Journal article
Uncovering the Peptide-Binding Specificities of HLA-C: A General Strategy To Determine the Specificity of Any MHC Class I Molecule
University of Copenhagen1
Institut national de la santé et de la recherche médicale2
Department of Systems Biology, Technical University of Denmark3
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark4
Immunological Bioinformatics, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark5
MHC class I molecules (HLA-I in humans) present peptides derived from endogenous proteins to CTLs. Whereas the peptide-binding specificities of HLA-A and -B molecules have been studied extensively, little is known about HLA-C specificities. Combining a positional scanning combinatorial peptide library approach with a peptide-HLA-I dissociation assay, in this study we present a general strategy to determine the peptide-binding specificity of any MHC class I molecule.
We applied this novel strategy to 17 of the most common HLA-C molecules, and for 16 of these we successfully generated matrices representing their peptide-binding motifs. The motifs prominently shared a conserved C-terminal primary anchor with hydrophobic amino acid residues, as well as one or more diverse primary and auxiliary anchors at P1, P2, P3, and/or P7.
Matrices were used to generate a large panel of HLA-C-specific peptide-binding data and update our pan-specific NetMHCpan predictor, whose predictive performance was considerably improved with respect to peptide binding to HLA-C. The updated predictor was used to assess the specificities of HLA-C molecules, which were found to cover a more limited sequence space than HLA-A and -B molecules.
Assessing the functional significance of these new tools, HLA-C*07:01 transgenic mice were immunized with stable HLA-C*07:01 binders; six of six tested stable peptide binders were immunogenic. Finally, we generated HLA-C tetramers and labeled human CD8(+) T cells and NK cells. These new resources should support future research on the biology of HLA-C molecules.
The data are deposited at the Immune Epitope Database, and the updated NetMHCpan predictor is available at the Center for Biological Sequence Analysis and the Immune Epitope Database.
Language: | English |
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Publisher: | AAI |
Year: | 2014 |
Pages: | 4790-4802 |
ISSN: | 15506606 and 00221767 |
Types: | Journal article |
DOI: | 10.4049/jimmunol.1401689 |
ORCIDs: | 0000-0001-8363-1999 and Nielsen, Morten |
Alleles Amino Acid Sequence Animals CD8-Positive T-Lymphocytes Computational Biology Databases, Factual Epitopes Gene Expression HLA-A Antigens HLA-B Antigens HLA-C Antigens Humans Iodine Radioisotopes Killer Cells, Natural Mice Mice, Transgenic Molecular Sequence Data Multigene Family Peptide Library Protein Binding Protein Multimerization Recombinant Proteins