金属核酸酶及寡聚酰胺与双链DNA分子对接模式的理论研究  

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

作　　者：朱艳艳[1] 苏延伟[1] 漆遥[1] 谭宏伟[1] 王艳[1] 陈光巨[1] 

机构地区：[1]北京师范大学化学学院,北京100875

出　　处：《高等学校化学学报》2009年第4期781-785,共5页Chemical Journal of Chinese Universities

基　　金：国家重点"九七三"计划(批准号:G2004CB719900);国家自然科学基金(批准号:20673011;20631020;20503002和20771017)资助

摘　　要：采用分子对接软件AutoDock分别研究了金属核酸酶、寡聚酰胺与DNA对接模式.研究结果表明,金属核酸酶、寡聚酰胺与DNA对接结果与实验数据吻合得较好.在金属核酸酶与DNA的对接中,最优构型都是金属核酸酶对接在DNA的小沟内.随着中心金属上电荷的增加,最大对接能呈现上升趋势.尤其是配体体积较小的金属核酸酶,最佳对接位点受中心金属上电荷影响较大,即随着中心金属上电荷的从少到多,最佳对接位点呈现多样化的趋势.在柔性分子寡聚酰胺与双链DNA分子的对接中,分子随DNA小沟的柔性变形是对接结合的关键.其最佳的结合物位点也都是在DNA的小沟内,其对接结果与晶体结构一致.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 nuelease 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.

关 键 词：金属核酸酶 分子对接 寡聚酰胺 AutoDock程序 

分 类 号：O641[理学—物理化学]