PXD030038

PXD030038 is an original dataset announced via ProteomeXchange.

Title	Engineering human SH2 domains for targeted phospho-proteomics
Description	A comprehensive analysis of the phosphoproteome is essential for understanding molecular mechanisms of human diseases. However, current tools to enrich phosphotyrosine are limited in their applicability and scope. Here, we engineered new superbinder SH2 domains that enrich diverse sets of phosphotyrosine peptides. We used phage display to select a Fes SH2 domain variant with high affinity for phosphotyrosine (superFes-SH2, sFes1) and solved the structure of sFes1 bound to a phosphopeptide. We performed systematic structure-function analyses of the superbinding mechanisms of sFes1 and superSrc-SH2 (sSrc1), another SH2-superbinder. We grafted the superbinder motifs from sFes1 and sSrc1 into 17 additional SH2 domains and confirmed increased binding affinity for specific phosphopeptides. Using mass spectrometry, we demonstrated that SH2 superbinders have distinct specificity profiles and superior capabilities to enrich phosphotyrosine peptides. Finally, combinations of SH2 superbinders as affinity purification tools showed that unique subsets of phosphopeptides can be enriched with unparalleled depth and coverage.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:30:36.724.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ulrike Kusebauch
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	oxygenated residue; phosphorylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-29 03:13:55	ID requested
1	2023-01-13 19:02:16	announced
⏵ 2	2023-11-14 08:30:40	announced	2023-11-14: Updated project metadata.

Martyn GD, Veggiani G, Kusebauch U, Morrone SR, Yates BP, Singer AU, Tong J, Manczyk N, Gish G, Sun Z, Kurinov I, Sicheri F, Moran MF, Moritz RL, Sidhu SS, Engineered SH2 Domains for Targeted Phosphoproteomics. ACS Chem Biol, 17(6):1472-1484(2022) [pubmed]

submitter keyword: phosphoproteomics, synthetic biology, K562, Src Homology 2 Domains, SH2 superbinders, mass spectrometry, human, structural biology, protein engineering, phosphotyrosine

Robert L. Moritz
contact affiliation	Institute for Systems Biology, Seattle, WA, USA
contact email	rmoritz@systemsbiology.org
lab head
Ulrike Kusebauch
contact affiliation	Institute for Systems Biology, Seattle, WA, USA
contact email	ukusebauch@systemsbiology.org
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/2023/01/PXD030038

PRIDE project URI

• PRIDE
  1. PXD030038
     1. Label: PRIDE project
     2. Name: Engineering human SH2 domains for targeted phospho-proteomics