PXD004964

PXD004964 is an original dataset announced via ProteomeXchange.

Title	MHC Peptidomics: HLA-B*27 vs Mamu-B*08
Description	Indian rhesus macaques are arguably the most reliable animal models in AIDS research. In this species the MHC class I allele Mamu-B*08, among others, is associated with elite control of SIV replication. A similar scenario is observed in humans where the expression of HLA-B*27 or HLA-B*57 has been linked to slow or no progression to AIDS after HIV infection. Despite having large differences in their primary structure, it has been reported that HLA-B*27 and Mamu-B*08 display peptides with sequence similarity. To fine-map the Mamu-B*08 binding motif and assess its similarities with that of HLA-B*27 we affinity purified the peptidomes bound to these MHC class I molecules and analyzed them by LC-MS/MS identifying several thousands of endogenous ligands. Sequence analysis of both sets of peptides revealed a degree of similarity in their binding motifs, especially at peptide position 2 (P2) where arginine was present in the vast majority of ligands of both allotypes. In addition, several differences emerged from this analysis: (i) ligands displayed by Mamu-B*08 tended to be shorter and to have lower molecular weight, (ii) Mamu-B*08 showed a higher preference for glutamine at P2 as a suboptimal binding motif and (iii) the second major anchor position, found at P-omega, was much more restrictive in Mamu-B*08. In this regard, HLA-B*27 bound efficiently peptides with aliphatic, aromatic (including tyrosine) and basic C-terminal residues while Mamu-B*08 preferred peptides with leucine and phenylalanine in this position. These results deepen our understanding of the molecular basis of the presentation of peptides by Mamu-B*08 and can contribute to the detection of novel SIV epitopes restricted by this allotype.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_01:53:02.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miguel Marcilla
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2016-09-14 01:59:58	ID requested
1	2016-10-07 01:43:23	announced
2	2017-06-06 00:30:40	announced	Updated project metadata.
⏵ 3	2017-10-24 01:53:03	announced	Updated project metadata.

Marcilla M, Alvarez I, Ramos-Fern, á, ndez A, Lombard, í, a M, Paradela A, Albar JP, Comparative Analysis of the Endogenous Peptidomes Displayed by HLA-B*27 and Mamu-B*08: Two MHC Class I Alleles Associated with Elite Control of HIV/SIV Infection. J Proteome Res, 15(3):1059-69(2016) [pubmed]

ProteomeXchange project tag: Human Immuno-Peptidome Project (HUPO-HIPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

curator keyword: Biological, Biomedical

submitter keyword: Peptidomics, Peptides, LC-MS/MS, MHC, HLA-B*27, Mamu-B*08, HIV, SIV

Alberto Paradela
contact affiliation	Proteomics Unit. Spanish National Biotechnology Centre (CNB-CSC). Madrid. Spain.
contact email	alberto.paradela@cnb.csic.es
lab head
Miguel Marcilla
contact affiliation	Proteomics Unit - Dpt. of Macromolecular Structures - Spanish National Biotechnolgy Centre (CNB-CSIC)
contact email	mmarcilla@cnb.csic.es
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/2016/10/PXD004964

PRIDE project URI

• PRIDE
  1. PXD004964
     1. Label: PRIDE project
     2. Name: MHC Peptidomics: HLA-B*27 vs Mamu-B*08