Applications of the Fragment Molecular Orbital Method for Bio-Macromolecules

被引：17

作者：

Fukuzawa, Kaori ^{[1
]}

Nakano, Tatsuya ^{[2
,3
]}

Kato, Akifumi ^{[1
]}

Mochizuki, Yuji ^{[3
,4
]}

Tanaka, Shigenori ^{[3
,5
]}

机构：

[1] Mizuho Informat & Res Inst Inc, Chiyoda Ku, 2-3 Kanda Nishiki Cho, Tokyo 1018443, Japan

[2] Natl Inst Hlth Sci, Setagaya Ku, Tokyo 1588501, Japan

[3] Japan Sci & Technol Agcy, CREST, Kawaguchi, Saitama 3320012, Japan

[4] Rikkyo Univ, Toshima Ku, Tokyo 1718501, Japan

[5] Kobe Univ, Nada Ku, Kobe, Hyogo 6578501, Japan

来源：

JOURNAL OF COMPUTER CHEMISTRY-JAPAN | 2007年 / 6卷 / 03期

关键词：

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

D O I：

10.2477/jccj.6.185

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

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.

引用

页码：185 / 197

页数：13

共 34 条

[31] Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations
Tsukamoto, Koki
Shimizu, Hideaki
Ishida, Takashi
Akiyama, Yutaka
Nukina, Nobuyuki
[J]. JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 2006, 778 (1-3): : 85 - 95
[32] Watanabe T, 2005, ABSTR PAP AM CHEM S, V229, pU779
[33] Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital-interfragment interaction energy analysis
Yamagishi, K
Yamamoto, K
Yamada, S
Tokiwa, H
[J]. CHEMICAL PHYSICS LETTERS, 2006, 420 (4-6) : 465 - 468
[34] Vitamin D receptor: Ligand recognition and allosteric network
Yamamoto, K
Abe, D
Yoshimoto, N
Choi, M
Yamagishi, K
Tokiwa, H
Shimizu, M
Makishima, M
Yamada, S
[J]. JOURNAL OF MEDICINAL CHEMISTRY, 2006, 49 (04) : 1313 - 1324

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