活性肽与MHC结合能力预测的免疫信息学方法研究进展
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摘要
综述活性肽与MHC(主要组织相容性复合体,major histocompatibility complex)结合能力预测的免疫信息学方法的最新进展,介绍常用的肽与MHC分子结合预测的相关工具及方法,分析了各类方法的特点、研究重点和难点,以期为寻找免疫活性肽提供更快捷的方法。
In this paper,the latest advances in immune-informatics methods for predicting the binding ability of active peptides to MHC are reviewed.The related tools and methods for predicting the binding of commonly used peptides to MHC molecules are introduced.The characteristics,research focuses,and difficulties of various methods are analyzed.Finding immune-active peptides provides a faster method.
In this paper,the latest advances in immune-informatics methods for predicting the binding ability of active peptides to MHC are reviewed.The related tools and methods for predicting the binding of commonly used peptides to MHC molecules are introduced.The characteristics,research focuses,and difficulties of various methods are analyzed.Finding immune-active peptides provides a faster method.
引文
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[15]MARSH Steven,PETER Parham,LIN Barber.HLA facts book[M].[S.l.]:Academic Press,2000:208-236.
[16]WU Xin,MICHAEL G Walker,LUO Jing-chu,et al.GBA server:EST-based digital gene expression profiling[J].Nucleic Acids Research,2005,33(Web Server issue):673-676.
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[18]TATENO Yoshio,SAITOU Naruya,OKUBO Kousaku,et al.DDBJ in collaboration with mass-sequencing teams on annotation[J].Nucleic Acids Research,2005,33(Database issue):25-28.
[19]孙继丽,张工梁,陈仁彪.HLA数据库和HLA命名系统[J].中国输血杂志,2005,18(2):174-176.
[20]RAMMENSEE Hans-Georg,BACHMANN J,EMMERICH N P N,et al.SYFPEITHI:database for MHC ligands and peptide motifs[J].Immunogenetics,1999,50(4):213-219.
[21]WHEELER David L,CHURCH Deanna M,LASH Alex E,et al.Database resources of the National Center for Biotechnology Information[J].Nucleic Acids Research,2007,35(Database issue):5-12.
[22]ROBINSON James,WALLER Matthew,PARHAM Peter,et al.IMGT/HLA Database:a sequence database for the human major histocompatibility complex[J].Nucleic Acids Research,2000,55(3):210-213.
[23]BERMAN Helen,WESTBROOK John,FENG Z,et al.The protein data bank[J].Genetica,2000,28(1):235-242.
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[27]SCHNBACH Christian,KOH Judice L Y,FLOWER Darren,et al.FIMM,a database of functional molecular immunology[J].Nucleic Acids Research,2002,30(1):226-229.
[28]RECHE Pedro A,ZHANG Hong,GLUTTING John-Paul,et al.EPIMHC:a curated database of MHC-binding peptides for customized computational vaccinology[J].Bioinformatics,2005,21(9):2 140-2 141.
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[31]LEFRANC Marie-Paule,EHRENMANN Francois,GINESTOUX Chantal,et al.Use of IMGT(?)databases and tools for antibody engineering and humanization[J].Methods in Molecular Biology,2012,907:3-37.
[32]LIAO Shu-jie,ZHANG Wei-na,HU Xiao-ji,et al.Preparation of HPV18 E7peptide plus CpG vaccine and its immunologic effects in vitro[J].Chinese Medical Journal,2012,92(23):1 641-1 645.
[33]ZHAO Wei-peng,LONG Hai-xia,ZHU Bo,et al.Prediction of HLA-A 2.1-restricted CTL epitopes from IGFBP7antigen of lung carcinoma[J].中国人民解放军军医大学学报:英文版,2009,24(2):63-68.
[34]LI Zhang-qiu,ZHANG Mei-xia,HU Hai-yan,et al.[On predicting the T cell and B cell epitopes of platelet membrane glycoprotein II b/III a antibody from human and mice][J].Journal of Biomedical Engineering,2010,27(5):1 146-1 151.
[35]EVA Stodulková,NOVK Peter,DEININGER S9ren-Oliver,et al.LC MALDI-TOF MS/MS and LC ESI FTMS analyses of HLA-B27associated peptides isolated from peripheral blood cells[J].Immunology Letters,2008,116(1):79-85.
[36]BHASIN Manoj,LATA Sneh,RAGHAVA Gajendra Pal Singh.Searching and mapping of T-cell epitopes,MHC binders,and TAP binders[J].Methods in Molecular Biology,2007,409(409):95-112.
[37]SCHULER Mathias M,NASTKE Maria-Dorothea,STEVANOVIKC Stefan.SYFPEITHI:database for searching and T-cell epitope prediction[J].Methods in Molecular Biology,2007,409:75-93.
