基于RIVEM的人肠道病毒衣壳表面结构绘制流程
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摘要
RIVEM是一款通过球面投射的方式在平面上绘制二十面体病毒衣壳结构的软件工具,因为开发时间较早,目前无法直接识别RCSB PDB数据库中绝大多数肠道病毒的三维结构文件。为此本研究发展了将RCSB PDB坐标体系转换到RIVEM PDB坐标体系的算法,开发了基于RIVEM的人肠道病毒衣壳表面结构绘制流程,并将该流程应用到PSGL-1和SCARB2这两个重要的肠道病毒受体的研究中。结果显示:构建的流程成功的绘制了RCSB PDB数据库中人肠道病毒的衣壳表面结构。与PyMol相比,RIVEM绘制的衣壳表面结构具有信息量更大,更便于研究衣壳与受体和抗体之间的相互作用关系等优点。对于广大非结构生物学专业的病毒学研究者来说,该流程能够促进RIVEM在衣壳与受体、抗体和抗病毒药物的相互作用、抗原表位、结构蛋白变异的监测以及肠道病毒致病机制等研究领域中的应用。该流程也能直接推广到包括脊髓灰质炎病毒、甲肝病毒和口蹄疫病毒在内的其他小RNA病毒的研究中。
The computer program RIVEM was developed to project the capsid surface of an icosahedral virus onto a sphere.RIVEM was developed more than one decade ago,so it cannot import the three-dimensional(3 D)structures of most current human enteroviruses from the Research Collaboratory for Structural Bioinformatics Protein Data Bank(RCSB PDB)database.An algorithm was developed to convert the RCSB PDB coordinate system into the RIVEM PDB coordinate system.Based on this conversion,a routine mapping process for the capsid surfaces of human enteroviruses was built.This process was applied to the study of two important human enteroviruses' receptors:P-selectin glycoprotein ligand-1 and scavenger receptor class B,member 2.Results showed that the process mapped the capsid surfaces of human enteroviruses from the RCSB PDB database correctly.Compared with PyMol,the capsid surfaces mapped by RIVEM could integrate more properties of human enteroviruses readily,and were more straightforward for research on the binding relationship among capsids,receptors and neutralizing antibodies.For researchers without a background in structural biology,this process could help application of RIVEM for studies on:interaction among capsids,receptors and antibodies;antigenic epitopes;monitoring of the variations of structural proteins;the pathogenic mechanism of human enteroviruses.This process could also be extended to other icosahedral viruses,including the poliovirus,hepatitis A virus and foot-and-mouth disease virus.
The computer program RIVEM was developed to project the capsid surface of an icosahedral virus onto a sphere.RIVEM was developed more than one decade ago,so it cannot import the three-dimensional(3 D)structures of most current human enteroviruses from the Research Collaboratory for Structural Bioinformatics Protein Data Bank(RCSB PDB)database.An algorithm was developed to convert the RCSB PDB coordinate system into the RIVEM PDB coordinate system.Based on this conversion,a routine mapping process for the capsid surfaces of human enteroviruses was built.This process was applied to the study of two important human enteroviruses' receptors:P-selectin glycoprotein ligand-1 and scavenger receptor class B,member 2.Results showed that the process mapped the capsid surfaces of human enteroviruses from the RCSB PDB database correctly.Compared with PyMol,the capsid surfaces mapped by RIVEM could integrate more properties of human enteroviruses readily,and were more straightforward for research on the binding relationship among capsids,receptors and neutralizing antibodies.For researchers without a background in structural biology,this process could help application of RIVEM for studies on:interaction among capsids,receptors and antibodies;antigenic epitopes;monitoring of the variations of structural proteins;the pathogenic mechanism of human enteroviruses.This process could also be extended to other icosahedral viruses,including the poliovirus,hepatitis A virus and foot-and-mouth disease virus.
引文
[1]刘志芳,桂娟娟,华启航,董长征.人肠道病毒71型与手足口病的分子流行病学及其分子进化[J].遗传,2015,37(5):426-435.
[2]Mcminn P C.Recent advances in the molecular epidemiology and control of human enterovirus 71infection[J].Curr Opin Virol,2012,2(2):199-205.
[3]郭素杰,李琦涵.人肠道病毒71型与宿主相互作用研究进展[J].病毒学报,2011,27(5):505-509.
