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

作者：Xue, Tuo; Cui, Shanshan; Wang, Yan^*; Yang, Bo; Chen, Guangju

来源：Theoretical Chemistry Accounts, 2014, 134(1): 1603.

DOI：10.1007/s00214-014-1603-5

• AMBER force field parameters
• Photoinduced copper nucleases
• Ranges of force field parameters
• Parameter integration

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.

• 出版日期2014-12-10
• 单位北京师范大学