Computational docking simulations of a DNA-aptamer for argininamide and related ligands
Computational docking simulations of a DNA-aptamer for argininamide and related ligands
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DOI：
10.1007/s10822-015-9844-5
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发表时间：
2015-07-01
影响因子：
3.5
通讯作者：
Willner, Itamar
中科院分区：
文献类型：
--
作者：
Albada, H. Bauke;Golub, Eyal;Willner, Itamar
序列特异性核酸（适体）与低分子量配体、大分子甚至细胞的结合特性吸引了大量的科学兴趣。这些配体-DNA复合物在传感、纳米医学和DNA纳米技术中有不同的应用。然而，关于适体-配体复合物的结构信息是稀缺的，即使它将打开在复合物中设计新特征的可能性。在本研究中，我们应用分子对接模拟探测实验记录的L-烟酰胺适体复合物的功能。使用AutoDock 4.0和YASARA Structure软件进行对接模拟，这是一种非常适合用于跟踪生物分子（包括DNA）的分子间相互作用和结构的程序。我们探索了DNA适体与L-精氨酸酰胺和一系列精氨酸衍生物或精氨酸样配体的结合特征。我们发现，最好的对接结果后，得到的能量最小化的父配体-适体复合物。所有单取代的含胍配体的计算结合能显示出良好的相关性与实验确定的结合常数。这些结果为应用对接模拟预测适体-配体结构以及设计配体-适体复合物的新特征提供了有价值的指导。
The binding properties of sequence-specific nucleic acids (aptamers) to low-molecular-weight ligands, macromolecules and even cells attract substantial scientific interest. These ligand-DNA complexes found different applications for sensing, nanomedicine, and DNA nanotechnology. Structural information on the aptamer-ligand complexes is, however, scarce, even though it would open-up the possibilities to design novel features in the complexes. In the present study we apply molecular docking simulations to probe the features of an experimentally documented L-argininamide aptamer complex. The docking simulations were performed using AutoDock 4.0 and YASARA Structure software, a well-suited program for following intermolecular interactions and structures of biomolecules, including DNA. We explored the binding features of a DNA aptamer to L-argininamide and to a series of arginine derivatives or arginine-like ligands. We find that the best docking results are obtained after an energy-minimization of the parent ligand-aptamer complexes. The calculated binding energies of all mono-substituted guanidine-containing ligands show a good correlation with the experimentally determined binding constants. The results provide valuable guidelines for the application of docking simulations for the prediction of aptamer-ligand structures, and for the design of novel features of ligand-aptamer complexes.