光肩星天牛气味结合蛋白AglaOBP12同源建模及与乙酸-顺-3-己烯酯的分子对接研究
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摘要
【目的】研究光肩星天牛Anoplophora glabripennis气味结合蛋白AglaOBP12与寄主植物挥发物乙酸-顺-3-己烯酯的相互作用机制,为利用化学生态手段调控光肩星天牛行为提供理论依据。【方法】采用同源建模预测AglaOBP12三维结构,虚拟氨基酸突变构建两个突变子,利用Molegro Virtual Docker程序进行分子对接研究AglaOBP12与乙酸-顺-3-己烯酯的结合模式。模型的合理性评价采用GMQE、QMEAN、ramachandran图和Verify-3D。【结果】AglaOBP12的三维结构由6个α-螺旋构成且形成锥形疏水口袋结构。6个保守半胱氨酸在螺旋结构之间形成稳定结构的3个二硫键。AglaOBP12的C端疏水性氨基酸位于结合口袋的出口并对口袋形成一定的遮挡。乙酸-顺-3-己烯酯位于疏水口袋中与疏水性氨基酸发生作用,而亲水头部羰基氧原子则与Asn123产生氢键。在与突变子N123A的对接中,乙酸-顺-3-己烯酯更接近疏水口袋的出口,乙酸-顺-3-己烯酯与C端Phe135形成氢键。而在与突变子F135E/L136E/V137E的对接中,乙酸-顺-3-己烯酯位于疏水口袋较深处,但未发现与Asn123氢键作用,相比野生型,两个突变子的对接空间能和范德华尔能增大,结合稳定性下降。【结论】乙酸-顺-3-己烯酯位于AglaOBP12疏水口袋并通过氢键与Asn123形成稳定的复合物,AglaOBP12的Asn123和C端疏水氨基酸对结合乙酸-顺-3-己烯酯具有重要作用。
[Objectives] To investigate the binding mechanism between the Anoplophora glabripennis odorant binding protein AglaOBP12 and the host plant volatile cis-3-hexenyl acetate. [Methods] The three dimensional structure of AglaOBP was predicted by homology modeling. Two mutants were obtained by virtual amino acid mutation, and the binding mode of AglaOBP12 with cis-3-hexenyl acetate was analyzed with the Molegro Virtual Docker program. The model was evaluated by GMQE、QMEAN、Ramachandran plot and Verify-3D. [Results] AglaOBP12 has six helical structures that shape a hydrophobic pocket. Three disulphide connections in various helices caused by six conserved cysteines could be conducive to maintaining structural stability. The hydrophobic residues in the C terminus located at the export of the pocket restrained the ligand in the binding site. Cis-3-hexenyl acetate was bound in the hydrophobic pocket, and its carbonyl oxygen atom formed a hydrogen bond with Asn123 of AglaOBP12. Cis-3-hexenyl acetate was closer to the export in mutant N123A. Phe135 of AglaOBP12 was related to the hydrogen bond. No hydrogen bond was found between the ligand and the mutant F135E/L136E/V1237E. Both docked mutants had less negative potential energy than the wild type. [Conclusion] Cis-3-hexenyl acetate was located in the hydrophobic pocket ofAglaOBP12 and formed a stable complex with a hydrogen bond with Asn123.Asn123 and the hydrophobic residues in the C terminus play an important role in binding the host plant volatile cis-3-hexenyl acetate.
[Objectives] To investigate the binding mechanism between the Anoplophora glabripennis odorant binding protein AglaOBP12 and the host plant volatile cis-3-hexenyl acetate. [Methods] The three dimensional structure of AglaOBP was predicted by homology modeling. Two mutants were obtained by virtual amino acid mutation, and the binding mode of AglaOBP12 with cis-3-hexenyl acetate was analyzed with the Molegro Virtual Docker program. The model was evaluated by GMQE、QMEAN、Ramachandran plot and Verify-3D. [Results] AglaOBP12 has six helical structures that shape a hydrophobic pocket. Three disulphide connections in various helices caused by six conserved cysteines could be conducive to maintaining structural stability. The hydrophobic residues in the C terminus located at the export of the pocket restrained the ligand in the binding site. Cis-3-hexenyl acetate was bound in the hydrophobic pocket, and its carbonyl oxygen atom formed a hydrogen bond with Asn123 of AglaOBP12. Cis-3-hexenyl acetate was closer to the export in mutant N123A. Phe135 of AglaOBP12 was related to the hydrogen bond. No hydrogen bond was found between the ligand and the mutant F135E/L136E/V1237E. Both docked mutants had less negative potential energy than the wild type. [Conclusion] Cis-3-hexenyl acetate was located in the hydrophobic pocket ofAglaOBP12 and formed a stable complex with a hydrogen bond with Asn123.Asn123 and the hydrophobic residues in the C terminus play an important role in binding the host plant volatile cis-3-hexenyl acetate.
引文
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Ahmed T,Hang T,Wang Z,He K,Bai S,2017.Molecular cloning,expression profile,odorant affinity,and stability of two odorant binding proteins in Macrocentrus cingulum Brischke(Hymenoptera:Braconidae).Archives of Insect Biochemistry and Physiology,92(2):e21347.
Baker D,Sali A,2001.Protein structure prediction and structural genomics.Science,294(5540):93?96.
Benkert P,Biasin M,Schwede T,2011.Toward the estimation of the absolute quality of individual protein structure models.Bioinformatics,27(3):343?350.
Benkert P,Tosatto SCE,Schomburg D,2008.QMEAN:Acomprehensive scoring function for model quality assessment.Proteins,71(1):261?277.