[4]Wang X,Peng W,Ren J,Hu Z,Xu J,Lou Z,Li X,Yin W,Shen X,Porta C.A sensor-adaptor mechanism for enterovirus uncoating from structures of EV-A71[J].Nat Struct Mol Biol,2012,19(4):424-429.
[5]祝苗,张添方,高柳莺,董长征.人肠道病毒71型抗原表位的研究进展[J].中国细胞生物学学报,2017,39(9):1243-1250.
[6]Nishimura Y,Shimojima M,Tano Y,Miyamura T,Wakita T,Shimizu H.Human P-selectin glycoprotein ligand-1is a functional receptor for enterovirus 71[J].Nat Med,2009,15(7):794-797.
[7]Yamayoshi S,Yamashita Y,Li J,Hanagata N,Minowa T,Takemura T,Koike S.Scavenger receptor B2is a cellular receptor for enterovirus 71[J].Nat Med,2009,15(7):798-801.
[8]Kuo R L,Shih S R.Strategies to develop antivirals against enterovirus 71[J/OL].Virol J,2013,10(28).
[9]Nishimura Y,Mclaughlin N P,Pan J,Goldstein S,Hafenstein S,Shimizu H,Winkler J D,Bergelson J M.The suramin derivative NF449interacts with the 5-fold vertex of the enterovirus A71capsid to prevent virus attachment to PSGL-1and heparan sulfate[J/OL].PLoS Pathog,2015,11(10):e1005184.
[10]陈祥鹏,檀晓娟,许文波.柯萨奇病毒A组16型分子流行病学和疫苗研究进展[J].病毒学报,2014,30(4):483-488.
[11]黄克强,张勇,许文波.全球EV-A71的基因型分布[J].病毒学报,2017,33(3):469-476.
[12]刘向东,顾新蕊,冀天娇,郭悦,黄克强,刘俐,杨倩,祝双利,许文波.2013-2015年中国重症手足口病的流行病学特征和病原构成[J].病毒学报,2018,34(4):477-482.
[13]赵奇,朱俊萍.中国手足口病的流行状况及病原谱变化分析[J].病毒学报,2015,31(5):554-559.
[14]李洁,张勇,许文波.EV-A71感染导致的重症手足口病的机制及防控研究进展[J].病毒学报,2018,34(2):277-284.
[15]Xiao C,Rossmann M G.Interpretation of electron density with stereographic roadmap projections[J].J Struct Biol,2007,158(2):182-187.
[16]DeLano WL.2002.The PyMol molecular graphics system[CP].Delano Scientific LLC,San Carlos,CA.http://www.PyMol.org.
[17]Natarajan P,Lander G C,Shepherd C M,Reddy V S,Rd B C,Johnson J E.Exploring icosahedral virus structures with VIPER[J].Nat Rev Microbiol,2005,3(10):809-817.
[18]Carrillotripp M,Shepherd C M,Borelli I A,Venkataraman S,Lander G,Natarajan P,Johnson J E,Brooks C L 3rd,Reddy V S.VIPERdb2:an enhanced and web API enabled relational database for structural virology[J].Nucleic Acids Res,2009,37(Database issue):436-442.
[19]Nishimura Y,Wakita T,Shimizu H.Tyrosine sulfation of the amino terminus of PSGL-1is critical for enterovirus 71infection[J/OL].PLoS Pathog,2010,6(11):e1001174.
[20]Yamayoshi S,Ohka S,Fujii K,Koike S.Functional comparison of SCARB2and PSGL1as receptors for enterovirus 71[J].J Virol,2013,87(6):3335-3347.
[21]Nishimura Y,Lee H,Hafenstein S,Kataoka C,Wakita T,Bergelson J M,Shimizu H.Enterovirus 71binding to PSGL-1on leukocytes:VP1-145acts as a molecular switch to control receptor interaction[J/OL].PLoS Pathog,2013,9(7):e1003511.
[22]Lee H,Cifuente J O,Ashley R E,Conway J F,Makhov A M,Tano Y,Shimizu H,Nishimura Y,Hafenstein S.A strain-specific epitope of enterovirus 71identified by cryo-electron microscopy of the complex with Fab from neutralizing antibody[J].J Virol,2013,87(21):11363-11370.
[23]Dang M,Wang X,Wang Q,Wang Y,Lin J,Sun Y,Li X,Zhang L,Lou Z,Wang J,Rao Z.Molecular mechanism of SCARB2-mediated attachment and uncoating of EV-A71[J].Protein Sci,2014,5(9):692-703.
