大豆过敏原11S球蛋白G2中A2链结合表位的预测
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摘要
采用生物信息学软件NCBI Gen Bank数据库、PDB数据库、SWISS-MODEL、Deep View 4.1等预测11S球蛋白G2中A2链的二级结构和三级结构模型,使用Disco Tope 2.0 Server软件预测B细胞构象表位,发现构象表位多位于无规则卷曲处。定位B细胞线性结合表位,结果表明11S球蛋白G2中A2链的可能线性表位有:~(37)KPDNRIE~(43)、~(79)PSYTNGP~(85)、~(114)SQQRGRSQRP~(123)、~(52)WNPNNK~(57)、~(196)QQGGSQSQKGKQQE~(209)、~(241)QGENEEED~(248)、~(267)RKPQQEEDDDDEEEQ~(281)、~(287)TDKGC~(291)。此表位预测为后续制肽、免疫等操作找出更准确的肽序,以便建立适合我国大豆过敏人群的食品大豆过敏原的检测技术。
Adopting bioinformatics software, this study aimed to predict the secondary and tertiary structure model of the A2 chain of 11 S globulin G2 in order to locate the B cell epitopes. The results indicated that the conformational epitopes were mainly at the random coil areas and the probable linear epitopes may contain ~(37)KPDNRIE~(43)、~(79)PSYTNGP~(85)、~(114)SQQRGRSQRP~(123)、~(52)WNPNNK~(57)、~(196)QQGGSQSQKGKQQE~(209)、~(241)QGENEEED~(248)、~(267)RKPQQEEDDDDEEEQ~(281)、~(287)TDKGC~(291). This prediction can be utilized to find out accurate peptides sequences for subsequent peptide preparation and immunization so as to develop a technique to detect soybean allergens for people allergic to soybean foods in China.
Adopting bioinformatics software, this study aimed to predict the secondary and tertiary structure model of the A2 chain of 11 S globulin G2 in order to locate the B cell epitopes. The results indicated that the conformational epitopes were mainly at the random coil areas and the probable linear epitopes may contain ~(37)KPDNRIE~(43)、~(79)PSYTNGP~(85)、~(114)SQQRGRSQRP~(123)、~(52)WNPNNK~(57)、~(196)QQGGSQSQKGKQQE~(209)、~(241)QGENEEED~(248)、~(267)RKPQQEEDDDDEEEQ~(281)、~(287)TDKGC~(291). This prediction can be utilized to find out accurate peptides sequences for subsequent peptide preparation and immunization so as to develop a technique to detect soybean allergens for people allergic to soybean foods in China.
引文
[1]张绍伟.阶段性营养亏缺对大豆产量的影响[J].新农村(黑龙江),2013,69(15):29.DOI:10.3969/j.issn.1674-8409.2013.16.031.
[2]李慧静.超高静压协同酶法降低专用大豆分离蛋白致敏性的研究[D].无锡:江南大学,2013:23-46.
[3]单晓红.大豆和牛奶致敏原表位预测及加工对其抗原性和结构的影晌[D].无锡:江南大学,2013:1-23.
[4]宋宏新.食品免疫学[M].北京:中国轻工业出版社,2009:169-176.
[5]冯彦娟,袁娟丽,佟平,等.大豆过敏原的检测方法研究进展[J].食品科学,2012,33(23):365-369.
[6]李海侠.蛋白质抗原表位研究进展[J].微生物学免疫学进展,2007,35(1):54-58.DOI:10.13309/j.cnki.pmi.2007.01.015.
[7]王耀,邓瑞广,张改平,等.大豆过敏原免疫学检测方法研究进展[J].中国粮油学报,2015,30(8):143-146.DOI:10.3969/j.issn.1003-0174.2015.08.027.
[8]吴敬,吴梧桐.B细胞蛋白质抗原表位的研究方法进展[J].药物生物技术,2000,7(4):239-242.DOI:10.3969/j.issn.1005-8915.2000.04.013.
[9]黄健,郭建巍,蔡美英.B细胞表位预测[J].微生物学免疫学进展,2004,32(1):40-42.DOI:10.13309/j.cnki.pmi.2004.01.012.
