カノニカル分子軌道計算に基づく線形回帰法を用いたタンパク質原子電荷の開発 Development of atomic charges for proteins by using the linear regression method based on canonical molecular orbital calculation

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Abstract

RESP 電荷は分子の静電ポテンシャル(ESP)を再現する目的で提案され,現在広く分子力場や分子動力学計算に使われている.タンパク質RESP 電荷は計算サイズの問題により,アミノ酸残基毎にパラメータ化されたRESP 電荷を繋ぎ合わせたものを代用している.本研究は,タンパク質全体のカノニカル分子軌道計算に基づき,タンパク質本来のESP をよく再現する原子電荷計算法を開発し,原子電荷の高品位化を行った.定義に従ったRESP 電荷をはじめ,線形回帰法を原子電荷モデルに適用することで,ESP を高精度に再現する性質を保ちつつ様々な特徴を持つ,タンパク質の新たな原子電荷を作成することができた.

The RESP charge has been proposed for the purpose of reproducing the electrostatic potential (ESP) of molecules and widely used for the molecular mechanics or molecular dynamics simulation. Because the cost of the RESP charge determination by using full QM calculation is high, the protein RESP charge is substituted by the combination of parameterized RESP charge for each amino acid residue. In this study, we have developed the atomic charge calculation method which reproduce intrinsic ESP based on the canonical molecular orbital calculation of the entire protein and improved the quality of atomic charge. In addition to RESP charge followed by the original definition, the various atomic charges of protein were proposed by applying the linear regression method to the atomic charge model with keeping the property of accurate ESP reproductivity.

Journal

  • SEISAN KENKYU

    SEISAN KENKYU 68(3), 213-217, 2016

    Institute of Industrial Science The University of Tokyo

Codes

  • NII Article ID (NAID)
    130005153090
  • NII NACSIS-CAT ID (NCID)
    AN00127075
  • Text Lang
    ENG
  • Journal Type
    大学紀要
  • ISSN
    0037-105X
  • NDL Article ID
    027482104
  • NDL Call No.
    Z14-198
  • Data Source
    NDL  J-STAGE 
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