PXD080708

PXD080708 is an original dataset announced via ProteomeXchange.

Title	Programmable Bioorthogonal Crosslinking Enables Residue-Resolved Mapping of Protein Interactions-1
Description	To systematically evaluate the performance of CLIPX, a five‑part strategy was developed, encompassing the chemical characterization of the cross‑linker, genetic code expansion for site‑specific unnatural amino acid incorporation, mechanistic validation using a structurally defined model complex, latent interactome profiling of phase‑separating IDRs, and orthogonal biological validation of candidate interactions. Pros and cons of each part are discussed with respect to two key issues: programmable cross‑linking fidelity and interactome coverage. The chemical characterization established the cross‑linker’s rapid kinetics, high lysine selectivity, and excellent proteome‑wide reproducibility, providing a solid foundation for subsequent applications. Genetic code expansion enabled precise spatial control over cross‑link formation, as confirmed by biotin‑click labeling of the mutant proteins. Using a structurally defined model complex, MS/MS analysis unambiguously identified cross‑links that matched structural predictions, validating the mechanistic accuracy and residue‑level spatial resolution of the platform. When applied to multiple phase‑separating IDRs, CLIPX revealed extensive and selective interaction networks, recovering known interactions while identifying previously underappreciated candidate interactors—including shared molecular hubs across different IDR systems. Orthogonal GST pull‑down and confocal microscopy validated the biological authenticity of representative interactions, with colocalization patterns consistent with known subcellular distributions. The concordance among CLIPX proteomics, structural prediction, biochemical binding, and cellular imaging—across five independent experimental paradigms—demonstrates that CLIPX faithfully captures weak and transient interactions that are often inaccessible to conventional affinity purification methods. Collectively, these results establish CLIPX as a robust and generalizable chemical platform for decoding dynamic IDR‑mediated interactomes.
HostingRepository	iProX
AnnounceDate	2026-07-07
AnnouncementXML	Submission_2026-07-08_00:01:33.538.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Long Chen
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2026-07-07 23:57:44	ID requested
⏵ 1	2026-07-08 00:01:34	announced

Dataset with its publication pending

submitter keyword: Bioorthogonal crosslinking，Intrinsically disordered regions (IDRs)，Genetic code expansion，Phase separation

Lin Li
contact affiliation	School of Pharmaceutical Sciences, Shanghai Jiao Tong University
contact email	linli.sjtu@sjtu.edu.cn
lab head
Long Chen
contact affiliation	School of Pharmaceutical Sciences, Shanghai Jiao Tong University
contact email	longchen0720@sjtu.edu.cn
dataset submitter

iProX dataset URI