Yuko Matsuda
Japan
Research Article
Exhaustive Characterization of TCR–pMHC Binding Energy Estimated by the String Model and Miyazawa-Jernigan Matrix
Author(s): Hiromichi Tsurui, Takuya Takahashi, Yuko Matsuda, Qingshun Lin, Aya Sato-Hayashizaki and Sachiko HiroseHiromichi 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 .. View More»