[24]Ye X,Fan C,Ku Z,Zuo T,Kong L,Zhang C,Shi J,Liu Q,Chen T,Zhang Y,Jiang W,Zhang L,Huang Z,Cong Y.Structural basis for recognition of human enterovirus 71by a bivalent broadly neutralizing monoclonal antibody[J/OL].PLoS Pathog,2016,12(3):e1005454.
[25]Plevka P,Lim P Y,Perera R,Cardosa J,Suksatu A,Kuhn R J,Rossmann M G.Neutralizing antibodies can initiate genome release from human enterovirus 71[J].Proc Natl Acad Sci U S A,2014,111(6):2134-2139.
[26]Muckelbauer J K,Kremer M,Minor I,Diana G,Dutko F J,Groarke J,Pevear D C,Rossmann M G.The structure of coxsackievirus B3at 3.5Aresolution[J].Structure,1995,3(7):653-667.
[27]Xiao C,Bator-Kelly C M,Rieder E,Chipman P R,Craig A,Kuhn R J,Wimmer E,Rossmann M G.The crystal structure of coxsackievirus A21and its interaction with ICAM-1[J].Structure,2005,13(7):1019-1033.
[28]Plevka P,Perera R,Cardosa J,Kuhn R J,Rossmann M G.Crystal structure of human enterovirus 71[J].Science,2012,336(6086):1274.
[29]Rossmann M G,Palmenberg A C.Conservation of the putative receptor attachment site in picornaviruses[J].Virology,1988,164(2):373-382.
[30]Chapman M S.Mapping the surface properties of macromolecules[J].Protein Sci,1993,2(3):459-469.
[31]Pettersen E F,Goddard T D,Huang C C,Couch G S,Greenblatt D M,Meng E C,Ferrin T E.UCSF Chimera—A visualization system for exploratory research and analysis[J].J Comput Chem,2004,25(13):1605-1612.
[2]Mcminn P C.Recent advances in the molecular epidemiology and control of human enterovirus 71infection[J].Curr Opin Virol,2012,2(2):199-205.
[3]郭素杰,李琦涵.人肠道病毒71型与宿主相互作用研究进展[J].病毒学报,2011,27(5):505-509.
[4]Wang X,Peng W,Ren J,Hu Z,Xu J,Lou Z,Li X,Yin W,Shen X,Porta C.A sensor-adaptor mechanism for enterovirus uncoating from structures of EV-A71[J].Nat Struct Mol Biol,2012,19(4):424-429.
[5]祝苗,张添方,高柳莺,董长征.人肠道病毒71型抗原表位的研究进展[J].中国细胞生物学学报,2017,39(9):1243-1250.
[6]Nishimura Y,Shimojima M,Tano Y,Miyamura T,Wakita T,Shimizu H.Human P-selectin glycoprotein ligand-1is a functional receptor for enterovirus 71[J].Nat Med,2009,15(7):794-797.
[7]Yamayoshi S,Yamashita Y,Li J,Hanagata N,Minowa T,Takemura T,Koike S.Scavenger receptor B2is a cellular receptor for enterovirus 71[J].Nat Med,2009,15(7):798-801.
[8]Kuo R L,Shih S R.Strategies to develop antivirals against enterovirus 71[J/OL].Virol J,2013,10(28).
[9]Nishimura Y,Mclaughlin N P,Pan J,Goldstein S,Hafenstein S,Shimizu H,Winkler J D,Bergelson J M.The suramin derivative NF449interacts with the 5-fold vertex of the enterovirus A71capsid to prevent virus attachment to PSGL-1and heparan sulfate[J/OL].PLoS Pathog,2015,11(10):e1005184.
[10]陈祥鹏,檀晓娟,许文波.柯萨奇病毒A组16型分子流行病学和疫苗研究进展[J].病毒学报,2014,30(4):483-488.
[11]黄克强,张勇,许文波.全球EV-A71的基因型分布[J].病毒学报,2017,33(3):469-476.
[12]刘向东,顾新蕊,冀天娇,郭悦,黄克强,刘俐,杨倩,祝双利,许文波.2013-2015年中国重症手足口病的流行病学特征和病原构成[J].病毒学报,2018,34(4):477-482.
