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Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases

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Abstract

We describe the development of the AMBER force field parameters for 46 nucleases involving most kinds of copper nucleases with high DNA affinities and specificities by MINA approach that could evaluate accurate force constants for batch bonds/angles on the basis of energies of three adjacent lengths/angles geometries. The molecular mechanics (MM) and molecular dynamic simulations on adducts of the 21 representative copper-based nucleases with DNA are in excellent agreement with those of experimental results. Furthermore, to validate the evaluated parameters, the studied structures performed frequency analysis together with normal mode calculations in quantum mechanics and MM calculations. The force field parameters evaluated in this work provide an extension of AMBER force field, and the results of molecular dynamics simulations of adduct of copper nuclease and duplex DNA illustrate the potential utility of these parameters.

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Acknowledgments

We are grateful to thank Professor David A. Case and Dr. He Chen working at Rutgers University for his valuable comments on this paper. The authors acknowledge financial support from the National Natural Science Foundation of China (Nos. 21001095) and University Key Research Programs of Department of Education in Henan Province (Grant Nos. 15A150082 and 14A150033).

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  1. College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, 450001, Henan Province, People’s Republic of China

    Chunmei Liu, Bin Zhang, Yanyan Zhu & Mingsheng Tang

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  1. Chunmei Liu
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Correspondence to Yanyan Zhu.

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Liu, C., Zhang, B., Zhu, Y. et al. Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases. Struct Chem 27, 1449–1464 (2016). https://doi.org/10.1007/s11224-016-0764-3

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