Cε3-Cε4蛋白寡核苷酸适配子结合位点的预测与筛选

采用NPDock程序对Cε3-Cε4蛋白与其核酸适配子A1的结合位点进行了预测与筛选, 筛选出A1与Cε3-Cε4蛋白结合的关键位点. 同时, 根据蛋白与DNA片段复合物结合界面中氨基酸残基和碱基统计分析发现, 结合界面氨基酸富集碱基G能力最强, 富集碱基T和C能力次之. 本文建立了以NPDock程序虚拟对接为基础的高效适配子优化方法, 为相关研究提供了实验参考.

Structure Prediction and Screening of Oligonucleotide Aptamers Target Cε3-Cε4 Protein†

The prediction and selection of binding sites between aptamers and targets are the key steps in SELEX process, however, the conventional screening process is complicated. As a new convenient screening method, the virtual screening based on computer has widely used in aptamers screening. The nucleic acid-protein dock(NPDock) program was used to predict and screen the binding site of Cε3-Cε4 protein and its aptamer A1 based on their molecular docking, and the key site of binding to Cε3-Cε4 protein was screened. According to the amino acid residues and bases in the binding interface between the protein and the DNA complexes by virtual docking, the results showed that the amino acid in the binding interface is most capable of enriching the base G, followed by the ability of enriching the base T and the base C. An efficient optimization method was established based on NPDock docking, which would provide an experimental reference for related researches.