[38]刘盟梦,李银平,延海莹,等.基于BP神经网络的牡蛎抗氧化活性肽制备工艺优化[J].食品工业科技,2016,37(20):206-210.
[39]陈艳艳,侯虎,陈铁军,等.基于酶传感器-人工神经网络的胶原蛋白酶解监控模型[J].中国食品学报,2016,16(5):167-173.
[40]孙国威,乐国伟,施用晖.模拟酶解大豆7S、11S蛋白及其抗氧化活性的研究[J].食品工业科技,2010(7):101-104.
[41]陈征松,施用晖,乐国伟,等.活性肽搜寻与蛋白模拟水解数据库的建立[J].计算机与应用化学,2007,24(3):331-334.
[42]庞广昌.一种新型具抗菌作用的免疫活性肽及其抗菌机理[D].天津:天津大学,2007:68-76.
[2]程媛,曹慧,徐斐,等.食源性蛋白中免疫活性肽的研究进展[J].食品科学,2015,36(17):296-299.
[3]陈兆国,冯新港,米荣升,等.免疫信息学在抗原虫病疫苗研发中的应用进展[J].中国人兽共患病学报,2010,26(5):495-498.
[4]ORTUTAY Csaba,SIERMALA Markku,VIHINEN Mauno.Molecular characterization of the immune system:emergence of proteins,processes,and domains[J].Immunogenetics,2007,59(5):333-348.
[5]FLOWER Darren R.Vaccines in silico:the growth and power of immunoinformatics[J].Biochemist,2004,26(4):17-20.
[6]GROOT Anne S De,BERZOFSKY Jay A.From genome to vaccine—new immunoinformatics tools for vaccine design[J].Methods,2004,34(4):425-428.
[7]LEFRANC Marie-Paule.IMGT?,the International ImMunoGeneTics Information System?[J].Nucleic Acids Research,2009,37(Database issue):D1 006.
[8]LEFRANC Marie-Paule,CLEMENT O,KAAS Quentin,et al.IMGT-Choreography for Immunogenetics and Immunoinformatics[J].Immunogenetics,2004,27:55-77.
[9]OKUBO K,SUGAWARA H,GOJOBORI T,et al.DDBJ in preparation for overview of research activities behind data submissions[J].Nucleic Acids Research,2006,34(Database issue):D6.
[10]FOLCH G,BERTRAND J.IMGT/PRIMER-DB[J/OL].Information System,2004.[2018-02-17].http://www.imgt.org.
[11]ROBINSON James,WALLER Matthew,PARHAM Peter,et al.IMGT/HLA and IMGT/MHC:sequence databases for the study of the major histocompatibility complex[J].Nucleic Acid Research Medical Journal,2003,31(1):311-314.
[12]KAAS Quentin,RUIZ Manuel,LEFRANC Marie-Paule.IMGT/3Dstructure-DB and IMGT/Structural Query,a database and a tool for immunoglobulin,T cell receptor and MHC structural data[J].Nucleic Acids Research,2004,32(1):208-210.
[13]HORTON Roger,WILMING Laurens,RAND Vikki,et al.Gene map of the extended human MHC[J].Nature Reviews Genetics,2004,5(12):889.
[14]MCGINNIS M B C,CHADWICK R,CONRAD M,et al.Genetic diversity of HLA:functional and medical implication[J].Human Immunology,1997,59(9):580-587.
[15]MARSH Steven,PETER Parham,LIN Barber.HLA facts book[M].[S.l.]:Academic Press,2000:208-236.
[16]WU Xin,MICHAEL G Walker,LUO Jing-chu,et al.GBA server:EST-based digital gene expression profiling[J].Nucleic Acids Research,2005,33(Web Server issue):673-676.
[17]DENNIS A Benson,ILENE Karsch-Mizrachi,DAVID J Lipman,et al.GenBank:update[J].Nucleic Acids Research,2007,36(Database issue):25-30.
[18]TATENO Yoshio,SAITOU Naruya,OKUBO Kousaku,et al.DDBJ in collaboration with mass-sequencing teams on annotation[J].Nucleic Acids Research,2005,33(Database issue):25-28.
[19]孙继丽,张工梁,陈仁彪.HLA数据库和HLA命名系统[J].中国输血杂志,2005,18(2):174-176.
[20]RAMMENSEE Hans-Georg,BACHMANN J,EMMERICH N P N,et al.SYFPEITHI:database for MHC ligands and peptide motifs[J].Immunogenetics,1999,50(4):213-219.
