Docking stability and electronic structure of azurin–cytochrome c551 complex system

Authors

  • Ayumu Sugiyama,

    Corresponding author
    1. Division of Mathematical and Physical Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
    • Division of Mathematical and Physical Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
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  • Yuichiro Takamatsu,

    1. Division of Mathematical and Physical Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
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  • Keigo Nishikawa,

    1. Division of Mathematical and Physical Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
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  • Hidemi Nagao,

    1. Division of Mathematical and Physical Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
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  • Kiyoshi Nishikawa

    1. Division of Mathematical and Physical Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
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Abstract

We investigate the docking structure between cytochrome c551 and azurin proteins by quantum mechanical calculation and molecular dynamics (MD). A model for the docking structure of the cytochrome–azurin complex is presented. We calculate the charge distribution around the active site for each protein and force field parameters to simulate the complex system by MD. We estimate some physical properties, such as binding free energy and the dynamical cross-correlation map. We discuss the stability of the cytochrome c551–azurin complex system. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

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