Molecular Docking Studies on the Metallonucleases and Polyamides with Double-strand DNA Molecules

Abstract

Abstract:

The studies on molecular docking of metallonucleases and polyamides with DNA were investigated via AutoDock program. Our studies demonstrate that the results of docking metal nucleases and poly-amides with double-strand DNA are consistent with those of the experiments. The characteristics of the optimal conformations for the two copper nucleases with DNA are that the two copper nucleases are docked into the minor groove of DNA. With the increase of the charges at copper center, the biggest docked energies for the two copper nucleases increase gradually. For BPA ligand, the nuclease with the different charges on copper center is docked into the different sites in the minor groove. However, for IDB ligand, the nuclease is docked into the similar site in the minor groove even if the charges on the copper center are changed from 0.5 e to 2.0 e. The feature of the optimal conformations of the flexible molecule-polyamide with double-strand DNA is that the polyamides are also docked into the minor groove of DNA, which agrees with the experimental estimation.

Key words: Metallonuclease, Molecular docking, Polyamide, AutoDock program

TrendMD:

ZHU Yan-Yan, SU Yan-Wei, QI Yao, TAN Hong-Wei, WANG Yan*, CHEN Guang-Ju*. Molecular Docking Studies on the Metallonucleases and Polyamides with Double-strand DNA Molecules[J]. Chem. J. Chinese Universities, 2009, 30(4): 781.

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