Specific interactions between lactose repressor protein and DNA affected by ligand binding: Ab initio molecular orbital calculations

Authors

  • Tatsuya Ohyama,

    1. Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
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  • Masato Hayakawa,

    1. Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
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  • Shin Nishikawa,

    1. Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
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  • Noriyuki Kurita

    Corresponding author
    1. Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
    • Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
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Abstract

Transcription mechanisms of gene information from DNA to mRNA are essentially controlled by regulatory proteins such as a lactose repressor (LacR) protein and ligand molecules. Biochemical experiments elucidated that a ligand binding to LacR drastically changes the mechanism controlled by LacR, although the effect of ligand binding has not been clarified at atomic and electronic levels. We here investigated the effect of ligand binding on the specific interactions between LacR and operator DNA by the molecular simulations combined with classical molecular mechanics and ab initio fragment molecular orbital methods. The results indicate that the binding of anti-inducer ligand strengthens the interaction between LacR and DNA, which is consistent with the fact that the binding of anti-inducer enhances the repression of gene transcription by LacR. It was also elucidated that hydrating water molecules existing between LacR and DNA contribute to the specific interactions between LacR and DNA. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

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