title: Theoretical studies on binding modes of copper-based nucleases with DNA.
abstract: In the present work, molecular simulations were performed for the purpose of predicting the binding modes of four types of copper nucleases (a total 33 compounds) with DNA. Our docking results accurately predicted the groove binding and electrostatic interaction for some copper nucleases with B-DNA. The intercalation modes were also reproduced by "gap DNA". The obtained results demonstrated that the ligand size, length, functional groups and chelate ring size bound to the copper center could influence the binding affinities of copper nucleases. The binding affinities obtained from the docking calculations herein also replicated results found using MM-PBSA approach. The predicted DNA binding modes of copper nucleases with DNA will ultimately help us to better understand the interaction of copper compounds with DNA.
authors.affiliation: College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China.
authors.forename: Chunmei
authors.initials: C
authors.lastname: Liu
authors.affiliation: College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China. Electronic address: zhuyan@zzu.edu.cn.
authors.forename: Yanyan
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China. Electronic address: mstang@zzu.edu.cn.
authors.forename: Mingsheng
authors.initials: M
authors.lastname: Tang
mesh_terms: D003300:Copper / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D003851:Deoxyribonucleases / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D021281:Quantitative Structure-Activity Relationship; D015203:Reproducibility of Results
chemical_list: D003300:Copper; D004247:DNA; D003851:Deoxyribonucleases
keywords: Binding mode; Copper nuclease; DNA; MD simulation; Molecular docking