高等学校化学学报 ›› 2019, Vol. 40 ›› Issue (1): 83-89.doi: 10.7503/cjcu20180428

• 有机化学 • 上一篇    下一篇

Cε3-Cε4蛋白寡核苷酸适配子结合位点的预测与筛选

刘中成1,2, 刘世芳1,2, 张苏1,2, 杨艳蕾1,2, 李飞1,2, 张楠1,2, 袁欣1,2, 张艳芬2,3   

  1. 1. 河北大学药学院, 保定 071002
    2. 河北省药物质量分析控制实验室, 保定 071002
    3. 河北大学科学技术处, 保定 071002
  • 收稿日期:2018-06-11 出版日期:2019-01-10 发布日期:2018-12-03
  • 作者简介:联系人简介: 张艳芬, 女, 副教授, 主要从事微生物生化药学方面的研究. E-mail: zhangjing@hbu.edu.cn
  • 基金资助:
    国家自然科学基金(批准号: 81202338)、 河北省自然科学基金(批准号: H2016201121)、 河北省高等学校科学技术研究项目(批准号: ZD2017010)和国家级大学生创新创业训练计划项目(批准号: 201610075007, 201710075016)资助.

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

LIU Zhongcheng1,2, LIU Shifang1,2, ZHANG Su1,2, YANG Yanlei1,2, LI Fei1,2, ZHANG Nan1,2, YUAN Xin1,2, ZHANG Yanfen2,3,*   

  1. 1. College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China
    2. Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Baoding 071002, China
    3. Offices of Science and Technology, Hebei University, Baoding 071002, China
  • Received:2018-06-11 Online:2019-01-10 Published:2018-12-03
  • Contact: ZHANG Yanfen
  • Supported by:
    † Supported by the National Natural Science Foundation of China(No.812022338), the Natural Science Foundation of Hebei Province, China(No.H2016201121), the Hebei Provincial Department of Education Key Research Project, China(No.ZD2017010) and the National College Students Innovation and Entrepreneurship Training Program, China(Nos.201610075007, 201710075016 ).

摘要:

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.

关键词: Cε3-Cε4蛋白;, NPDock程序, 分子对接, 适配子筛选

Abstract:

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.

Key words: Cε3-Cε4 protein ;, Nucleic acid-protein dock program, Molecular docking, Aptamers screening

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