinities of interactomes
Description	~500,000 protein interactions have been identified in human but most binding affinities remain unknown, limiting quantitative investigation of interactome-function relationships. This gap can be filled by systematically measuring the affinities of minimal interacting protein fragments, the building blocks of interactomes. As a proof of principle, we experimentally measured 65,000 affinities involving 266 human PDZ domains (practically the complete "PDZome"), 424 human PDZ-Binding Motifs (~10% of the "PBMome") and 24 viral motifs. We determined binding constants for ~18,000 interactions that passed the detection threshold. Independent AP-MS experiments and database surveys demonstrated the strong agreement of quantitative fragmentomics with full-length protein interactomics. We evidence hot spots for viral interference, which allow a viral PBM, such as that of HPV-E6 oncoprotein, to impact the cell proteome way beyond its immediate binders. We propose to distinguish interactomes and complexomes, viewed as intrinsic and extrinsic properties linked by the law of mass action.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:32:04.220.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Luc Negroni
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-05 09:59:53	ID requested
1	2022-10-14 09:18:20	announced
⏵ 2	2023-11-14 08:32:05	announced	2023-11-14: Updated project metadata.

Gogl G, Zambo B, Kostmann C, Cousido-Siah A, Morlet B, Durbesson F, Negroni L, Eberling P, Jan, é P, Nomin, é Y, Zeke A, Ø, stergaard S, Monsellier É, Vincentelli R, Trav, é G, Quantitative fragmentomics allow affinity mapping of interactomes. Nat Commun, 13(1):5472(2022) [pubmed]

submitter keyword: complexome,PDZ, domain-motif interaction, interactome

Gergo Gogl
contact affiliation	Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch CEDEX, France
contact email	goglg@igbmc.fr
lab head
Luc Negroni
contact affiliation	CNRS
contact email	luc.negroni@igbmc.fr
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/2022/10/PXD027743

PRIDE project URI

• PRIDE
  1. PXD027743
     1. Label: PRIDE project
     2. Name: Quantitative fragmentomics to map affinities of interactomes