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

Abstract

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, 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 PΩ, 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. Finally, in silico estimations of binding efficiency and competitive binding assays to Mamu-B*08 of several selected peptides revealed a good correlation between the characterized anchor motif and binding affinity. 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.

Human Leukocyte Antigen (HLA)-DRB1*15:01 and HLA-DRB5*01:01 Present Complementary Peptide Repertoires

“…All the peptides associated with DR2a or DR2b were analyzed with NetMHCIIpan 3.1 Software ( 27 ) to predict the binding core of each peptide. After the elimination of the redundant cores in nested sets, the remaining 9-mer cores were analyzed as previously described ( 28 , 29 ). Preferences in residue usage were determined by comparing the observed frequency of each amino acid at each peptide position (fobs) with the frequency of the same amino acid in the database (fexp), named as deviation from mean in proteome (DMP) using a binomial test with Bonferroni’s correction.…”

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

“…Identification-Peptide identification was carried out as previously described (18). Raw MS/MS data were converted to mgf files with Peakview 1.…”

Identification of Functional mimotopes of human Vasorin Ectodomain by Biopanning

“…VASN(C432-C441) located in the epidermal growth factor (EGF)-like domain, and Cys 432 and Cys 441 formed a disulfide bond. Interestingly, the peptide SLTLPPFTGLAG, named V21P1, also has some similarity with SLTLGIEPVSPTS, the residues 463-475 of VASN, which was identified as a B-cell epitope by mass spectrometry combined with a multiengine search approach 25 . Furthermore, competitive ELISA was carried out to assess the specificity of binding between the positive phage clones and the antibodies.…”