[13]赵奇,朱俊萍.中国手足口病的流行状况及病原谱变化分析[J].病毒学报,2015,31(5):554-559.
[14]李洁,张勇,许文波.EV-A71感染导致的重症手足口病的机制及防控研究进展[J].病毒学报,2018,34(2):277-284.
[15]Xiao C,Rossmann M G.Interpretation of electron density with stereographic roadmap projections[J].J Struct Biol,2007,158(2):182-187.
[16]DeLano WL.2002.The PyMol molecular graphics system[CP].Delano Scientific LLC,San Carlos,CA.http://www.PyMol.org.
[17]Natarajan P,Lander G C,Shepherd C M,Reddy V S,Rd B C,Johnson J E.Exploring icosahedral virus structures with VIPER[J].Nat Rev Microbiol,2005,3(10):809-817.
[18]Carrillotripp M,Shepherd C M,Borelli I A,Venkataraman S,Lander G,Natarajan P,Johnson J E,Brooks C L 3rd,Reddy V S.VIPERdb2:an enhanced and web API enabled relational database for structural virology[J].Nucleic Acids Res,2009,37(Database issue):436-442.
[19]Nishimura Y,Wakita T,Shimizu H.Tyrosine sulfation of the amino terminus of PSGL-1is critical for enterovirus 71infection[J/OL].PLoS Pathog,2010,6(11):e1001174.
[20]Yamayoshi S,Ohka S,Fujii K,Koike S.Functional comparison of SCARB2and PSGL1as receptors for enterovirus 71[J].J Virol,2013,87(6):3335-3347.
[21]Nishimura Y,Lee H,Hafenstein S,Kataoka C,Wakita T,Bergelson J M,Shimizu H.Enterovirus 71binding to PSGL-1on leukocytes:VP1-145acts as a molecular switch to control receptor interaction[J/OL].PLoS Pathog,2013,9(7):e1003511.
[22]Lee H,Cifuente J O,Ashley R E,Conway J F,Makhov A M,Tano Y,Shimizu H,Nishimura Y,Hafenstein S.A strain-specific epitope of enterovirus 71identified by cryo-electron microscopy of the complex with Fab from neutralizing antibody[J].J Virol,2013,87(21):11363-11370.
[23]Dang M,Wang X,Wang Q,Wang Y,Lin J,Sun Y,Li X,Zhang L,Lou Z,Wang J,Rao Z.Molecular mechanism of SCARB2-mediated attachment and uncoating of EV-A71[J].Protein Sci,2014,5(9):692-703.
[24]Ye X,Fan C,Ku Z,Zuo T,Kong L,Zhang C,Shi J,Liu Q,Chen T,Zhang Y,Jiang W,Zhang L,Huang Z,Cong Y.Structural basis for recognition of human enterovirus 71by a bivalent broadly neutralizing monoclonal antibody[J/OL].PLoS Pathog,2016,12(3):e1005454.
[25]Plevka P,Lim P Y,Perera R,Cardosa J,Suksatu A,Kuhn R J,Rossmann M G.Neutralizing antibodies can initiate genome release from human enterovirus 71[J].Proc Natl Acad Sci U S A,2014,111(6):2134-2139.
[26]Muckelbauer J K,Kremer M,Minor I,Diana G,Dutko F J,Groarke J,Pevear D C,Rossmann M G.The structure of coxsackievirus B3at 3.5Aresolution[J].Structure,1995,3(7):653-667.
[27]Xiao C,Bator-Kelly C M,Rieder E,Chipman P R,Craig A,Kuhn R J,Wimmer E,Rossmann M G.The crystal structure of coxsackievirus A21and its interaction with ICAM-1[J].Structure,2005,13(7):1019-1033.
[28]Plevka P,Perera R,Cardosa J,Kuhn R J,Rossmann M G.Crystal structure of human enterovirus 71[J].Science,2012,336(6086):1274.
[29]Rossmann M G,Palmenberg A C.Conservation of the putative receptor attachment site in picornaviruses[J].Virology,1988,164(2):373-382.
[30]Chapman M S.Mapping the surface properties of macromolecules[J].Protein Sci,1993,2(3):459-469.
[31]Pettersen E F,Goddard T D,Huang C C,Couch G S,Greenblatt D M,Meng E C,Ferrin T E.UCSF Chimera—A visualization system for exploratory research and analysis[J].J Comput Chem,2004,25(13):1605-1612.