Study of the binding mechanism of aptamer to palytoxin by docking and molecular simulation
Study of the binding mechanism of aptamer to palytoxin by docking and molecular simulation
复制标题
通过对接和分子模拟研究适体与海藻毒素的结合机制
DOI：
10.1038/s41598-019-52066-z
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发表时间：
2019-10-29
影响因子：
4.6
通讯作者：
Jiao, Binghua
中科院分区：
文献类型：
--
作者：
Hu, Bo;Zhou, Rong;Jiao, Binghua
本文为核酸适体与小分子的分子结构分析及相互作用机理研究提供了一个可行的模型。在本研究中，分别对单链DNA适配子(P-18S2)和靶标(毒素，PTX)进行了建模和动态模拟。然后，预测了DNA与PTX之间的复杂结构，对接结果表明，PTX可以通过较强的氢键和静电相互作用稳定地结合在DNA模型的凹槽顶部。因此，我们通过仿真对P-18S2进行了截断和优化。同时，通过实验验证了仿真结果的可靠性。结合实验和计算结果，本研究对P-18S2与PTX的高亲和力和特异性结合提供了更合理的解释，为进一步优化和开发适配子在分子诊断和治疗应用中的应用奠定了基础。
This paper provides a feasible model for molecular structure analysis and interaction mechanism of aptamer and micromolecule. In this study, modeling and dynamic simulation of ssDNA aptamer (P-18S2) and target (Palytoxin, PTX) were performed separately. Then, the complex structure between DNA and PTX was predicted, and docking results showed that PTX could combine steadily at the groove’s top of DNA model by strong hydrogen-bonds and electrostatic interaction. Thus, we truncated and optimized P-18S2 by simulating. At the same time, we also confirmed the reliability of simulation results by experiments. With the experimental and computational results, the study provided a more reasonable interpretation for the high affinity and specific binding of P-18S2 and PTX, which laid the foundation for further optimization and development of aptamers in molecular diagnostics and therapeutic applications.