DNA and estrogen receptor interaction revealed by the fragment molecular orbital method - Implementation of SCF convergence

被引：0

作者：

Watanabe, T ^{[1
]}

Inadomi, Y ^{[1
]}

Tanaka, S ^{[1
]}

Nagashima', U ^{[1
]}

机构：

[1] JST, Kawaguchi 3320012, Japan

来源：

NSTI NANOTECH 2004, VOL 1, TECHNICAL PROCEEDINGS | 2004年

关键词：

estrogen receptor; DNA binding domain; zinc finger; fragment molecular orbital;

D O I：

暂无

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

The fragment molecular orbital (FMO) method was applied to evaluate the interaction between estrogen response element (ERE) in DNA and DNA binding domain (DBD) of estrogen receptor (ER). In order to calculate the whole electronic state of DNA-ERE and ER-DBD, we developed the SCC-DIIS method and the field scaling method. The SCC-DIIS method is for acceleration of the self-consistent charge (SCC) convergence, and the field scaling method changes the field effect from other fragments for stable convergence. Hybridization of these two methods made it possible to calculate the whole electronic state of DNA-ERE and ER-DBD.

引用

页码：176 / 179

页数：4

共 50 条

[1] DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations
Watanabe, Toshio
Inadomi, Yuichi
Fukuzawa, Kaori
Nakano, Tatsuya
Tanaka, Shigenori
Nilsson, Lennart
Nagashima, Umpei
JOURNAL OF PHYSICAL CHEMISTRY B, 2007, 111 (32): : 9621 - 9627
[2] DNA and estrogen receptor interaction revealed by the fragment molecular orbital calculation.
Watanabe, T
Inadomi, V
Tanaka, S
Fukuzawa, K
Nakano, T
Nilsson, L
Nagashima, U
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2005, 229 : U779 - U779
[3] Analysis of ligand binding specificity of estrogen receptor by the fragment molecular orbital method
Seki, Yuya
Kato, Tsukasa
Furuishi, Takayuki
Fukuzawa, Kaori
Yone, Etsuo
JOURNAL OF COMPUTER CHEMISTRY-JAPAN, 2018, 17 (03) : 160 - 162
[4] Fragment molecular orbital (FMO) method for studying actinide/lanthanide interaction with DNA/protein
Tsushima, S.
Mochizuki, Y.
Fahmy, K.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2019, 48 : S208 - S208
[5] Fragment molecular orbital study of the binding energy of ligands to the estrogen receptor
Fukuzawa, K
Kitaura, K
Nakata, K
Kaminuma, T
Nakano, T
PURE AND APPLIED CHEMISTRY, 2003, 75 (11-12) : 2405 - 2410
[6] Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method
Fukuzawa, Kaori
Mochizuki, Yuji
Tanaka, Shigenori
Kitaura, Kazuo
Nakano, Tatsuya
JOURNAL OF PHYSICAL CHEMISTRY B, 2006, 110 (32): : 16102 - 16110
[7] Efficient implementation of the three-dimensional reference interaction site model method in the fragment molecular orbital method
Yoshida, Norio
JOURNAL OF CHEMICAL PHYSICS, 2014, 140 (21):
[8] Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy
Fukuzawa, Kaori
Watanabe, Chiduru
Kurisaki, Ikuo
Taguchi, Naoki
Mochizuki, Yuji
Nakano, Tatsuya
Tanaka, Shigenori
Komeiji, Yuto
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 2014, 1034 : 7 - 16
[9] The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications
Fedorov, Dmitri G.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2017, 7 (06)
[10] Fragment molecular orbital method with density functional theory and DIIS convergence acceleration
Sugiki, SI
Kurita, N
Sengoku, Y
Sekino, H
CHEMICAL PHYSICS LETTERS, 2003, 382 (5-6) : 611 - 617

← 1 2 3 4 5 →