白蛾周氏啮小蜂气味结合蛋白CcOBP3的生物信息学分析
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摘要
为了探究白蛾周氏啮小蜂气味结合蛋白CcOBP3的结合特性,利用Bio Edit、SignalP3.0 Serve、HMMTop对CcOBP3的碱基序列进行了预测分析,用Swiss-Model对CcOBP3蛋白进行同源建模,从Pubchem下载美国白蛾的5种蛹挥发物(邻苯二甲酸二甲酯、正戊醛、十六烷、正十五烷、正十四烷)及3种植物挥发物(苊、3-蒈烯和丁酸丁酯)的结构,利用maestro10.2软件进行分子对接.对CcOBP3碱基序列的分析结果表明,CcOBP3具有昆虫气味结合蛋白的典型特征,即相对分子质量小,有6个保守的半胱氨酸位点,在N端有信号肽.通过Swiss-Model构建的CcOBP3的结构模型中有Arg32-Thr51 (α1)、Leu54-Asn63 (α2)、Pro69-Leu81 (α3)、Ala93-Ile102 (α4)、Ile108-Val116(α5)、Pro128-Glu142 (α6)6个α螺旋结构,拉氏构象和PROSA能量评价结果均表明模型构象合理.分子对接结果表明,CcOBP3与3-蒈烯的结合特性最好,与美国白蛾的挥发物邻苯二甲酸二甲酯和正戊醛的结合特性也较好.推测CcOBP3的功能可能与引诱作用相关. CcOBP3与3-蒈烯主要通过范德华力、碳磷键、碳碳键等进行结合.
To explore the binding characteristics of CcOBP3 of the Chouioia cunea Yang,the base sequences of CcOBP3 were predicted and analyzed by Bio Edit、SignalP3.0 Serve and HMMTop. Homology modeling for CcOBP3 was conducted through Swiss-Model and the 3D structure of five kinds of pupae volatile(Dimethyl phthalate,Valeraldehyde,n-Hexadecane,n-Pentadecane,Etradecane)from Hyphantria cunea(Drury)and three kinds of plant volatile(Acenaphthene,3-Carene,n-Butyl butyrate)were downloaded from Pubchem. Molecular docking was done using maestro 10.2 software. The results of the analysis of CcOBP3 base sequences showed that CcOBP3 had typical characteristics of insect odorant binding protein,i.e.low molecular weight,six conserved cysteine sites and signal peptide at N-terminus. The 3D model of CcOBP3 built by Swiss-Model consisted six α-helices located between residues,i.e. Arg32-Thr51(α1),Leu54-Asn63(α2),Pro69-Leu81(α3),Ala93-Ile102(α4),Ile108-Val116(α5),Pro128-Glu142(α6). Ramachandran plot and PROSA energy evaluation results showed that the model conformation is reasonable. The molecular docking results showed that CcOBP3 had the best binding affinity with 3-Carene and better binding offinity with Dimethyl phthalate and Valeraldehyde,which are the volatiles of Hyphantria cunea(Drury). Therefore,it was speculated that the function of CcOBP3 might be related to attraction. CcOBP3 and 3-Carene are mainly combined by Van der Waals force,carbon-phosphorus bond and carbon-carbon bond.
To explore the binding characteristics of CcOBP3 of the Chouioia cunea Yang,the base sequences of CcOBP3 were predicted and analyzed by Bio Edit、SignalP3.0 Serve and HMMTop. Homology modeling for CcOBP3 was conducted through Swiss-Model and the 3D structure of five kinds of pupae volatile(Dimethyl phthalate,Valeraldehyde,n-Hexadecane,n-Pentadecane,Etradecane)from Hyphantria cunea(Drury)and three kinds of plant volatile(Acenaphthene,3-Carene,n-Butyl butyrate)were downloaded from Pubchem. Molecular docking was done using maestro 10.2 software. The results of the analysis of CcOBP3 base sequences showed that CcOBP3 had typical characteristics of insect odorant binding protein,i.e.low molecular weight,six conserved cysteine sites and signal peptide at N-terminus. The 3D model of CcOBP3 built by Swiss-Model consisted six α-helices located between residues,i.e. Arg32-Thr51(α1),Leu54-Asn63(α2),Pro69-Leu81(α3),Ala93-Ile102(α4),Ile108-Val116(α5),Pro128-Glu142(α6). Ramachandran plot and PROSA energy evaluation results showed that the model conformation is reasonable. The molecular docking results showed that CcOBP3 had the best binding affinity with 3-Carene and better binding offinity with Dimethyl phthalate and Valeraldehyde,which are the volatiles of Hyphantria cunea(Drury). Therefore,it was speculated that the function of CcOBP3 might be related to attraction. CcOBP3 and 3-Carene are mainly combined by Van der Waals force,carbon-phosphorus bond and carbon-carbon bond.
