分子对接比较随机RNA片段与同源建模蛋白及其模板的相互作用

Molecular docking study on interaction of random RNA fragment and escherichia coli homologous intimin

为了促进开发大肠杆菌O157∶H7快速检测适体生物传感器,对其鞭毛蛋白紧密黏附素以肠致病性大肠杆菌紧密黏附素为模板,进行空间结构同源建模并作为目标抗原,用不同对接方法模拟预测研究比较其与随机RNA序列的相互作用。方法可行性通过模拟研究已知亲和性同一RNA适体与不同物种凝血酶相互作用论证。结果表明,不同随机RNA序列与不同菌株的紧密黏附素空间相互作用的位点预测有一定差异,说明针对不同蛋白质进行高亲和适体筛选具有一定的可行性。分子对接研究表明因不同长度RNA所形成空间结构不同,而与大肠杆菌O157∶H7紧密黏附素结合位点存在一定差异、与PRIdictor预测位点结果接近;具有不同RNA结构模体的片段对紧密黏附素的亲和力不同,有从不同片段中筛选高亲和力的RNA适体的可能。分子模拟进一步研究RNA-紧密黏附素相互作用的方法具有一定的可行性,将有助于进一步通过设计合成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 of Escherichia coli O157 ： H7 detection aptamer biosensor, and based on the big achievements of biomacromolecule and bioinformation, different docking programs had been used to predict the interaction between random RNA fragment and Escherichia coli O157 ： H7 intimin, which 3D-structure had been already modelled. The methodology idea had been proved by in silicon presentation of the same reported RNA aptamer interacted both bovine and human thrombin. For the interaction site predicted by PRIdictor, though the sites and relative location were similar, different RNA should been interact with different intimin in vary site and structural domain, The docking result shown that different RNA performed variable affinity to the intimin, and RNA with the same length presented differences on the RNA primary sequences, 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.