alexa Exhaustive Characterization of TCRand#195;and#162;and#194;and#8364;and#194;and#8220;pMHC Binding Energy Estimated by the String Model and Miyazawa-Jernigan Matrix | Abstract
ISSN: 2327-5146

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Research Article

Exhaustive Characterization of TCR–pMHC Binding Energy Estimated by the String Model and Miyazawa-Jernigan Matrix

Hiromichi Tsurui1*, Takuya Takahashi2, Yuko Matsuda3, Qingshun Lin1, Aya Sato-Hayashizaki1,4 and Sachiko Hirose1
1Department of Pathology, School of Medicine, Juntendo University, 2-1-1 Bunkyo-ku, Hongo, Tokyo 113-8421, Japan
2Department of Bioscience and Bioinformatics, College of life science, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga-ken 525-8577, Japan
3Symbolic Systems, Inc., 1-33-6 Sinyosida-Higasi, Kohoku, YOKOHAMA, 223-0058, Japan
4F.G.J Co. Ltd., 3-25-18 Jingumae, Shibuya-ku, Tokyo 150-0001, Japan
Corresponding Author : Hiromichi Tsurui
Department of Pathology, School of Medicine
Juntendo University, 2-1-1 Hongo
Bunkyo-ku, Tokyo 113-8421, Japan
Tel: 81-3-5802-1671
E-mail: [email protected]
Received October 01, 2013; Accepted December 19, 2013; Published December 27, 2013
Citation: Tsurui H, Takahashi T, Matsuda Y, Lin Q, Sato-Hayashizaki A (2013) Exhaustive Characterization of TCR–pMHC Binding Energy Estimated by the String Model and Miyazawa-Jernigan Matrix. Gen Med (Los Angel) 2:126. doi: 10.4172/2327-5146.1000126
Copyright: © 2013 Tsurui H, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Abstract

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.

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