PXD051865-1

PXD051865 is an original dataset announced via ProteomeXchange.

Title	Molecular details of ligand binding to the intrinsically disordered N terminus of the neuropeptide Y receptor
Description	Neuropeptide Y (NPY) receptors comprise a family of rhodopsin-like G-protein coupled receptors (GPCRs) that participate in controlling food intake, memory retention, and circadian rhythm, making them highly attractive drug targets. However, the multiligand nature of NPY receptors, such as the NPY receptor type 2 (Y2R), requires a detailed understanding of the receptor’s interactions with their natural ligands. Binding assays have so far provided insights into multiple Y2R-NPY conformers with distinct binding affinities that might also be controlled by intracellular Y2R-Gi protein-protein interactions. However, structural biology approaches, such as X-ray crystallography or cryo-electron microscopy, have so far not been able to capture these Y2R-NPY conformers, nor have they been able to resolve the conformational states of Y2R’s N-terminus. The N-terminus of Y2R has been classified as intrinsically disordered region. Cross-linking mass spectrometry (XL-MS) was employed to characterize the different conformational states and binding modes of Y2R upon binding of its ligand NPY. Cross-linked peptide digests were analyzed on a timsTOF Pro instrument using Parallel Signal Accumulation and Fragmentation operated in data dependent acquisition (DDA) and data independent acquisition (DIA) modes. The combined effects of precursor ion accumulation in the TIMS cell, fragment ion current accumulation through fragmentation events stacking, and the additional ion mobility dimension of peptide separation by DDA-PASEF provided better fragment ion spectral evidence of low-intensity cross-linked peptides. At the same time, spectra generated by co-isolation of high-abundant unmodified peptides were minimized. The comprehensive evaluation of each cross-linked peptide’s chromatographic and ion mobility properties in Skyline, in addition to fragment ion spectra, greatly improved the confidence of filtered peptide identifications. For the Y2R-NPY interaction, multiple cross-linking sites were identified between Y2R and NPY, involving the disordered N-terminal region of Y2R. The coexistence of different cross-linking sites between Y2R’s N-terminus and different amino acids in NPY point to multiple conformational states of Y2R’s N-terminus. Our results provide first insights into the interactions of NPY with Y2R at a molecular level.
HostingRepository	PanoramaPublic
AnnounceDate	2025-08-25
AnnouncementXML	Submission_2025-08-25_13:15:47.691.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	supported by repository but incomplete data and/or metadata
PrimarySubmitter	Juan Camilo Rojas Echeverri
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Sus scrofa; NCBI TaxID: 9823;
ModificationList	Oxidation
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-29 17:11:41	ID requested
⏵ 1	2025-08-25 13:15:48	announced

no publication

submitter keyword: Cross-linking mass spectrometry, timsTOF, PASEF, GPCR

Andrea Sinz
contact affiliation	Department of Pharmaceutical Chemistry & Bioanalytics and Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg
contact email	andrea.sinz@pharmazie.uni-halle.de
lab head
Juan Camilo Rojas Echeverri
contact affiliation	Research Assistant
contact email	juank1892@gmail.com
dataset submitter

Panorama Public dataset URI