PXD054249

PXD054249 is an original dataset announced via ProteomeXchange.

Title	SMAP3-ID for identification of protein-protein interactions in native cells
Description	Proteins regulate biological functions through formation of distinct protein complexes. Identification and characterization of these protein-protein interactions are critical to decipher their mechanism of action. Different antibody- or crosslinking-based methods have been developed to identify the protein-protein interactions. However, these methods require genetic engineering and/or other means to disrupt the native environments. To circumvent this limitation, we introduce here SMAP3-ID (Small Molecule Assisted identification of Protein-Protein interactions through Proximity) method to identify protein-protein interactions in native cells. This method entails a selective ligand for binding to a protein of interest for photocrosslinking, a live-cell compatible bioorthogonal click reaction with a trifunctional chemical probe and a final photocrosslinking reaction to covalently capture the interacting proteins. Using SMAP3-ID method and nuclear lamin as an example, we identified lamin-interactors in native cells. Significantly, we identified a number of mitochondrial enzymes as novel lamin A (LA)-interactors. The interactions between mitochondrial enzymes and LA were further validated, which provides mechanistic insights underlying the metabolic alterations caused by mutations in LA. We conclude that SMAP3-ID is a powerful and generalizable method to identify protein-protein interactions in the native cellular environment.
HostingRepository	PRIDE
AnnounceDate	2025-05-25
AnnouncementXML	Submission_2025-05-25_08:48:22.892.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Phillip Wilmarth
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-25 15:22:28	ID requested
⏵ 1	2025-05-25 08:48:23	announced

10.1021/jacsau.4c00988;

Warren J, Wang J, Dhoro F, Chao B, Reddy A, Petrie SK, David LL, Xiao X, Li BX, SMAP3-ID for Identification of Endogenous Protein-Protein Interactions Reveals Regulation of Mitochondrial Activity by Lamins. JACS Au, 5(1):302-319(2025) [pubmed]

submitter keyword: lamin, SMAP3-ID, protein-protein interaction, LBL1-PCF, native

Dr. Xiangshu Xiao
contact affiliation	Department of Chemical Physiology and Biochemistry Oregon Health & Science University Portland, OR, USA.
contact email	xiaoxi@ohsu.edu
lab head
Phillip Wilmarth
contact affiliation	OHSU
contact email	wilmarth@ohsu.edu
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/2025/05/PXD054249

PRIDE project URI

• PRIDE
  1. PXD054249
     1. Label: PRIDE project
     2. Name: SMAP3-ID for identification of protein-protein interactions in native cells