[21]WHEELER David L,CHURCH Deanna M,LASH Alex E,et al.Database resources of the National Center for Biotechnology Information[J].Nucleic Acids Research,2007,35(Database issue):5-12.
[22]ROBINSON James,WALLER Matthew,PARHAM Peter,et al.IMGT/HLA Database:a sequence database for the human major histocompatibility complex[J].Nucleic Acids Research,2000,55(3):210-213.
[23]BERMAN Helen,WESTBROOK John,FENG Z,et al.The protein data bank[J].Genetica,2000,28(1):235-242.
[24]BRUSIC Vladimir,RUDY George,KYNE Anthony P,et al.MHCPEP,a database of MHC-binding peptides:update 1996[J].Nucleic Acids Research,1998,26(1):3 663-3 665.
[25]BHASIN Manoj,SINGH Harpreet,RAGHAVA Gajendra Pal Singh.MHCBN:a comprehensive database of MHC binding and non-binding peptides[J].Bioinformatics,2003,19(5):665-666.
[26]BLYTH Martin J,DOYTCHINOVA Irini A,FLOWER Darren.JenPep:a database of quantitative functional peptide data for immunology[J].Bioinformatics,2002,18(3):434-439.
[27]SCHNBACH Christian,KOH Judice L Y,FLOWER Darren,et al.FIMM,a database of functional molecular immunology[J].Nucleic Acids Research,2002,30(1):226-229.
[28]RECHE Pedro A,ZHANG Hong,GLUTTING John-Paul,et al.EPIMHC:a curated database of MHC-binding peptides for customized computational vaccinology[J].Bioinformatics,2005,21(9):2 140-2 141.
[29]Tripos Associates Inc.SYBYL Software,Version 6.9[CP].Morris,Peters,St.Louis:Tripos Associates Inc,1985.
[30]HOLCOMB Cherie L,RASTROU Melinda,WILLIAMS T C,et al.Next-generation sequencing can reveal in vitro-generated PCR crossover products:some artifactual sequences correspond to HLA alleles in the IMGT/HLA database[J].Tissue Antigens,2014,83(1):32-40.
[31]LEFRANC Marie-Paule,EHRENMANN Francois,GINESTOUX Chantal,et al.Use of IMGT(?)databases and tools for antibody engineering and humanization[J].Methods in Molecular Biology,2012,907:3-37.
[32]LIAO Shu-jie,ZHANG Wei-na,HU Xiao-ji,et al.Preparation of HPV18 E7peptide plus CpG vaccine and its immunologic effects in vitro[J].Chinese Medical Journal,2012,92(23):1 641-1 645.
[33]ZHAO Wei-peng,LONG Hai-xia,ZHU Bo,et al.Prediction of HLA-A 2.1-restricted CTL epitopes from IGFBP7antigen of lung carcinoma[J].中国人民解放军军医大学学报:英文版,2009,24(2):63-68.
[34]LI Zhang-qiu,ZHANG Mei-xia,HU Hai-yan,et al.[On predicting the T cell and B cell epitopes of platelet membrane glycoprotein II b/III a antibody from human and mice][J].Journal of Biomedical Engineering,2010,27(5):1 146-1 151.
[35]EVA Stodulková,NOVK Peter,DEININGER S9ren-Oliver,et al.LC MALDI-TOF MS/MS and LC ESI FTMS analyses of HLA-B27associated peptides isolated from peripheral blood cells[J].Immunology Letters,2008,116(1):79-85.
[36]BHASIN Manoj,LATA Sneh,RAGHAVA Gajendra Pal Singh.Searching and mapping of T-cell epitopes,MHC binders,and TAP binders[J].Methods in Molecular Biology,2007,409(409):95-112.
[37]SCHULER Mathias M,NASTKE Maria-Dorothea,STEVANOVIKC Stefan.SYFPEITHI:database for searching and T-cell epitope prediction[J].Methods in Molecular Biology,2007,409:75-93.
[38]刘盟梦,李银平,延海莹,等.基于BP神经网络的牡蛎抗氧化活性肽制备工艺优化[J].食品工业科技,2016,37(20):206-210.
[39]陈艳艳,侯虎,陈铁军,等.基于酶传感器-人工神经网络的胶原蛋白酶解监控模型[J].中国食品学报,2016,16(5):167-173.
[40]孙国威,乐国伟,施用晖.模拟酶解大豆7S、11S蛋白及其抗氧化活性的研究[J].食品工业科技,2010(7):101-104.
[41]陈征松,施用晖,乐国伟,等.活性肽搜寻与蛋白模拟水解数据库的建立[J].计算机与应用化学,2007,24(3):331-334.
[42]庞广昌.一种新型具抗菌作用的免疫活性肽及其抗菌机理[D].天津:天津大学,2007:68-76.