引文
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[13]张新玥,王凤竹,范伟健,等.白蛾周氏啮小蜂普通气味受体OR1的进化分析[J].天津师范大学学报(自然科学版),2018,38(2):29-34.ZHANG X Y,WANG F Z,FAN W J,et al. Evolutionary analysis of the common odorant receptor OR1 of the Chouioia cunea Yang[J]. Journal of Tianjin Normal University(Natural Science Edition),2018,38(2):29-34(in Chinese).
[14]王凤竹,张新玥,范伟健,等.周氏啮小蜂气味结合蛋白I基因的进化分析[J].天津师范大学学报(自然科学版),2017,37(1):46-50.WANG F Z,ZHANG X Y,FAN W J,et al. Phylogenetic analysis on the odorant binding proteinⅠgene of Chouioia cunea Yang[J]. Journal of Tianjin Normal University(Natural Science Edition),2017,37(1):46-50(in Chinese).
[15],CAFLISCH A. Protein structure-based drug design:From docking to molecular dynamics[J]. Current Opinion in Structural Biology,2017,48:93-102.
[16] LI H L,ZHANG L Y,NI C X,et al. Molecular recognition of floral volatile with two olfactory related proteins in the Eastern honeybee(Apis cerana)[J]. International Journal of Biological Macromolecules,2013,56(5):114-121.
[17] DU S Q,YANG Z K,QIN Y G,et al. Computational investigation of the molecular conformation-dependent binding mode of(E)-β-farnesene analogs with a heterocycle to aphid odorant-binding proteins[J]. Journal of Molecular Modeling,2018,24(3):70.
[18]李得宇.桃和李子挥发物对桃蛀螟的引诱作用[D].北京:北京农学院,2014.LI D Y. Attractive Effect of Volatiles from Peach and Plum on Conogethes punctiferalis(Guenée)[D]. Beijing:Beijing University of Agriculture,2014(in Chinese).
[19] HE L Z,WANG J,ZHAO Z D,et al. Research progress on resources and bioactivity applications of 3-carene[J]. Chemistry&Industry of Forest Products,2011,31(3):122-126.
[20]侯林林.不同抗性品种向日葵挥发物成分分析及对欧洲葵螟性诱剂诱捕作用的影响[D].呼和浩特:内蒙古农业大学,2017.HOU L L. Analysis of Volatile Components of Sunflower Varieties with Different Resistance and Their Effects on the Homoeosoma nebulellum Hübner by Sexual Attractants[D]. Hohhot:Inner Mongolia Agricultural University,2017(in Chinese).
[21] SCHWEDE T,KOPP J,GUEX N,et al. SWISS-MODEL:An automated protein homology-modeling server[J]. Nucleic Acids Research,2003,31(13):3381-3385.
[22] RAMACHANDRAN G N,RAMAKRISHNAN C,SASISEKHARAN V.Stereochemistry of polypeptide chain configurations[J]. Journal of Molecular Biology,1963,7(1):95-99.
[23] WANG Y L,BRYANT S H,CHEN T J,et al. PubChem bioAssay:2017update[J]. Nucleic Acids Research,2016,45(D1):955-963.
[24] XIANG Z X. Advances in homology protein structure modeling[J]. Current Protein and Peptide Science,2006,7(3):217-227.
