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Ab initio fragment molecular orbital calculations on specific interactions between aryl hydrocarbon receptor and dioxin
Author(s) -
Miyagi Satoshi,
Sawamura Satoshi,
Yoshikawa Eri,
Dedachi Kenichi,
Itoh Satoshi,
IshiharaSugano Mitsuko,
Kurita Noriyuki
Publication year - 2012
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.23212
Subject(s) - fragment molecular orbital , aryl hydrocarbon receptor , aryl hydrocarbon receptor nuclear translocator , chemistry , molecular mechanics , ab initio , molecular dynamics , aryl , homology modeling , molecular orbital , computational chemistry , ligand (biochemistry) , stereochemistry , receptor , molecule , gene , transcription factor , biochemistry , organic chemistry , enzyme , alkyl
Aryl hydrocarbon receptor (AhR) regulates expression of genes in a ligand‐dependent manner. Although AhR was found to contain basic helix‐loop‐helix and Per‐Arnt‐Sim (PAS) domains, three‐dimensional structures of AhR and its complex with ligand have not been determined yet. We here obtain some modeled structures for the PAS domain of mouse AhR by using homology modeling and classical molecular mechanics methods. In addition, the stable structure of solvated AhR–dioxin complex is determined by the protein–ligand docking and the classical molecular dynamics simulations, and the specific interactions between AhR and dioxin are investigated at an electronic level by using ab initio fragment molecular orbital method. The computed results highlight the important amino acid residues of AhR for the binding between AhR and dioxin. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012