多样性结构适体结合链霉素的分子动力学模拟  

Molecular dynamics simulations of diverse structural aptamers bound to streptomycin

作　　者：张云礼 向阳可佳 广毅 俞志刚 ZHANG Yunli;XIANG Yangkejia;GUANG Yi;YU Zhigang(School of Materials Science and Engineering,College of Chemical and Environmental Engineering,Harbin University of Science and Technology,Harbin 150040,China;Post-Doctoral Research Center of Chongqing Key Laboratory of Inorganic Special Functional Materials,College of Chemistry and Chemical Engineering,Yangtze Normal University,Chongqing 408100,China)

机构地区：[1]哈尔滨理工大学材料科学与化学工程学院,哈尔滨150040 [2]无机特种功能材料重庆市重点实验室博士后科研工作站,长江师范学院化学化工学院,重庆408100

出　　处：《分析试验室》2024年第9期1296-1301,共6页Chinese Journal of Analysis Laboratory

基　　金：重庆市教委重点(KJZD-K202101401);重庆市自然科学基金(CSTB2023NSCQ-MSX0477)项目资助。

摘　　要：采用分子动力学模拟方法研究了多样性结构适体与靶标链霉素(STR)分子的结合模式。通过Mfold网络平台预测适体多样性二级结构并基于RNAComposer创建3D结构,分别运用Autodock和Gromacs软件进行分子对接和模拟优势对接构象结合作用的动力学变化过程。结果显示,4个多样性结构适体(Apt-1,Apt-2,Apt-3和Apt-4)结合体系显示为总体相似的个性差异,主要包括氢键、π-烷基疏水和静电3种作用力类型,其中以静电为主,结合特征推断为通过静电吸引诱导的契合作用模式,对应结合自由能分别为-2458,-2601,-2377,-2524和-2176 kJ/mol。研究从分子层面明晰了适体与靶标STR分子的结合特性,其有效结论可为适体传感器的目标性设计与构建及药物载运与释放等提供参考。The molecular dynamics simulation method was used to study the binding mode of diverse structural aptamers to target streptomycin(STR)molecules.The Mfold network platform was applied to predict the aptamer's diverse secondary structures with the corresponding 3D structures constructed based on RNA Composer.Autodock was used for molecular docking,and the Gromacs software was used to simulate the dynamic change process for the docking dominant conformation.The research results show that the binding systems of 4 diverse structural aptamers(Apt-1,Apt-2,Apt-3,and Apt-4)exhibit overall similar personality differences,which mainly include 3 types of forces:hydrogen bonding,π-alkyl hydrophobic interaction,and electrostatic force,among which electrostatic force is the main.The binding characteristic is inferred as a fit mode induced by electrostatic attraction.The corresponding binding free energy is-2458,-2601,-2377,-2524,and-2176 kJ/mol,respectively.The study clarifies the binding characteristics of the aptamer to its target streptomycin at the molecular level.Its effective conclusions can be a reference for the application of this binding system in the targetoriented design and construction of aptasensors and drug delivery and release.

关 键 词：分子动力学模拟 适体 链霉素 结合模式 

分 类 号：O657.37[理学—分析化学]