[25] KELSEY R G,WESTLIND D J. Attraction of red turpentine beetle and other Scolytinae to ethanol,3-carene or ethanol+3-carene in an Oregon pine forest[J]. Agricultural&Forest Entomology,2017,20(2):272-278.
[26] REN L L,BALAKRISHNAN K,LUO Y Q,et al. EAG response and behavioral orientation of Dastarcus helophoroides(Fairmaire)(Coleoptera:Bothrideridae)to synthetic host-associated volatiles[J]. Plos One,2017,12(12):e0190067.
[2]张向欣,王正军.外来入侵种美国白蛾的研究进展[J].安徽农业科学,2009,37(1):215-219.ZHANG X X,WANG Z J. Research progress of exotic invasive species Hyphantria cunea[J]. Anhui Agricultural Sciences,2009,37(1):215-219(in Chinese).
[3]季荣,谢宝瑜,李欣海,等.外来入侵种——美国白蛾的研究进展[J].应用昆虫学报,2003,40(1):13-18.JI R,XIE B Y,LI X H,et al. Research progress on exotic invasive species:Hyphantria cunea[J]. Chinese Journal of Applied Entomology,2003,40(1):13-18(in Chinese).
[4]杨忠岐,张永安.重大外来入侵害虫——美国白蛾生物防治技术研究[J].应用昆虫学报,2007,44(4):465-471.YANG Z Q,ZHANG Y A. Study on biological control technology of Hyphantria cunea,a major invasive pest[J]. Chinese Journal of Applied Entomology,2007,44(4):465-471(in Chinese).
[5]杨忠岐.中国寄生于美国白蛾的啮小蜂—新属—新种(膜翅目,姬小蜂科,啮小蜂亚科)[J].昆虫分类学报,1989(增1):117-130.YANG Z Q. A new genus and species of Eulophidae(Hymenoptera:Chalcidoidea)parasitizing Hyphantria cunea(Drury)(Lepidoptera:Arctiidae)in China[J]. Entomotaxonomia,1989(Suppl1):117-130(in Chinese).
[6]苏智,杨忠岐,魏建荣,等.白蛾周氏啮小蜂转主寄主的研究[J].林业科学,2004,40(4):106-116.SU Z,YANG Z Q,WEI J R,et al. Studies on alternate hosts of the parasiotid Chouioia cunea(Hymenoptera:Eulophidae)[J]. Scientia Silvae Sinicae,2004,40(4):106-116(in Chinese).
[7]杨忠岐,王小艺,王传珍,等.白蛾周氏啮小蜂可持续控制美国白蛾的研究[J].林业科学,2005,41(5):72-80.YANG Z Q,WANG X Y,WANG C Z,et al. Study on sustainable control of Hyphantria cunea by Chouioia cunea[J]. Scientia Silvae Sinicae,2005,41(5):72-80(in Chinese).
[8]万新龙,杜永均.昆虫嗅觉系统结构与功能研究进展[J].昆虫学报,2015,58(6):688-698.WAN X L,DU Y J. Research progress in the structure and function of insect olfactory system[J]. Acta Entomologica Sinica,2015,58(6):688-698(in Chinese).
[9] LEAL W S. Odorant reception in insects:Roles of receptors,binding proteins,and degrading enzymes[J]. Annu Rev Entomol,2013,58:373-391.
[10] ZHAO Y N,WANG F Z,ZHANG X Y,et al. Transcriptome and expression patterns of chemosensory genes in antennae of the parasitoid wasp Chouioia cunea[J]. Plos One,2016,11(2):e0148159.
[11] ZHU G P,PAN L N,ZHAO Y N,et al. Chemical investigations of volatile kairomones produced by Hyphantria cunea(Drury),a host of the parasitoid Chouioia cunea Yang[J]. Bulletin of Entomological Research,2016,107(2):1-7.
