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An integrating strategy of AMBER force field parameters for the photoinduced copper nucleases

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Abstract

In this research study, we develop a theoretical method for the determination of the AMBER force field parameters that are associated with the ten representative photoinduced copper nucleases. First, the ten nuclease compounds were grouped into three classes based on the same decisive ligands and similar ligand environments. The AMBER force field parameters around the central coppers for these compounds were calculated using the three-point method. Then, three sets of the ranges of force field parameters for the three classes of compounds were, respectively, summarized by taking into account the structural and ligand-environmental similarity in a same class. The ranges of force field parameters were successfully applied in the molecular mechanic calculations and the molecular dynamics simulations for some nucleases and nuclease–DNA systems. The influences of structural, electronic, and polarized factors on the ranges of force field parameters were discussed for the three classes of compounds.

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Acknowledgments

The authors acknowledge research support from the National Science Foundation of China (No. 21271029, 21131003, 21073015, and 20973024) and the Major State Basic Research Development Programs (Grant No. 2011CB808500).

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Authors and Affiliations

  1. Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Xinjiekouwai Street 19#, Haidian District, Beijing, 100875, China

    Tuo Xue, Shanshan Cui, Yan Wang & Guangju Chen

  2. Library, Beijing Normal University, Beijing, 100875, China

    Bo Yang

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  1. Tuo Xue
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  2. Shanshan Cui
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  3. Yan Wang
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Correspondence to Yan Wang, Bo Yang or Guangju Chen.

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Xue, T., Cui, S., Wang, Y. et al. An integrating strategy of AMBER force field parameters for the photoinduced copper nucleases. Theor Chem Acc 134, 1603 (2015). https://doi.org/10.1007/s00214-014-1603-5

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