Theoretical Chemistry, Organic Chemistry Institute, Westfälische Wilhelms-Universität Münster, Corrensstr. 40, 48149 Münster, Germany.
J Inorg Biochem. 2013 Oct;127:203-10. doi: 10.1016/j.jinorgbio.2013.03.009. Epub 2013 Mar 28.
A series of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations was performed on models of a DNA duplex with artificial silver(I)-mediated imidazole base pairs. The optimized structures were compared to the original experimental NMR structure (Nat. Chem. 2 (2010) 229-234). The metal⋯metal distances are significantly shorter (~0.5Å) in the QM/MM model than in the original NMR structure. As a result, argentophilic interactions are feasible between the silver(I) ions of neighboring metal-mediated base pairs. Using the computationally determined metal⋯metal distances, a re-refined NMR solution structure of the DNA duplex was obtained. In this new NMR structure, all experimental constraints remain fulfilled. The new NMR structure shows less deviation from the regular B-type conformation than the original one. This investigation shows that the application of QM/MM models to generate additional constraints to be used during NMR structural refinements represents an elegant approach to obtaining high-resolution NMR structures.
对具有人工银（I）介导的咪唑碱基对的 DNA 双链体模型进行了一系列混合量子力学/分子力学（QM/MM）计算。将优化后的结构与原始实验 NMR 结构（Nat. Chem. 2 (2010) 229-234）进行了比较。QM/MM 模型中的金属···金属距离明显短于原始 NMR 结构（~0.5Å）。因此，相邻金属介导的碱基对之间可能存在银（I）离子之间的银相互作用。使用计算确定的金属···金属距离，获得了 DNA 双链体的重新-refined NMR 溶液结构。在这个新的 NMR 结构中，所有实验约束都得到了满足。与原始 NMR 结构相比，新的 NMR 结构显示出更小的偏离常规 B 型构象。这项研究表明，应用 QM/MM 模型生成要在 NMR 结构精修过程中使用的附加约束代表了获得高分辨率 NMR 结构的一种优雅方法。