[10]章辉,朱荫昌.B细胞表位预测的研究进展[J].中国血吸虫病防治杂志,2006,18(3):236-239.DOI:10.16250/j.32.1374.2006.03.032.
[11]梁瑾,王靖飞.B细胞表位预测方法研究进展[J].生命科学,2009,21(2):320-323.DOI:10.13376/j.cbls/2009.02.016.
[12]RUDOLPH R,TSCHESCHE H.Modern methods in protein and nucleic acid research[M].New York:Walter de Gruger Berlin,1990,231.
[13]HOOP T P,WOODS K R.Prediction of protein antigenic determinants from amino acid sequences[J].Proceedings of the National Academy of Sciences,1981,78(6):3824-3828.
[14]KARPLUS P A,SCHULZ G E.Prediction of chain flexibility in proteins[J].Naturwissenschaften,1985,72(4):212-213.
[15]髙冶.基于二级结构的蛋白质三维结构预测方法研究[D].海口:海南大学,2013:12-15.
[16]CHEN J,LIU H,YANG J,et al.Prediction of linear B-cell epitopes using amino acid pair antigenicity scale[J].Amino Acids,2007,33:423-428.DOI:10.1007/s00726-006-0485-9.
[17]EL-MANZALAWY Y,DOBBS D,HONAVAR V.Predicting linear B-cell epitopes using string kernels[J].Journal of Molecular Recognition,2008,21(4):243-255.DOI:10.1002/jmr.893.
[18]ANDERSEN P H,NIELSEN M,LUND O.Prediction of residues in discontinuous B-cell epitopes using protein 3D structure[J].Protein Science,2006,15(11):2558-2567.DOI:10.1110/ps.062405906.
[19]SORIA-GUERRA R E,NIETO-GOMEZ R,GOVEA-ALONSO DO,et al.An overview of bioinformatics tools for epitope prediction:implications on vaccine development[J].Journal of Biomedical Informatics,2015,53:405-414.DOI:10.1016/j.jbi.2014.11.003.
[20]闫慧丽.大豆主要过敏原Gly m bd 28K IgG结合表位的定位研究[D].郑州:河南工业大学,2016:1-12;25-35.
[21]GOVINDARAJ D,SHARMA S,GAUR S N,et al.Immunogenic peptides:B&T cell epitopes of Per a 10 allergen of Periplaneta americana[J].Molecular Immunology,2016,80:24-32.DOI:10.1016/j.molimm.2016.10.007.
[22]MAO H Y,CAO M J,MALEKI S J,et al.Structural characterization and IgE epitope analysis of arginine kinase from Scylla paramamosain[J].Molecular Immunology,2013,56(4):463-470.DOI:10.1016/j.molimm.2013.04.016.
[23]PATWARY N I,ISLAM M S,SOHEL M,et al.In silico structure analysis and epitope prediction of E3 CR1-beta protein of Human Adenovirus E for vaccine design[J].Biomedical Journal,2016,39(6):382-390.DOI:10.1016/j.bj.2016.11.004.
[24]BIASINI M,BIENERT S,WATERHOUSE A,et al.SWISS-MODEL:modelling protein tertiary and quaternary structure using evolutionary information[J].Nucleic Acids Research,2014,42:252-258.DOI:10.1093/nar/gku340.
[25]谌容,陈敏,杨春贤.基于SWISS-MODEL的蛋白质三维结构建模[J].生命的化学,2006,26(1):54-55.DOI:10.3969/j.issn.1000-1336.2006.01.021.
[26]李江英,白雪娟,梁艳,等.用DNAStar软件预测Rv1410c结核分枝杆菌蛋白抗原表位[J].细胞与分子免疫学杂志,2015,31(4):474-477.DOI:10.13423/j.cnki.cjcmi.007316.
[27]GEOURJON C,DELéAGE G.SOPMA:significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments[J].Computer Applications in the Biosciences,1995,11(6):681-684.
[28]张海霞.蛋白质二级结构预测方法研究[D].大连:大连理工大学,2004:20.
[29]景楠.基于神经网络方法蛋白质二级结构预测的研究[D].长春:吉林大学,2004:7-13.
