PXD046825

PXD046825 is an original dataset announced via ProteomeXchange.

Title	Mass spectrometric profiling of HLA-B44 peptidomes provides evidence for tapasin-mediated tryptophan editing
Description	The extreme polymorphisms of human leukocyte antigen (HLA) class I proteins result in structural variations in their peptide binding sites to achieve diversity in antigen presentation. External factors could independently constrict or alter HLA class I peptide repertoires. Such effects of the assembly factor tapasin were assessed for HLA-B*44:05 (Y116) and a close variant, HLA-B*44:02 (D116), which have low and high tapasin dependence, respectively, for their cell surface expression. Analyses of the HLA-B*44:05 peptidomes in the presence and absence of tapasin reveal that peptides with C-terminal tryptophans and higher predicted affinities are preferentially selected by tapasin, coincident with reduced frequencies of peptides with other C-terminal amino acids, including leucine. Comparisons of the HLA-B*44:05 and HLA-B*44:02 peptidomes indicate the expected structure-based alterations near the peptide C-termini, but also C-terminal amino acid frequency and predicted affinity changes among the unique and shared peptide groups for B*44:02 and B*44:05. Overall, these findings indicate that the presence of tapasin and the tapasin-dependence of assembly alter HLA class I peptide binding preferences at the peptide C-terminus. The particular C-terminal amino acid preferences that are altered by tapasin are expected to be determined by the intrinsic peptide binding specificities of HLA class I allotypes. Additionally, the findings suggest that tapasin deficiency and reduced tapasin dependence expand the permissive affinities of HLA class I bound peptides, consistent with prior findings that HLA class I allotypes with low tapasin dependence have increased breadth of CD8+ T cell epitope presentation and are more protective in HIV infections.
HostingRepository	PRIDE
AnnounceDate	2024-07-15
AnnouncementXML	Submission_2024-07-15_13:42:23.819.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD046825
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Malini Raghavan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-09 13:50:01	ID requested
⏵ 1	2024-07-15 13:42:24	announced

10.4049/jimmunol.2300232;

10.6019/PXD046825;

Kaur A, Surnilla A, Zaitouna AJ, Mumphrey MB, Basrur V, Grigorova I, Cieslik M, Carrington M, Nesvizhskii AI, Raghavan M, Mass Spectrometric Profiling of HLA-B44 Peptidomes Provides Evidence for Tapasin-Mediated Tryptophan Editing. J Immunol, 211(9):1298-1307(2023) [pubmed]

submitter keyword: HLA-B*44:02, HLA-B*44:05, Tapasin, peptide binding affinity, Tryptophan, Peptide loading complex,HLA class I, Immunopeptidome, Half-life, MHC class I

MALINI RAGHAVAN
contact affiliation	Department of Microbiology and Immunology University of Michigan Medical School, Ann Arbor, MI 48109.
contact email	malinir@umich.edu
lab head
Malini Raghavan
contact affiliation	University of Michigan
contact email	malinir@umich.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD046825
     1. Label: PRIDE project
     2. Name: Mass spectrometric profiling of HLA-B44 peptidomes provides evidence for tapasin-mediated tryptophan editing