Ab initio fragment molecular orbital calculations on specific interactions between aryl hydrocarbon receptor and dioxin

Authors

  • Satoshi Miyagi,

    1. Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
    Search for more papers by this author
  • Satoshi Sawamura,

    1. Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
    Search for more papers by this author
  • Eri Yoshikawa,

    1. Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
    Search for more papers by this author
  • Kenichi Dedachi,

    1. Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
    Search for more papers by this author
  • Satoshi Itoh,

    1. Corporate Research & Development Center, Toshiba Corporation, 1, Komukai-Toshiba-cho, Saiwai-ku, Kawasaki 212-8582, Japan
    Search for more papers by this author
  • Mitsuko Ishihara-Sugano,

    1. Corporate Research & Development Center, Toshiba Corporation, 1, Komukai-Toshiba-cho, Saiwai-ku, Kawasaki 212-8582, Japan
    Search for more papers by this author
  • Noriyuki Kurita

    Corresponding author
    1. Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
    • Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
    Search for more papers by this author

Abstract

Aryl hydrocarbon receptor (AhR) regulates expression of genes in a ligand-dependent manner. Although AhR was found to contain basic helix-loop-helix and Per-Arnt-Sim (PAS) domains, three-dimensional structures of AhR and its complex with ligand have not been determined yet. We here obtain some modeled structures for the PAS domain of mouse AhR by using homology modeling and classical molecular mechanics methods. In addition, the stable structure of solvated AhR–dioxin complex is determined by the protein–ligand docking and the classical molecular dynamics simulations, and the specific interactions between AhR and dioxin are investigated at an electronic level by using ab initio fragment molecular orbital method. The computed results highlight the important amino acid residues of AhR for the binding between AhR and dioxin. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

Ancillary