生物信息分析细粒棘球绦虫EgA31蛋白T细胞及B细胞的优势抗原表位
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摘要
背景:EgA 31蛋白是参与成虫吸盘肌收缩的一类蛋白,是细粒棘球蚴绦虫保护性免疫中重要的候选疫苗分子。目的:应用生物信息学方法对细粒棘球绦虫EgA31蛋白进行分析,预测其可能的T细胞及B细胞优势抗原表位。方法:从GenB ank中获取EgA31蛋白的氨基酸序列(GenB ank登记号为AAC21558.1),利用ProtParam在线程序分析EgA31蛋白的分子质量、理论等电点、氨基酸组成、原子组成、消光系数、不稳定系数和总平均疏水性,DNAstar Protein模块、SOPMA在线服务器分析蛋白二级结构,Phyre的同源建模服务器预测其蛋白质三级结构,最后通过ABCpred、BepiPred、SYFPEITHI、IDBE等软件联合预测细粒棘球绦虫EGA31蛋白的T细胞及B细胞的优势抗原表位。结果与结论:(1)EgA31蛋白由601个氨基酸组成,其中含有112个强碱性氨基酸,121个强酸性氨基酸,归类为不稳定且亲水性蛋白;(2)在线分析发现,EgA31蛋白的二级结构中α-螺旋约占82.36%,延长链约占4.16%,β-转角约占3.16%,无规则卷曲约占10.32%;(3)通过ABCpred、Bepi Pred、SYFPEITHI、IDBE等软件联合分析后预测了4段优势T细胞抗原、6段优势B细胞抗原以及1段T-B细胞联合表位;(4)生物学信息方法能较为全面地预测细粒棘球绦虫EgA31蛋白的优势T细胞及B细胞抗原表位,为进一步研制疫苗和检测试剂奠定了基础。
BACKGROUND: EgA31 protein participates in acetabulum muscle contraction, and is an important candidate vaccine in the protective immunity of Echinococcus granulosus. OBJECTIVE: To analyze the EgA31 protein of the Echinococcus granulosus using bioinformatics and to predict the potential dominant T cell and B cell epitopes. METHODS: The amino acid sequence of EgA31 from the NCBI GenBank database was obtained. The molecular mass, theory isoelectric point, amino acid composition, atomic composition, extinction coefficient, instability coefficient, and total average hydrophobicity were analyzed using ProtParam online program. The secondary structure of EgA31 protein was analyzed using protein module of DNAstar software and SOPMA online services. The tertiary structure model of EgA31 protein was established Phyre server. Finally, the dominant T cell and B cell epitopes were predicted using ABCpred, BepiPred, SYFPEITHI, and IDBE software. RESULTS AND CONCLUSION: EgA31 protein consisted of 601 amino acids, including 112 negatively charged residues and 121 positively charged residues, which were classified as the unstable and hydrophilic protein. Online service analysis revealed that the second structure of EgA31 protein comprised 82.36% of α-helixs, 4.16% of β-sheets, 3.16% of β-turns and 10.32% of random coils. According to ABCpred, BepiPred, SYFPEITHI and IDBE databases, four dominant T cell epitopes, six dominant T cell epitopes, and one T-B combined epitopes were predicted successfully. Bioinformatics can comprehensively predict the dominant T cell and B cell epitopes in EgA31 protein of the Echinococcus granulosus, which lays a foundation for developing vaccine and reagent in the future.
BACKGROUND: EgA31 protein participates in acetabulum muscle contraction, and is an important candidate vaccine in the protective immunity of Echinococcus granulosus. OBJECTIVE: To analyze the EgA31 protein of the Echinococcus granulosus using bioinformatics and to predict the potential dominant T cell and B cell epitopes. METHODS: The amino acid sequence of EgA31 from the NCBI GenBank database was obtained. The molecular mass, theory isoelectric point, amino acid composition, atomic composition, extinction coefficient, instability coefficient, and total average hydrophobicity were analyzed using ProtParam online program. The secondary structure of EgA31 protein was analyzed using protein module of DNAstar software and SOPMA online services. The tertiary structure model of EgA31 protein was established Phyre server. Finally, the dominant T cell and B cell epitopes were predicted using ABCpred, BepiPred, SYFPEITHI, and IDBE software. RESULTS AND CONCLUSION: EgA31 protein consisted of 601 amino acids, including 112 negatively charged residues and 121 positively charged residues, which were classified as the unstable and hydrophilic protein. Online service analysis revealed that the second structure of EgA31 protein comprised 82.36% of α-helixs, 4.16% of β-sheets, 3.16% of β-turns and 10.32% of random coils. According to ABCpred, BepiPred, SYFPEITHI and IDBE databases, four dominant T cell epitopes, six dominant T cell epitopes, and one T-B combined epitopes were predicted successfully. Bioinformatics can comprehensively predict the dominant T cell and B cell epitopes in EgA31 protein of the Echinococcus granulosus, which lays a foundation for developing vaccine and reagent in the future.
