分子模拟研究不同随机RNA片段适体与大肠杆菌紧密黏附素的相互作用

Study on different random RNA fragment and enteropathogenic Escherichia coli intimin interaction by molecular modelling

为了促进开发大肠杆菌快速检测适体生物传感器,通过对已知RNA-蛋白质相互作用原理和复合物结构的分析,在对相关文献资料和基于分子模拟技术的网络资源充分了解的基础上,模拟预测研究了随机RNA序列与肠致病性大肠杆菌紧密黏附素蛋白的相互作用。结果表明,RNA高级结构主要依赖于其一级结构的序列信息。NPDock模拟不同随机RNA序列与紧密黏附素相互作用时,不同长度RNA序列均可与紧密黏附素发生相互作用,但作用位点和相互位置有一定差异;对于相同长度不同排布的RNA序列,相互作用的差异性主要与序列排布信息有关。对于分子模拟研究RNA-紧密黏附素相互作用方法的可行性,通过RNA-蛋白质相互作用位点在线预测方法(PRIdictor)进行验证,结果表明,预测出的蛋白质、RNA相互作用位点均位于相互作用预测结构的接触面上,说明对于RNA-蛋白质相互作用的模拟预测研究方法具有一定的可行性,将有助于通过设计合成RNA改进适体筛选、研发的相关生物技术推广,以及应用创新。

In order to improve the development ofEscherichia coli detection aptamer biosensor, and based on the achievements ofbio- macromolecule and bioinformation emerge in large number, the molecular modeling method had been used to predict the interaction between random RNA fragment and enteropathogenic Escherichia coli intimin. The result shown that there was a correlation exists be- tween the high levels of RNA structure and its primary sequences. For the prediction result, though the sites and relative location were different, RNA with different length should been interact with intimin, and RNA with the same length presented differences on the RNA primary sequences. The prediction result had been verified by PRIdictor, the result shown that the predicted sites mostly belong to the interaction face of the RNA-protein complex. Moleculor modeling method can been used to predict the interaction of RNA and protein, which would to improve the study and usage ofRNA aptamer.