Hiromichi Tsurui, Takuya Takahashi, Yuko Matsuda, Qingshun Lin, Aya Sato-Hayashizaki and Sachiko Hirose
Accurate calculations of protein–protein binding free energies based on rigorous models, which consider the binding complex structure in atomic detail, are computationally expensive and impracticable to apply to T cell repertoire formation that occurs in the thymus because this process involves the interactions among numerous combinations of T cell receptors (TCRs) and presented peptides. By comparison, an evaluation of binding free-energy using a combination of the string model and Miyazawa-Jernigan matrix is very efficient and was therefore applied to estimate interaction energies between T cell receptor–peptide–MHC (TCR–pMHC) complexes, which appeared to successfully explain the effects of binding capacity of MHC on repertoire–formation and the reason for the presence of elite-controllers of some viral infections. However, this evaluation method is overly simplified and requires more detailed considerations when applied to evaluating TCR-pMHC interactions. In this study, we examined this method exhaustively and revealed the limitations of the method. Following features necessitate cautious attitude when interpreting the calculation results: first, the apparent increase in the number of hot spots in accordance with an increase of educational epitope pool size does not mean an increased TCR specificity of surviving clones; second, strong binders to any TCR converge to some limited sequences that are determined by the physical nature of the Miyazawa-Jernigan matrix.