Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method

Ikuo Kurisaki*, Kaori Fukuzawa, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Janine Imada, Aneta Chmielewski, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

*この研究の対応する著者

研究成果: Article査読

43 被引用数 (Scopus)

抄録

A visualization method for inter-fragment interaction energies (IFIEs) of biopolymers is presented on the basis of the fragment molecular orbital (FMO) method. The IFIEs appropriately illustrate the information about the interaction energies between the fragments consisting of amino acids, nucleotides and other molecules. The IFIEs are usually analyzed in a matrix form called an IFIE matrix. Analyzing the IFIE matrix, we detect important fragments for the function of biomolecular systems and quantify the strength of interaction energies based on quantum chemistry, including the effects of charge transfer, electronic polarization and dispersion force. In this study, by analyzing a protein-DNA complex, we report a visual representation of the IFIE matrix, a so-called IFIE map. We comprehensively examine what information the IFIE map contains concerning structures and stabilities of the protein-DNA complex.

本文言語English
ページ(範囲)1-9
ページ数9
ジャーナルBiophysical Chemistry
130
1-2
DOI
出版ステータスPublished - 2007 10月
外部発表はい

ASJC Scopus subject areas

  • 生物理学
  • 生化学
  • 有機化学

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