Peptide‐MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity

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Abstract
Efficient presentation of peptide‐MHC class I (pMHC‐I) complexes to immune T cells should benefit from a stable peptide‐MHC‐I interaction. However, it has been difficult to distinguish stability from other requirements for MHC‐I binding, for example, affinity. We have recently established a high‐throughput assay for pMHC‐I stability. Here, we have generated a large database containing stability measurements of pMHC‐I complexes, and re‐examined a previously reported unbiased analysis of the relative contributions of antigen processing and presentation in defining cytotoxic T lymphocyte (CTL) immunogenicity [Assarsson et al., J. Immunol. 2007. 178: 7890–7901]. Using an affinity‐balanced approach, we demonstrated that immunogenic peptides tend to be more stably bound to MHC‐I molecules compared with nonimmunogenic peptides. We also developed a bioinformatics method to predict pMHC‐I stability, which suggested that 30% of the nonimmunogenic binders hitherto classified as “holes in the T‐cell repertoire” can be explained as being unstably bound to MHC‐I. Finally, we suggest that nonoptimal anchor residues in position 2 of the peptide are particularly prone to cause unstable interactions with MHC‐I. We conclude that the availability of accurate predictors of pMHC‐I stability might be helpful in the elucidation of MHC‐I restricted antigen presentation, and might be instrumental in future search strategies for MHC‐I epitopes.