HPV53进化关系分析及B细胞与T细胞抗原表位预测

Phylogenetic Analyses of HPV53 and Prediction of B and T Cell Epitopes

目的基于全长序列分析人乳头瘤病毒(human papillomavirus,HPV)53不同分离株的进化关系,并对代表性分离株病毒蛋白(E1、E2、E4、E6、E7、L1和L2)的理化性质、二级结构及B细胞与T细胞抗原表位进行预测。方法检索美国国立生物技术信息中心(National Center for Biotechnology Information,NCBI)数据库,获取HPV53全长序列并构建进化树。采用ProtParam软件分析蛋白的理化性质,PSIPRED和SOPMA软件预测其二级结构。采用ABCpred和IEDB软件预测B、T细胞抗原表位,并结合肽段柔韧性、亲水性、表面可及性、抗原性及Vaxijen评分等参数进一步筛选潜在的优势抗原表位;最后对潜在优势抗原表位与13个高危型HPV进行同源性分析。结果检索NCBI数据库共下载54条HPV53全长序列,经去重后保留48条,来自不同国家/地区的HPV53分离株可划分为A、B、C三个主要进化分支。三个分支代表株病毒的蛋白理化性质相似,E1、E6和E7蛋白的二级结构以α螺旋为主,E2、E4、L1和L2以无规则卷曲为主。经预测和筛选后,共得到6个B细胞潜在优势抗原表位和9个T细胞潜在优势抗原表位,同源性分析发现,E4和E6区域的B细胞抗原表位TTPIRPPPPPRPWAPT和CYRCQHPLTPEEKQLH,及L2区域的T细胞抗原表位SGVHSYEEIPMQ与HPV56具有较高同源性(均>90%)。结论通过生物信息学方法分析和预测发现HPV53分离株可分为A、B、C三个主要进化分支,其理化性质相似,二级结构存在部分小差异,且病毒蛋白中含有B、T细胞抗原表位,为HPV53相关多肽形式的疫苗和抗体药物开发提供了更多理论依据。

Objective To construct phylogenetic trees based on HPV53 full length sequences,and pre⁃dict the physical and chemical parameters,secondary structure,B and T cell epitopes of HPV53 proteins(E1,E2,E4,E6,E7,L1,and L2).Methods The full⁃length sequences of HPV53 variants were retrieved from the National Center for Biotechnology Information(NCBI),and a phylogenetic tree was constructed to delineate variant lineages.The physical and chemical parameters of HPV53 proteins were analyzed by ProtParam.The secondary structure of proteins was analyzed using PSIPRED and SOPMA.The B and T cell epitopes for HPV53 proteins were predicted by the IEDB analysis server and the ABCpred server,respectively.Then,to select the potential dominant B and T cell epitopes,more parameters including flexibility,hydrophi⁃licity,surface accessibility,antigenicity of predicted B and T cell epitopes were further predicted by bioinfor⁃matic methods such as VaxiJen.Finally,for homology analysis,the potential dominant B and T cell epitopes were compared with the 13 high⁃risk HPV subtypes using NCBI BLAST tool.Results A total of 54 full⁃length HPV53 sequences were retrieved from the NCBI database,with 48 entries remaining after deduplication.These 48 HPV53 isolates from different countries/regions were clustered into three main evolutionary branches labeled as lineages A,B,and C.The physicochemical properties of three different HPV53 variants(representing A,B,and C lineages,respectively)were similar.The secondary structure of the E1,E6,and E7 proteins was predominantlyα⁃helices,while E2,E4,L1,and L2 predominantly exhibited random coils.After prediction and screening,a total of 6 potential B⁃cell epitopes and 9 potential T⁃cell epitopes were identified on HPV53 proteins.Among these epitopes,B cell epitopes TTPIRPPPPPRPWAPT in E4 region,CYRCQHPLTPEEKQLH in E6 region,and T cell epitopes SGVHSYEEIPMQ in L2 region showed high homologous to HPV56(all>90%).Conclusions Bioinformatics analysis and prediction revealed that HPV53 isolates could be clus⁃tered into three main evolutionary branches labeled as A,B,and C.These branches exhibited similar physico⁃chemical properties,with minor differences in their secondary structure.Moreover,HPV53 viral proteins con⁃tained both B⁃cell and T⁃cell antigenic epitopes.These results lay the foundation for further research on vaccines and drugs based on HPV53⁃related peptides.