Applications of the Fragment Molecular Orbital Method for Bio-Macromolecules

Kaori FUKUZAWAa*, Tatsuya NAKANOb, c, Akifumi KATOa, Yuji MOCHIZUKIc, d and Shigenori TANAKAc, e

aMizuho Information & Research Institute, Inc.
2-3 Kanda-Nishiki-cho, Chiyoda-ku, Tokyo 101-8443, Japan
bNational Institute of Health Sciences
1-18-1 Kami-Yoga, Setagaya-ku, Tokyo 158-8501, Japan
cJapan Science and Technology Agency, CREST
4-1-8 Honcho, Kawaguchi, Saitama 332-0012
dRikkyo University
3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
eKobe University
1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan

(Received: April 5, 2007; Accepted for publication: May 10, 2007; Published on Web: June 29, 2007)

This review introduces the application of the Fragment molecular orbital (FMO) method. The ABINIT-MP and BioStation Viewer programs have been used for such applications. The FMO method was applied for problems of transcriptional regulation, including interactions of nuclear receptor, ligand, transcription factor, and DNA. Detailed interactions between biomolecules and the roles of each amino acid residue were revealed through analyses of inter-fragment interaction energy (IFIE), charge distribution, and orbital configuration. Electrostatic and van der Waals dispersion interactions were found to be equally important in molecular recognition. It was found that the inclusion of electron correlation was essential to obtain appropriate pictures. Other applications such as the photo-excitation process are also introduced.

Keywords: Fragment molecular orbital method, ABINIT-MP, BioStation Viewer, Bio-macromolecule, Molecular recognition, Nuclear receptor, DNA

Abstract in Japanese

Text in Japanese

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