引文
[1]贾海英,丁剑冰,傅玉才.细粒棘球绦虫EgA31疫苗的分子生物学特征[J].中国病原生物学杂志,2008,(7):552-555.
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[14]Saha S,Raghava GP.Prediction of continuous B-cell epitopes in an antigen using recurrent neural network.Proteins.2006;65(1):40-48.
[15]Larsen JE,Lund O,Nielsen M.Jens Erik Pontoppidan Larsen,Ole Lund and Morten Nielsen.Improved method for predicting linear B-cell epitopes.Immunome Res.2006;2:2.
[16]Keong B,Wilkie B,Sutherland T,et al.Hepatic cystic echinococcosis in Australia:an update on diagnosis and management.ANZ J Surg.2017 Oct 11.[Epub ahead of print]
[17]Craig PS,Hegglin D,Lightowlers MW,et al.Echinococcosis:Control and Prevention.Adv Parasitol.2017;96:155-158.
[18]鲍佳春,袁凤来,陆伟国.包虫病治疗进展[J].中国血吸虫病防治杂,2010,22(2):197-199.
[19]Grubor NM,Jovanova-Nesic KD,Shoenfeld Y.Liver cystic echinococcosis and human host immune and autoimmune follow-up:A review.World J Hepatol.2017;9(30):1176-1189.
[20]Jazouli M,Lightowlers M,Gauci CG,et al.Vaccination Against Hydatidosis:Molecular Cloning and Optimal Expression of the EG95NC(-)Recombinant Antigen in Escherichia coli.Protein J.2017;36(6):472-477.
[21]Alvarez Rojas CA,Gauci CG,Lightowlers MW.Antigenic differences between the EG95-related proteins from Echinococcus granulosus G1 and G6 genotypes:implications for vaccination.Parasite Immunol.2013;35(2):99-102.
[22]安梦婷,吾拉木·马木提,马海梅,等.细粒棘球蚴AgB 1、AgB2、AgB4抗原表位的特性分析[J].新疆医科大学学报,2016,39(12):1541-1546,1553.
[23]Fu Y,Saint-AndréMarchal I,Marchal T,et al.Cellular immune response of lymph nodes from dogs following the intradermal injection of a recombinant antigen corresponding to a 66 kDa protein of Echinococcus granulosus.Vet Immunol Immunopathol.2000;74(3-4):195-208.
[24]Saboulard D,Lahmar S,Petavy AF,et al.The Echinococcus granulosus antigen EgA31:localization during development and immunogenic properties.Parasite Immunol.2003;25(10):489-501.
[25]Ma X,Zhou X,Zhu Y,et al.The prediction of T-and B-combined epitope and tertiary structure of the Eg95 antigen of Echinococcus granulosus.Exp Ther Med.2013;6(3):657-662.
[26]Ma X,Zhao H,Zhang F,et al.Activity in mice of recombinant BCG-EgG1Y162 vaccine for Echinococcus granulosus infection.Hum Vaccin Immunother.2016;12(1):170-175.
[27]Shen CM,Zhu BF,Deng YJ,et al.Allele polymorphism and haplotype diversity of HLA-A,-B and-DRB1 loci in sequence-based typing for Chinese Uyghur ethnic group.PLo S One.2010;5(11):e13458.
[2]李玉娇,王晶,赵慧,等.细粒棘球绦虫Eg95抗原表位的生物信息学预测[J].中国人兽共患病学报,2011,27(10):892-896,900.
[3]Zhang FB,Lu XB,Guo N,et al.The prediction of T-and B-combined epitope of Ag85B antigen of Mycobacterium tuberculosis.Int J Clin Exp Med.2016;9:1408-1421
[4]Fu Y,Martinez C,Chalar C,et al.A new potent antigen from Echinococcus granulosus associated with muscles and tegument.Mol Biochem Parasitol.1999;102(1):43-52.
[5]李玉娇,杨晶,赵慧,等.细粒棘球绦虫EgA31重组蛋白的抗原表位分析预测[J].中国寄生虫学与寄生虫病杂志,2012,30(1):78-80.