[30]LARSEN J E,LUND O,NIELSEN M.Improved method for predicting linear B-cell epitopes[J].Immunome Research,2006,2:2.DOI:10.1186/1745-7580-2-2.
[31]黄影.隐马尔科夫模型在生物信息学中的应用[J].电子科技,2015,28(8):185-189.DOI:10.16180/j.cnki.issn1007-7820.2015.08.052.
[32]SAHA S,RAGHAVA G P.Prediction of continuous B-cell epitopes in an antigen using recurrent neural network[J].Proteins,2006,65(1):40-48.DOI:10.1002/prot.21078.
[33]KRINGELUM J V,LUNDEGAARD C,LUND O,et al.Reliable Bcell epitope predictions:impacts of method development and improved benchmarking[J].PLoS Computational Biology,2012,8:1-10.DOI:10.1371/journal.pcbi.1002829.
[34]RUSSI R C,BOURDIN E,GARCíA M I,et al.In silico prediction of T-and B-cell epitopes in PmpD:first step towards to the design of a Chlamydia trachomatis vaccine[J].Biomedical Journal,2018,41(2):109-117.DOI:10.1016/j.bj.2018.04.007.
[35]柯丕余.应用蛋白质拉氏图信息提高谷氨酸脱羧酶催化性能的研究[D].杭州:浙江大学,2015:15-17.
[2]李慧静.超高静压协同酶法降低专用大豆分离蛋白致敏性的研究[D].无锡:江南大学,2013:23-46.
[3]单晓红.大豆和牛奶致敏原表位预测及加工对其抗原性和结构的影晌[D].无锡:江南大学,2013:1-23.
[4]宋宏新.食品免疫学[M].北京:中国轻工业出版社,2009:169-176.
[5]冯彦娟,袁娟丽,佟平,等.大豆过敏原的检测方法研究进展[J].食品科学,2012,33(23):365-369.
[6]李海侠.蛋白质抗原表位研究进展[J].微生物学免疫学进展,2007,35(1):54-58.DOI:10.13309/j.cnki.pmi.2007.01.015.
[7]王耀,邓瑞广,张改平,等.大豆过敏原免疫学检测方法研究进展[J].中国粮油学报,2015,30(8):143-146.DOI:10.3969/j.issn.1003-0174.2015.08.027.
[8]吴敬,吴梧桐.B细胞蛋白质抗原表位的研究方法进展[J].药物生物技术,2000,7(4):239-242.DOI:10.3969/j.issn.1005-8915.2000.04.013.
[9]黄健,郭建巍,蔡美英.B细胞表位预测[J].微生物学免疫学进展,2004,32(1):40-42.DOI:10.13309/j.cnki.pmi.2004.01.012.
[10]章辉,朱荫昌.B细胞表位预测的研究进展[J].中国血吸虫病防治杂志,2006,18(3):236-239.DOI:10.16250/j.32.1374.2006.03.032.
[11]梁瑾,王靖飞.B细胞表位预测方法研究进展[J].生命科学,2009,21(2):320-323.DOI:10.13376/j.cbls/2009.02.016.
[12]RUDOLPH R,TSCHESCHE H.Modern methods in protein and nucleic acid research[M].New York:Walter de Gruger Berlin,1990,231.
[13]HOOP T P,WOODS K R.Prediction of protein antigenic determinants from amino acid sequences[J].Proceedings of the National Academy of Sciences,1981,78(6):3824-3828.
[14]KARPLUS P A,SCHULZ G E.Prediction of chain flexibility in proteins[J].Naturwissenschaften,1985,72(4):212-213.
[15]髙冶.基于二级结构的蛋白质三维结构预测方法研究[D].海口:海南大学,2013:12-15.
[16]CHEN J,LIU H,YANG J,et al.Prediction of linear B-cell epitopes using amino acid pair antigenicity scale[J].Amino Acids,2007,33:423-428.DOI:10.1007/s00726-006-0485-9.
[17]EL-MANZALAWY Y,DOBBS D,HONAVAR V.Predicting linear B-cell epitopes using string kernels[J].Journal of Molecular Recognition,2008,21(4):243-255.DOI:10.1002/jmr.893.
