吉林大学学报(医学版) ›› 2024, Vol. 50 ›› Issue (3): 739-748.doi: 10.13481/j.1671-587X.20240318

• 基础研究 • 上一篇    

基于幽门螺杆菌hp0169基因三维结构的生物信息学分析

林玲辉1,李娜1,尹晓燕1,王晓凌1,胡亚平1,刘威2,费瑞3(),田新利1()   

  1. 1.邢台医学高等专科学校病原生物学与免疫学教研室,河北 邢台 054000
    2.陆军军医大学基础医学院全军免疫学研究所,重庆 400038
    3.吉林大学基础医学院细胞生物学系,吉林 长春 130021
  • 收稿日期:2023-06-02 出版日期:2024-05-28 发布日期:2024-07-01
  • 通讯作者: 费瑞,田新利 E-mail:feirui@jlu.edu.cn;xttxl66@163.com
  • 作者简介:林玲辉(1984-),男,河北省邢台市人,副教授,医学硕士,主要从事原核细胞结构生物学方面的研究。
  • 基金资助:
    河北省卫健委医学科学研究项目(20201591)

Bioinformatics anlysis based on three-dimensional structure of Helicobacter pylori hp0169 gene

Linghui LIN1,Na LI1,Xiaoyan YIN1,Xiaoling WANG1,Yaping HU1,Wei LIU2,Rui FEI3(),Xinli TIAN1()   

  1. 1.Department of Pathogenic Biology and Immunology,Xingtai Medical College,Xingtai 054000,China
    2.Institute of Immunology,School of Basic Medical Scienes,Army Medical University,Chongqing 400038,China
    3.Department of Cell Biology,School of Basic Medical Scienes,Jilin University,Changchun 130021,China
  • Received:2023-06-02 Online:2024-05-28 Published:2024-07-01
  • Contact: Rui FEI,Xinli TIAN E-mail:feirui@jlu.edu.cn;xttxl66@163.com

摘要:

目的 克隆幽门螺杆菌(Hp)hp0169基因并进行晶体学研究,分析其二级结构和三维结构。 方法 由UniProt数据库中检索Hp NCTC26695菌株hp0169基因及其编码蛋白序列,采用生物信息学方法分析Hp重组胶原蛋白酶(HpPrtC)蛋白理化性质,SOPMA和DNAStrar软件预测HpPrtC蛋白二级结构特征,SWISS-MOPEL软件构建HpPrtC蛋白三维结构,IEDB和ABCpred软件预测HpPrtC蛋白B淋巴细胞抗原表位,SYFPEITHI网站预测T淋巴细胞抗原表位,专家库(EP)算法和随机森林(RF)算法预测HpPrtC蛋白可结晶性。原核表达HpPrtC重组蛋白,经Ni2+亲和层析和分子筛技术纯化蛋白,结晶试剂盒筛选HpPrtC的结晶条件。 结果 hp0169基因共包含1 269个碱基配对,编码蛋白全长422个氨基酸,理论等电点为7.64,相对分子质量为47 300。HpPrtC蛋白为亲水性、可溶性蛋白。HpPrtC蛋白α螺旋的氨基酸数量占全部氨基酸数量百分率为35.78%,β片层为18.72%,β转角为6.87%,无规则卷曲为38.63%。抗原表位分析,HpPrtC蛋白含有B淋巴细胞的5个优势线性表位和3个构象表位及多个T淋巴细胞潜在优势抗原表位。同源建模,HpPrtC蛋白呈二聚体,单体由β折叠围成桶状结构,周围被α螺旋和无规则卷曲围绕。HpPrtC蛋白为中等难度结晶,且无信号肽和跨膜螺旋,在0.2 mol·L-1 氯化镁、0.1 mol·L-1 三羟甲基氨基甲烷(Tris)、3.4 mol·L-1 己二醇和pH 8.5条件下出现细小成簇的针状晶体。 结论 HpPrtC是一种亲水型蛋白,呈二聚体构造,在适宜条件下呈细小成簇针状晶体,其具有T淋巴细胞和B淋巴细胞优势抗原表位,可作为Hp疫苗设计的抗原,用于构建多价融合疫苗或多表位疫苗,本研究结果为Hp的防治提供了实验基础。

关键词: 幽门螺杆菌, hp0169基因, 抗原表位, 蛋白结晶, 生物信息学

Abstract:

Objective To clone the Helicobacter pyloriHp) hp0169 gene and conduct the crystallographic study, and to clarify its secondary and tertiary structures. Methods The hp0169 gene and its encoded protein sequence of the Hp NCTC26695 strain were retrieved from the UniProt database. Bioinformatics method was used to analyze the physicochemical properties of the Hp recombinant protease (HpPrtC) protein; SOPMA and DNAStrar softwares were used to predict the secondary structure characteristics of HpPrtC protein; SWISS-MODEL software was used to construct the tertiary structure of the HpPrtC protein; IEDB and ABCpred softwares were used to predict the antigenic epitopes of the B lymphocytes HpPrtC protein; SYFPEITMI website was used to predict the antigenic epitopes of the T lymphocytes of HpPrtC protein; the expert pool (EP) and random forest (RF) algorithms were used to predict the crystallizability of the HpPrtC protein;the HpPrtC recombinant protein was expressed in the prokaryotic system; the HpPrtC recombinant protein was purified by Ni2+ affinity chromatography and size-exclusion chromatography;the crystallization conditions for HpPrtC were screened by crystallization kit. Results The hp0169 gene contained 1 269 base pairs and encoded the protein of 422 amino acids, the theoretical isoelectric point was 7.64 and the relative molecular weight was 47 300. HpPrtC was a hydrophilic and soluble protein. The number of amino acids of alpha helices of HpPrtC accounted for 35.78%, beta sheets 18.72%, beta turns 6.87%, and random coils 38.63%. The antigen epitope analysis results showed that HpPrtC contained five dominant linear epitopes of B lymphocytes, three conformational epitopes, and multiple potential dominant epitopes of T lymphocytes. The homology modeling results showed that HpPrtC formed a dimer, and each monomer displayed a barrel structure surrounded by β sheets, alpha helices, and random coils. HpPrtC was predicted to have moderate crystallizability without signal peptides and transmembrane helices. Small clustered needle-like crystals of HpPrtC were obtained under the conditions of 0.2 mol·L-1 magnesium chloride, 0.1 mol·L-1 tris (hydroxymethyl) amino methane(Tris), 3.4 mol·L-1 hexanediol, and pH=8.5. Conclusion HpPrtC is a hydrophilic protein that forms a dimeric structure and crystallizes into small clustered needle-like crystals under suitable conditions. HpPrtC contains dominant antigenic epitopes of the T lymphocytes and B lymphocytes and can serve as an antigen for the design of Hp vaccines to establish the multivalent fusion vaccines or multi-epitope vaccines; the results provide an experimental basis for the prevention and control of Hp.

Key words: Helicobacter pylori, hp0169 gene, Crystallization, Antigenic epitope, Bioinformatics

中图分类号: 

  • R378.99