caa a22 4500 605488118 CHVBK 20210128100454.0 cr unu---uuuuu 210128e20150801xx s 000 0 eng 10.1007/s00214-015-1700-0 doi (NATIONALLICENCE)springer-10.1007/s00214-015-1700-0 Theoretical study on binding models of copper nucleases containing pyridyl groups to DNA [Elektronische Daten] [Xuening Zhang, Mingsheng Tang, Fangfang Li, Yanyan Zhu, Chunmei Liu, Wenjing Zhang, Donghui Wei] Molecular dynamic simulations have been performed to investigate the DNA binding affinities and cleavage activities of a new class of copper nucleases with similar ligand structures, including Cu(pzdpy)2+, Cu(hpzpy)2+, Cu(pmea)2+, Cu(pmap)2+, Cu(tepa)2+ and Cu(tpa)2+, in this present study. The obtained results reveal that the five copper nucleases bind to DNA in the minor groove, while the favorable binding sites for Cu(tepa)2+ locate in the DNA major groove. Analyses of binding free energies, all possible hydrogen bonds and favorable interactions between copper nucleases and DNA suggest that DNA binding affinities of the six copper nucleases are in the order of Cu(pzdpy)2+>Cu(hpzpy)2+>Cu(pmea)2+>Cu(tepa)2+>Cu(tpa)2+>Cu(pmap)2+, which is good agreement with the experimental results. Meanwhile, the simulated results demonstrated that significant difference in frequency distribution of the DNA helical parameters was observed between the unbound B-DNA and the bound DNA by the copper nucleases, which causes the inhibition of transcription and replication. Furthermore, RDF analyses suggest that the activities of the studied copper nucleases decrease in the order of Cu(pzdpy)2+, Cu(pmea)2+, Cu(hpzpy)2+, Cu(tpa)2+, Cu(pmap)2+ and Cu(tepa)2+, consisting with the experimental results. The present study provides detailed information to help us understand a new congeneric class of copper nucleases with different nuclease properties. Springer-Verlag Berlin Heidelberg, 2015 Artificial metallonucleases nationallicence Binding affinity nationallicence MD simulations nationallicence Zhang Xuening College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut Tang Mingsheng College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut Li Fangfang College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut Zhu Yanyan College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut Liu Chunmei College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut Zhang Wenjing College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut Wei Donghui College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut Theoretical Chemistry Accounts Springer Berlin Heidelberg 134/8(2015-08-01), 1-15 1432-881X 134:8<1 2015 134 214 https://doi.org/10.1007/s00214-015-1700-0 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00214-015-1700-0 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Zhang Xuening College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut NATIONALLICENCE 700 1- Tang Mingsheng College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut NATIONALLICENCE 700 1- Li Fangfang College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut NATIONALLICENCE 700 1- Zhu Yanyan College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut NATIONALLICENCE 700 1- Liu Chunmei College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut NATIONALLICENCE 700 1- Zhang Wenjing College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut NATIONALLICENCE 700 1- Wei Donghui College of Chemistry and Molecular Engineering, Zhengzhou University, 450001, Zhengzhou, Henan Province, People's Republic of China aut NATIONALLICENCE 773 0- Theoretical Chemistry Accounts Springer Berlin Heidelberg 134/8(2015-08-01), 1-15 1432-881X 134:8<1 2015 134 214