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

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• 作者：Chunmei Liu ; Bin Zhang ; Yanyan Zhu ; Mingsheng Tang
• 关键词：Force field parameter ; Copper ; based nuclease ; DNA binding ; MINA ; Molecular dynamics simulation
• 刊名：Structural Chemistry
• 出版年：2016
• 出版时间：October 2016
• 年：2016
• 卷：27
• 期：5
• 页码：1449-1464
• 全文大小：2,895 KB
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Computer Applications in Chemistry
  Physical Chemistry
  Theoretical and Computational Chemistry
  
• 出版者：Springer Netherlands
• ISSN：1572-9001
• 卷排序：27

文摘

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.