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医学信息[ISSN:1006-1959/CN:61-1278/R]

卷:

37卷

期数:

2024年04期

页码:

1-7

栏目:

生物信息学

出版日期:

2024-02-15

文章信息/Info

Title:

Bioinformatics Analysis of PipD Protein Structure and Epitope of Salmonella Typhimurium PipD

文章编号:

1006-1959（2024）04-0001-07

作者:

宋晓蕊; 刘玉春; 丁 聪; 等

（郑州大学附属儿童医院河南省儿童感染性疾病国际联合实验室1，耳鼻咽喉头颈外科2，河南 郑州 450000）

Author(s):

SONG Xiao-rui; LIU Yu-chun; DING Cong; et al.

(Henan International Joint Laboratory of Children’s Infectious Diseases1,Department of Otorhinolaryngology Head and Neck Surgery2,Children’s Hospital Affiliated to Zhengzhou University,Zhengzhou 450000,Henan,China)

关键词:

鼠伤寒沙门菌; PipD; 生物信息; 蛋白结构; 抗原表位

Keywords:

Salmonella typhimurium; PipD; Bioinformatics; Protein structure; Antigenic epitope

分类号:

S852.6

DOI:

10.3969/j.issn.1006-1959.2024.04.001

文献标志码:

A

摘要:

目的 用生物信息学方法预测分析沙门菌PipD蛋白的结构和抗原表位，为沙门菌相关疾病的诊疗和疫苗的研发提供理论依据。方法 通过NCBI数据库获得沙门菌典型致病血清型：鼠伤寒沙门菌（Salmonella typhimurium）ATCC 14028S标准菌株STM14_1240基因的核苷酸序列及其编码蛋白PipD 的氨基酸序列，运用ProtParam、ProtScale、SignalP 4.1 Server、TMHMM Serverv.2.0、Netphos 3.1 Server、NetNGlyc-1.0、NCBI BLAST、SOMPA、SWISSMODEL、ABCpred、SYFPEITHI和UniProt等生物信息学工具分别对鼠伤寒沙门菌PipD蛋白的理化性质、亲疏水特性、信号肽、跨膜区、磷酸化位点、糖基化位点、结构域、二级结构、三级结构、B细胞抗原表位、T细胞抗原表位及蛋白同源性进行预测分析。结果 PipD是由520个氨基酸组成的亲水蛋白，分子式为C2608H3963N721O780S16，理论相对分子质量为58.4 kDa，理论等电点为7.34，脂溶指数为67.81，平均亲水系数为-0.508。PipD蛋白无信号肽序列，在其35~57氨基酸残基位置含1个长度为23个氨基酸的跨膜螺旋，属于跨膜蛋白。预测PipD蛋白含有 57个磷酸化位点和1个糖基化位点。PipD蛋白二级结构以无规则卷曲居多，占36.35%，其次为α螺旋、β折叠、β转角分别占15.77%、3.27%、44.62%。预测PipD蛋白可形成22个B细胞优势抗原表位，17个CTL细胞优势表位和30个Th细胞优势表位。PipD蛋白与人类基因BCLA3、SCRN2和MRPL4的编码蛋白同源性分别为29%、24.6%和31.8%，同源性较低。结论 PipD蛋白为亲水蛋白，热稳定性好；存在多个B细胞和T细胞抗原表位，与人类宿主蛋白同源性低，不易发生交叉免疫反应，可作为鼠伤寒沙门菌血清学诊断和疫苗候选蛋白。

Abstract:

Objective To predict and analyze the structure and antigenic epitopes of Salmonella PipD protein by bioinformatics methods, and to provide a theoretical basis for the diagnosis and treatment of Salmonella-related diseases and the development of vaccines.Methods The nucleotide sequence of Salmonella typhimurium ATCC 14028S standard strain STM14_1240 gene and the amino acid sequence of its encoded protein PipD were obtained by NCBI database. Bioinformatics tools such as ProtParam, ProtScale, SignalP 4.1 Server, TMHMM Serverv.2.0, Netphos 3.1 Server, NetNGlyc-1.0, NCBI BLAST, SOMPA, SWISSMODEL, ABCpred, SYFPEITHI and UniProt were used to predict and analyze the physicochemical properties, hydrophilicity and hydrophobicity, signal peptide, transmembrane region, phosphorylation site, glycosylation site, domain, secondary structure, tertiary structure, B cell epitope, T cell epitope and protein homology of Salmonella typhimurium PipD protein.Results PipD was a hydrophilic protein composed of 520 amino acids, the molecular formula was C2608H3963N721O780S16, the theoretical relative molecular mass was 58.4 kDa, the theoretical isoelectric point was 7.34, the fat solubility index was 67.81, and the average hydrophilic coefficient was -0.508. PipD protein had no signal peptide sequence, and contained a transmembrane helix with a length of 23 amino acids at its 35-57 amino acid residues, which belonged to transmembrane protein. It was predicted that PipD protein contained 57 phosphorylation sites and 1 glycosylation site. The secondary structure of PipD protein was mostly random coil, accounting for 36.35%, followed by α-helix, β-sheet and β-turn, accounting for 15.77%, 3.27% and 44.62%, respectively. It was predicted that PipD protein could form 22 B cell dominant epitopes, 17 CTL cell dominant epitopes and 30 Th cell dominant epitopes. The homology of PipD protein with human genes BCLA3, SCRN2 and MRPL4 was 29%, 24.6% and 31.8%, respectively.Conclusion PipD protein is a hydrophilic protein with good thermal stability. There are multiple B cell and T cell epitopes, which have low homology with human host proteins and are not prone to cross-immune reactions. It can be used as a candidate protein for serological diagnosis and vaccine of Salmonella typhimurium.

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