[6]Pan Pang,Fengbo Zhang,Bin Jia,et al.Bioinformatics analysis of T-and B-combined epitopes of OMP31 protein of Brucella melitensis in Xinjiang,China.Int J Clin Exp Med.2017;10(9):13320-13330.
[7]Gasteiger E,Hoogland C,Gattiker A,et al.Protein Identification and Analysis Tools on the ExPASy Server.The Proteomics Protocols Handbook,Humana Press.2005:571-607
[8]Chen H,Gu F,Liu F.Predicting protein secondary structure using continuous wavelet transform and Chou-Fasman method.Conf Proc IEEE Eng Med Biol Soc.2005,3:2603-2606.
[9]Deléage G.ALIGNSEC:viewing protein secondary structure predictions within large multiple sequence alignments.Bioinformatics.2017;33(24):3991-3992.
[10]Kelley LA,Mezulis S,Yates CM,et al.The Phyre2 web portal for protein modeling,prediction and analysis.Nat Protoc.2015;10(6):845-858.
[11]Pikora M,Gieldon A.RASMOL AB-new functionalities in the program for structure analysis.Acta Biochim Pol.2015;62(3):629-631.
[12]Schuler MM,Nastke MD,Stevanovik?S.SYFPEITHI:database for searching and T-cell epitope prediction.Methods Mol Biol.2007;409:75-93.
[13]Karosiene E,Lundegaard C,Lund O,et al.NetMHCcons:a consensus method for the major histocompatibility complex class I predictions.Immunogenetics.2012;64(3):177-186.
[14]Saha S,Raghava GP.Prediction of continuous B-cell epitopes in an antigen using recurrent neural network.Proteins.2006;65(1):40-48.
[15]Larsen JE,Lund O,Nielsen M.Jens Erik Pontoppidan Larsen,Ole Lund and Morten Nielsen.Improved method for predicting linear B-cell epitopes.Immunome Res.2006;2:2.
[16]Keong B,Wilkie B,Sutherland T,et al.Hepatic cystic echinococcosis in Australia:an update on diagnosis and management.ANZ J Surg.2017 Oct 11.[Epub ahead of print]
[17]Craig PS,Hegglin D,Lightowlers MW,et al.Echinococcosis:Control and Prevention.Adv Parasitol.2017;96:155-158.
[18]鲍佳春,袁凤来,陆伟国.包虫病治疗进展[J].中国血吸虫病防治杂,2010,22(2):197-199.
[19]Grubor NM,Jovanova-Nesic KD,Shoenfeld Y.Liver cystic echinococcosis and human host immune and autoimmune follow-up:A review.World J Hepatol.2017;9(30):1176-1189.
[20]Jazouli M,Lightowlers M,Gauci CG,et al.Vaccination Against Hydatidosis:Molecular Cloning and Optimal Expression of the EG95NC(-)Recombinant Antigen in Escherichia coli.Protein J.2017;36(6):472-477.
[21]Alvarez Rojas CA,Gauci CG,Lightowlers MW.Antigenic differences between the EG95-related proteins from Echinococcus granulosus G1 and G6 genotypes:implications for vaccination.Parasite Immunol.2013;35(2):99-102.
[22]安梦婷,吾拉木·马木提,马海梅,等.细粒棘球蚴AgB 1、AgB2、AgB4抗原表位的特性分析[J].新疆医科大学学报,2016,39(12):1541-1546,1553.
[23]Fu Y,Saint-AndréMarchal I,Marchal T,et al.Cellular immune response of lymph nodes from dogs following the intradermal injection of a recombinant antigen corresponding to a 66 kDa protein of Echinococcus granulosus.Vet Immunol Immunopathol.2000;74(3-4):195-208.
[24]Saboulard D,Lahmar S,Petavy AF,et al.The Echinococcus granulosus antigen EgA31:localization during development and immunogenic properties.Parasite Immunol.2003;25(10):489-501.
[25]Ma X,Zhou X,Zhu Y,et al.The prediction of T-and B-combined epitope and tertiary structure of the Eg95 antigen of Echinococcus granulosus.Exp Ther Med.2013;6(3):657-662.
[26]Ma X,Zhao H,Zhang F,et al.Activity in mice of recombinant BCG-EgG1Y162 vaccine for Echinococcus granulosus infection.Hum Vaccin Immunother.2016;12(1):170-175.
[27]Shen CM,Zhu BF,Deng YJ,et al.Allele polymorphism and haplotype diversity of HLA-A,-B and-DRB1 loci in sequence-based typing for Chinese Uyghur ethnic group.PLo S One.2010;5(11):e13458.