结核分枝杆菌潜伏抗原Rv2628的生物信息学分析

Bioinformatics analysis of the Mycobacterium tuberculosis latency-associated protein Rv2628

目的运用生物信息学的方法分析结核分枝杆菌潜伏相关蛋白Rv2628的结构与功能。方法自NCBI网站获取Rv2628蛋白的基本信息;利用Protparam、ProtScale预测Rv2628蛋白的理化性质、亲疏水性;应用Signal 6.0 Server、TMHMM Server V.2.0、NLStradamus、PSORTb预测Rv2628蛋白的信号肽、跨膜区域、核定位信号及亚细胞定位;使用NetNGlyc1.0、NetPhos Server v.3.1预测Rv2628蛋白的糖基化位点及磷酸化位点;利用SOPMA分析Rv2628蛋白的二级结构,使用SWISS-MODEL对其进行三级结构同源建模;使用ABCpred、SYFPEITHI预测Rv2628蛋白的相关抗原表位;利用MEGA构建Rv2628蛋白的分子进化树;使用STRING数据库预测与Rv2628蛋白可能发生互作的蛋白;使用autodock实现Rv2628蛋白与化合物的分子对接。结果Rv2628基因全长363 bp,由120个氨基酸构成,分子式为C575H906N178O168S4,等电点(pI)为9.09;Rv2628蛋白亚细胞定位于细胞质,无跨膜结构、信号肽及糖基化位点,存在12个磷酸化位点,包括6个苏氨酸、5个丝氨酸和1个酪氨酸磷酸化位点;该蛋白的二级结构以α-螺旋(41.67%)、无规则卷曲(35.83%)为主;Rv2628蛋白含有10个B细胞、6个Th细胞和6个CTL候选表位,三级结构同源建模的GMQE为0.72;苯基香豆素化合物10可以稳定的与Rv2628蛋白结合并发挥抑制作用;此外,Rv2628蛋白可能与Rv1733c、rip3、hrp1、devR、hspX等蛋白存在相互作用,参与结核分枝杆菌潜伏休眠的过程,诱导Th1免疫反应。结论Rv2628蛋白为亲水性蛋白,存在多个磷酸化位点并能够与多种蛋白相互作用,具有高度免疫原性,包含多个优势B细胞、T细胞抗原表位,可作为结核病诊断的候选蛋白。

Objective This study aims to analyze the structure and function of Rv2628 protein of Mycobacterium tuberculosis(Mtb)using bioinformatics methods.Methods Basic information of the Rv2628 protein was retrieved from the NCBI website.Protparam and ProtScale were employed to predict its physicochemical properties and hydrophobicity.Signal 6.0 Server,TMHMM Server V.2.0,NLStradamus,and PSORTb were utilized to predict its signal peptide,transmembrane regions,nuclear localization signals,and subcellular localization.NetNGlyc1.0 and NetPhos Server v.3.1 were employed to predict its glycosylation and phosphorylation sites.SOPMA was used to analyze its secondary structure,while SWISS-MODEL was employed for tertiary structure homology modeling.ABCpred and SYFPEITHI were utilized to predict its relevant antigenic epitopes.MEGA was employed to construct its molecular evolutionary tree.STRING database was used to predict proteins potentially interacting with Rv2628,and autodock was used to implement molecular docking of Rv2628 protein with compounds.Results The full length of the Rv2628 gene is 363 bp,encoding 120 amino acids,with a molecular formula of C_(575)H_(906)N_(178)O_(168)S_4,and an isoelectric point(pI)of 9.09.This protein is subcellularly localized in the cytoplasm,lacking transmembrane structures,signal peptides and glycosylation sites,and containing 12 phosphorylation sites,including 6 threonine,5 serine,and 1 tyrosine.Its secondary structure is primarily composed ofα-helices(41.67%)and random coils(35.83%).Rv2628 protein contains 10 B cell,6 Th cell and 6 CTL candidate epitopes.The homology modeling of tertiary structure has a GMQE of 0.72.Compound 10 of benzopyran compounds could stably bind to Rv2628 protein and exert inhibitory effects.Additionally,Rv2628 protein may interact with proteins such as Rv1733c,rip3,hrp1,devR,and hspX,participating in the process of Mycobacterium tuberculosis dormancy and inducing Th1 immune responses.Conclusion Rv2628 protein is hydrophilic,containing multiple phosphorylation sites,and capable of interacting with various proteins.It exhibits high immunogenicity,containing multiple dominant B cell and T cell antigenic epitopes.Therefore,Rv2628 protein could be served as a candidate protein for tuberculosis diagnosis.