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Updated: Mar 26, 2026
Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis
Published on: October 15, 2021
Comparative Analysis of the Endogenous Peptidomes Displayed by HLA-B*27 and Mamu-B*08: Two MHC Class I Alleles
Miguel Marcilla1, Iñaki Alvarez2, Antonio Ramos-Fernández3
1Proteomics Unit, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049 Madrid, Spain.
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.
Insights
Indian rhesus macaques and humans share similarities in controlling viral replication through specific MHC class I alleles. Researchers found Mamu-B*08 and HLA-B*27 share peptide binding motifs, aiding SIV epitope discovery.
Area of Science:
- Immunology
- Virology
- Genetics
Background:
- Indian rhesus macaques are crucial animal models for AIDS research.
- MHC class I alleles like Mamu-B*08 in macaques and HLA-B*27/HLA-B*57 in humans are associated with control of SIV/HIV infection.
- Previous studies suggest sequence similarity in peptides displayed by Mamu-B*08 and HLA-B*27.
Purpose of the Study:
- To precisely map the peptide-binding motif of Mamu-B*08.
- To compare the Mamu-B*08 binding motif with that of HLA-B*27.
- To understand the molecular basis of peptide presentation by Mamu-B*08 for SIV epitope identification.
Main Methods:
- Affinity purification of peptidomes bound to Mamu-B*08 and HLA-B*27.
- Liquid chromatography-mass spectrometry (LC-MS) analysis of endogenous ligands.
- Sequence analysis of identified peptides to determine binding motifs.
- In silico binding efficiency estimation and competitive binding assays.
Main Results:
- Thousands of endogenous ligands were identified for Mamu-B*08 and HLA-B*27.
- Both allotypes showed a preference for arginine at peptide position 2 (P2).
- Mamu-B*08 displayed shorter, lower molecular weight peptides, preferred glutamine at P2, and had a more restrictive C-terminal anchor (PΩ) preference (leucine, phenylalanine) compared to HLA-B*27.
- In silico and binding assays confirmed the correlation between the characterized motif and binding affinity.
Conclusions:
- The study fine-mapped the Mamu-B*08 binding motif, revealing similarities and key differences with HLA-B*27.
- Understanding these motifs enhances knowledge of peptide presentation by Mamu-B*08.
- This research can facilitate the discovery of novel SIV epitopes restricted by the Mamu-B*08 allotype.