[18]ANDERSEN P H,NIELSEN M,LUND O.Prediction of residues in discontinuous B-cell epitopes using protein 3D structure[J].Protein Science,2006,15(11):2558-2567.DOI:10.1110/ps.062405906.
[19]SORIA-GUERRA R E,NIETO-GOMEZ R,GOVEA-ALONSO DO,et al.An overview of bioinformatics tools for epitope prediction:implications on vaccine development[J].Journal of Biomedical Informatics,2015,53:405-414.DOI:10.1016/j.jbi.2014.11.003.
[20]闫慧丽.大豆主要过敏原Gly m bd 28K IgG结合表位的定位研究[D].郑州:河南工业大学,2016:1-12;25-35.
[21]GOVINDARAJ D,SHARMA S,GAUR S N,et al.Immunogenic peptides:B&T cell epitopes of Per a 10 allergen of Periplaneta americana[J].Molecular Immunology,2016,80:24-32.DOI:10.1016/j.molimm.2016.10.007.
[22]MAO H Y,CAO M J,MALEKI S J,et al.Structural characterization and IgE epitope analysis of arginine kinase from Scylla paramamosain[J].Molecular Immunology,2013,56(4):463-470.DOI:10.1016/j.molimm.2013.04.016.
[23]PATWARY N I,ISLAM M S,SOHEL M,et al.In silico structure analysis and epitope prediction of E3 CR1-beta protein of Human Adenovirus E for vaccine design[J].Biomedical Journal,2016,39(6):382-390.DOI:10.1016/j.bj.2016.11.004.
[24]BIASINI M,BIENERT S,WATERHOUSE A,et al.SWISS-MODEL:modelling protein tertiary and quaternary structure using evolutionary information[J].Nucleic Acids Research,2014,42:252-258.DOI:10.1093/nar/gku340.
[25]谌容,陈敏,杨春贤.基于SWISS-MODEL的蛋白质三维结构建模[J].生命的化学,2006,26(1):54-55.DOI:10.3969/j.issn.1000-1336.2006.01.021.
[26]李江英,白雪娟,梁艳,等.用DNAStar软件预测Rv1410c结核分枝杆菌蛋白抗原表位[J].细胞与分子免疫学杂志,2015,31(4):474-477.DOI:10.13423/j.cnki.cjcmi.007316.
[27]GEOURJON C,DELéAGE G.SOPMA:significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments[J].Computer Applications in the Biosciences,1995,11(6):681-684.
[28]张海霞.蛋白质二级结构预测方法研究[D].大连:大连理工大学,2004:20.
[29]景楠.基于神经网络方法蛋白质二级结构预测的研究[D].长春:吉林大学,2004:7-13.
[30]LARSEN J E,LUND O,NIELSEN M.Improved method for predicting linear B-cell epitopes[J].Immunome Research,2006,2:2.DOI:10.1186/1745-7580-2-2.
[31]黄影.隐马尔科夫模型在生物信息学中的应用[J].电子科技,2015,28(8):185-189.DOI:10.16180/j.cnki.issn1007-7820.2015.08.052.
[32]SAHA S,RAGHAVA G P.Prediction of continuous B-cell epitopes in an antigen using recurrent neural network[J].Proteins,2006,65(1):40-48.DOI:10.1002/prot.21078.
[33]KRINGELUM J V,LUNDEGAARD C,LUND O,et al.Reliable Bcell epitope predictions:impacts of method development and improved benchmarking[J].PLoS Computational Biology,2012,8:1-10.DOI:10.1371/journal.pcbi.1002829.
[34]RUSSI R C,BOURDIN E,GARCíA M I,et al.In silico prediction of T-and B-cell epitopes in PmpD:first step towards to the design of a Chlamydia trachomatis vaccine[J].Biomedical Journal,2018,41(2):109-117.DOI:10.1016/j.bj.2018.04.007.
[35]柯丕余.应用蛋白质拉氏图信息提高谷氨酸脱羧酶催化性能的研究[D].杭州:浙江大学,2015:15-17.