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

Research output: Contribution to journalArticlepeer-review

32 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)1-9
Number of pages9
JournalBiophysical Chemistry
Volume130
Issue number1-2
DOIs
Publication statusPublished - 2007 Oct
Externally publishedYes

Keywords

  • Ab initio quantum chemical calculation
  • Cyclic AMP receptor protein (CRP)
  • DNA-binding protein
  • Fragment molecular orbital (FMO) method
  • Sequence-specific recognition
  • Transcription factor

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Organic Chemistry

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