Journal article
A combined prediction strategy increases identification of peptides bound with high affinity and stability to porcine MHC class I molecules SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01
National Veterinary Institute, Technical University of Denmark1
University of Copenhagen2
Immunological Bioinformatics, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark3
Department of Systems Biology, Technical University of Denmark4
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark5
Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark6
Affinity and stability of peptides bound by major histocompatibility complex (MHC) class I molecules are important factors in presentation of peptides to cytotoxic T lymphocytes (CTLs). In silico prediction methods of peptide-MHC binding followed by experimental analysis of peptide-MHC interactions constitute an attractive protocol to select target peptides from the vast pool of viral proteome peptides.
We have earlier reported the peptide binding motif of the porcine MHC-I molecules SLA-1*04:01 and SLA-2*04:01, identified by an ELISA affinity-based positional scanning combinatorial peptide library (PSCPL) approach. Here, we report the peptide binding motif of SLA-3*04:01 and combine two prediction methods and analysis of both peptide binding affinity and stability of peptide-MHC complexes to improve rational peptide selection.
Using a peptide prediction strategy combining PSCPL binding matrices and in silico prediction algorithms (NetMHCpan), peptide ligands from a repository of 8900 peptides were predicted for binding to SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01 and validated by affinity and stability assays. From the pool of predicted peptides for SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01, a total of 71, 28, and 38 % were binders with affinities below 500 nM, respectively.
Comparison of peptide-SLA binding affinity and complex stability showed that peptides of high affinity generally, but not always, produce complexes of high stability. In conclusion, we demonstrate how state-of-the-art prediction and in vitro immunology tools in combination can be used for accurate selection of peptides for MHC class I binding, hence providing an expansion of the field of peptide-MHC analysis also to include pigs as a livestock experimental model.
Language: | English |
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Publisher: | Springer Berlin Heidelberg |
Year: | 2016 |
Pages: | 157-165 |
ISSN: | 14321211 and 00937711 |
Types: | Journal article |
DOI: | 10.1007/s00251-015-0883-9 |
ORCIDs: | Nielsen, Morten , Jungersen, Gregers and 0000-0001-8363-1999 |
Alleles Allergology Amino Acid Motifs Animals Biomedicine Cell Biology Epitope Mapping Epitopes, T-Lymphocyte Gene Function Histocompatibility Antigens Class I Human Genetics Humans Peptide Library Peptides Position-Specific Scoring Matrices Protein Binding Protein Stability Recombinant Proteins SC3 beta 2-Microglobulin