DNA and Estrogen Receptor Interaction Revealed by the Fragment Molecular Orbital Method -Implementation of SCF Convergence-
T. Watanabe, Y. Inadomi, S. Tanaka and U. Nagashima
National Institute of Advanced Industrial and Science and Technology, JP
Keywords: estrogen receptor, DNA binding domain, zinc finger, fragment molecular orbital
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.
Nanotech 2004 Conference Technical Program Abstract