结核分枝杆菌panD蛋白功能预测及生物信息学分析

Bioinformatic analysis and prediction of the structure and function of the panD protein from Mycobacterium tuberculosis

目的研究结核分枝杆菌panD(Rv3601c)基因及其编码蛋白的结构和功能,为耐药结核的治疗提供参考依据。方法运用ClustalX 2.1、MEGA 6.06软件以及ExPASy、NCBI等在线工具分析结核分枝杆菌panD基因信息,同时分析其进化特征、编码蛋白质的理化性质、信号肽、磷酸化位点、结构特点并预测其功能;利用BepiPred 1.0Server和NetMHCIIpan 3.1Server预测panD蛋白的B细胞和T细胞抗原表位。结果结核分枝杆菌panD基因全长420bp,不同菌株panD基因序列相似度100%,具有高度同源性,进化关系较近,编码139个氨基酸。panD蛋白不稳定系数为8.72,亲水性平均系数为0.147,为稳定、疏水性蛋白、无跨膜区与信号肽,存在9个磷酸化位点。二级结构中以无规则卷曲为主,结构较疏松。三级结构同源建模成功。该蛋白具有多个潜在的B细胞抗原表位和T细胞抗原表位。结论panD蛋白作为脱羧酶,在结核分枝杆菌合成β-丙氨酸过程中具有重要作用。panD蛋白序列保守稳定,具有多个优势抗原表位,是治疗耐药结核的潜在新靶标。

Objectives To analyze the panD gene from Mycobacterium tuberculosis and to predict the structure and function of the protein that panD codes for （L-aspartate α-decarboxytase） in order to evaluate its potential value as a target for treatment of drug-resistant tuberculosis. Methods The software ClustalX 2. 1 and MEGA 6. 06 and online tools from ExPASy and the NCBI were used to analyze information on the panD gene of M. tuberculosis and its evolutionary characteristics and the physical and chemical properties of panD protein and to predict the signal peptides, phosphorylation sites, structural features, and functions of that protein. BepiPred 1.0 Server and NetMHCIIpan 3.1 Server were used to predict B-cell and T-cell epitopes. Results The panD gene of M. tuberculosis was 420 bp in length. The panD gene se- quence of different M. tuberculosis strains was 100% similar, which indicates that the panD gene of M. tuberculosis is highly homologous and has a close evolutionary relationship to other M. tuberculosis stains. The panD gene of M. tuber culosis encodes 139 amino acids. The panD protein has an instability coefficient of 8.72 and an average coefficient of hy- drophilicity was 0. 147, which suggests that the protein is stable and hydrophobic. The protein contains multiple hydro- philic and hydrophobic regions, but those regions are not clumped together. The protein has no transmembrane regions or signal peptides, though it has 9 phosphorylation sites and its phosphorylation occurs via O-phosphate modification. Its secondary structure mostly consists of random coils, which account for about 33.81% of the structure and suggest that the panD protein has a loose structure. A homology-based model of the tertiary structure of the panD protein was success- fully constructed, and the protein is presumed to belong to the Asp decarbox family. The panD protein has multiple po- tential B cell and T-cell epitopes Conclusion The PanD protein, is a decarboxylase that plays an important role in the synthesis of beta alanine to facilitate growth of M. tuberculosis. The PanD protein sequence is stable and has a number of dominant epitopes, so the protein represents a new potential target for the treatment of drug-resistant tuberculosis.