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PXD039583 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleGlycosite mapping and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE
DescriptionMucin-domain glycoproteins are densely O-glycosylated and play key roles in a host of biological functions. In particular, the T-cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, 3, 4) decorate immune cells and act as key checkpoint inhibitors in cancer. However, their dense O-glycosylation remains enigmatic both in glycoproteomic landscape and structural dynamics, primarily due to the challenges associated with studying mucin domains. Here, we present a mucinase (SmE) and demonstrate its ability to selectively cleave along the mucin glycoprotein backbone, similar to others of its kind. Unlike other mucinases, though, SmE harbors the unique ability to cleave at residues bearing extremely complex glycans, which enabled improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we performed molecular dynamic (MD) simulations of TIM-3 and 4 to demonstrate how glycosylation affects structural features of these proteins. Overall, we present a powerful workflow to better understand the detailed molecular structures of the mucinome.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAlexandra Steigmeyer
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; O-glycosylated residue; deamidated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Eclipse
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-01-20 03:33:18ID requested
12023-09-27 12:35:03announced
22023-11-14 08:28:29announced2023-11-14: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: O-glycoprotein, TIM-1, cancer, mucinase, TIM-4, TIM-3, O-glycosylation, immune checkpoint, T-cell immunoglobulin and mucin-domain containing, LC-MS/MS, molecular dynamics, mucinome,mucin, O-glycoproteomics, mucin domain, checkpoint inhibitor, O-glycoprotease
Contact List
Stacy A. Malaker
contact affiliationDepartment of Chemistry, Yale University, New Haven, CT 06511, USA
contact emailstacy.malaker@yale.edu
lab head
Alexandra Steigmeyer
contact affiliationYale University, Department of Chemistry
contact emailalexandra.steigmeyer@yale.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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