[12]赵燕妮,刘强,李敏.周氏啮小蜂非典型气味受体基因的cDNA序列及进化分析[J].应用昆虫学报,2014(4):1026-1034.ZHAO Y N,LIU Q,LI M. Identification and evolution of the Or83b olfactory gene of Chouioia cunea Yang[J]. Chinese Journal of Applied Entomology,2014,51(4):1026-1034(in Chinese).
[13]张新玥,王凤竹,范伟健,等.白蛾周氏啮小蜂普通气味受体OR1的进化分析[J].天津师范大学学报(自然科学版),2018,38(2):29-34.ZHANG X Y,WANG F Z,FAN W J,et al. Evolutionary analysis of the common odorant receptor OR1 of the Chouioia cunea Yang[J]. Journal of Tianjin Normal University(Natural Science Edition),2018,38(2):29-34(in Chinese).
[14]王凤竹,张新玥,范伟健,等.周氏啮小蜂气味结合蛋白I基因的进化分析[J].天津师范大学学报(自然科学版),2017,37(1):46-50.WANG F Z,ZHANG X Y,FAN W J,et al. Phylogenetic analysis on the odorant binding proteinⅠgene of Chouioia cunea Yang[J]. Journal of Tianjin Normal University(Natural Science Edition),2017,37(1):46-50(in Chinese).
[15],CAFLISCH A. Protein structure-based drug design:From docking to molecular dynamics[J]. Current Opinion in Structural Biology,2017,48:93-102.
[16] LI H L,ZHANG L Y,NI C X,et al. Molecular recognition of floral volatile with two olfactory related proteins in the Eastern honeybee(Apis cerana)[J]. International Journal of Biological Macromolecules,2013,56(5):114-121.
[17] DU S Q,YANG Z K,QIN Y G,et al. Computational investigation of the molecular conformation-dependent binding mode of(E)-β-farnesene analogs with a heterocycle to aphid odorant-binding proteins[J]. Journal of Molecular Modeling,2018,24(3):70.
[18]李得宇.桃和李子挥发物对桃蛀螟的引诱作用[D].北京:北京农学院,2014.LI D Y. Attractive Effect of Volatiles from Peach and Plum on Conogethes punctiferalis(Guenée)[D]. Beijing:Beijing University of Agriculture,2014(in Chinese).
[19] HE L Z,WANG J,ZHAO Z D,et al. Research progress on resources and bioactivity applications of 3-carene[J]. Chemistry&Industry of Forest Products,2011,31(3):122-126.
[20]侯林林.不同抗性品种向日葵挥发物成分分析及对欧洲葵螟性诱剂诱捕作用的影响[D].呼和浩特:内蒙古农业大学,2017.HOU L L. Analysis of Volatile Components of Sunflower Varieties with Different Resistance and Their Effects on the Homoeosoma nebulellum Hübner by Sexual Attractants[D]. Hohhot:Inner Mongolia Agricultural University,2017(in Chinese).
[21] SCHWEDE T,KOPP J,GUEX N,et al. SWISS-MODEL:An automated protein homology-modeling server[J]. Nucleic Acids Research,2003,31(13):3381-3385.
[22] RAMACHANDRAN G N,RAMAKRISHNAN C,SASISEKHARAN V.Stereochemistry of polypeptide chain configurations[J]. Journal of Molecular Biology,1963,7(1):95-99.
[23] WANG Y L,BRYANT S H,CHEN T J,et al. PubChem bioAssay:2017update[J]. Nucleic Acids Research,2016,45(D1):955-963.
[24] XIANG Z X. Advances in homology protein structure modeling[J]. Current Protein and Peptide Science,2006,7(3):217-227.
[25] KELSEY R G,WESTLIND D J. Attraction of red turpentine beetle and other Scolytinae to ethanol,3-carene or ethanol+3-carene in an Oregon pine forest[J]. Agricultural&Forest Entomology,2017,20(2):272-278.
[26] REN L L,BALAKRISHNAN K,LUO Y Q,et al. EAG response and behavioral orientation of Dastarcus helophoroides(Fairmaire)(Coleoptera:Bothrideridae)to synthetic host-associated volatiles[J]. Plos One,2017,12(12):e0190067.