Biessmann H,Andronopoulou E,Biessmann MR,Douris V,Dimitratos SD,Eliopoulos E,2010.The Anopheles gambiae odorant binding protein 1(AgamOBP1)mediates indole recognition in the antennae of female mosquitoes.PLoS ONE,5(3):e9471.
Brito NF,Moreira MF,Melo AC,2016.A look inside odorantbinding proteins in insect chemoreception.Journal of Insect Physiology,95:51?65.
Damberger FF,Ishida Y,Leal WS,Wüthrich K,2007.Structural basis of ligand binding and release in insect pheromone-binding proteins:NMR structure of Antheraea polyphemus PBP1 at pH 4.5.Journal of Molecular Biology,373(4):811?819.
Du HF,Wang PX,Xu HC,Zhang WW,Wang ZW,2016.EAGresponses of Asian longhorn beetle Anoplophora glabripennis(Coleoptera:Cerambycidae)to volatiles of hickory.Journal of Zhejiang A&F University,33(1):166?171.[杜和芬,王佩星,徐华潮,张娓娓,王紫薇,2016.光肩星天牛对山核桃挥发物组分的触角电位分析.浙江农林大学学报,33(1):166?171.]
Eisenberg D,Luthy R,Bowie JU,1997.VERIFY3D:assessment of protein models with three-dimensional profiles.Methods in Enzymology,277:396?404.
Gong DP,Zhang HJ,Zhao P,Liu Y,Xia QY,Xiang ZH,2007.Identification and expression pattern of the chemosensory protein gene family in the silkworm,Bombyx mori.Insect Biochemistry and Molecular Biology,37(3):266?277.
Hu P,Wang JZ,Cui MM,Tao J,Luo YQ,2016.Antennal transcriptome analysis of the Asian longhorned beetle Anoplophora glabripennis.Scientific Reports,6:26652.
Lautenschlager C,Leal WS,Clardy J,2005.Coil-to-helix transition and ligand release of Bombyx mori pheromone-binding protein.Biochemical and Biophysical Research Communications,335(4):1044?1050.
Leal WS,2013.Odorant reception in insects:roles of receptors,binding proteins,and degrading enzymes.Annual Review of Entomology,58(1):373?391.
Leal WS,Chen AM,Ishida Y,2005.Kinetics and molecular properties of pheromone binding and release.Proceedings of the National Academy of Sciences of the United States of America,102(15):5386?5391.
Li GH,Gao RT,Smith MT,Kong LC,2010.Study on dispersal of Anoplophora glabripennis(Motsch.)(Coleoptera:Cerambycidae)population.Forest Research,23(5):678?684.[李国宏,高瑞桐,Smith MT,孔令才,2010.光肩星天牛种群扩散规律的研究.林业科学研究,23(5):678?684.]
Li GW,Chen XL,Shang TC,2017a.Identification and tissue distribution of odorant binding proteins of female antennae Anoplophora nobilis Ganglbauer(Coleoptera:Cerambycidae).Chinese Journal of Ecology,36(6):1678?1689.[李广伟,陈秀琳,尚天翠,2017a黄斑星天牛雌虫触角气味结合蛋白基因的鉴定及组织分布.生态学杂志,36(6):1678?1689.]
Li GW,Lu YM,Chen XL,Shang TC,2017b.c DNA cloning,expression and ligand binding properties of the odorant binding protein AglaOBP12 in the Asian longhorned beetle,Anoplophora glabripennis(Coleoptera:Cerambycidae).Acta Entomologica Sinica,60(10):1141?1154.[李广伟,陈秀琳,尚天翠,2017b.光肩星天牛气味结合蛋白AglaOBP12的基因克隆、表达及配体结合特征.昆虫学报,60(10):1141?1154.]
Li GW,Lu Y,Chen XL,Shang TC,2017c.Extraction and identification of host-plant volatiles of Acer mono and EAGresponses of Anoplophora nobilis to the primary compounds of A.mono volatiles.Journal of Henan Normal University(Nature Science Edition),45(2):53?59.[李广伟,芦屹,陈秀琳,尚天翠,2017c.五角枫挥发物的提取鉴定及黄斑星天牛对主要组分的触角电位反应.河南师范大学学报(自然科学版),45(2):53?59.]
Maiti R,Van Domselaar GH,Zhang H,Wishart DS,2004.SuperPose:a simple server for sophisticated structural superposition.Nucleic Acids Research,32(Suppl.2):590?594.
Mao Y,Xu XZ,Xu W,Ishida Y,Leal WS,Ames JB,Clardy J,2010.Crystal and solution structures of an odorant-binding protein from the southern house mosquito complexed with an oviposition pheromone.Proceedings of the National Academy of Sciences of the United States of America,107(44):19102?19107.
Ramachandran GN,Ramakrishnan C,Sasisekharan V,1963.Stereochemistry of polypeptide chain configurations.Journal of Molecular Biology,7:95?99.
Thomsen R,Christensen MH,2006.MolDock:a new technique for high-accuracy molecular docking.Journal of Medicinal Chemistry,49(11):3315?3321.
Tzotzos G,Iley JN,Moore EA,2018.New insights on repellent recognition by Anopheles gambiae odorant-binding protein 1.PLoS ONE,13(4):e0194724.
Wang JZ,Hu P,Luo YQ,Tao J,2017.Identification and expression patterns of the pheromone binding protein genes AglaPBP1 and AglaPBP2 in Anoplophora glabripennis(Coleoptera:Cerambycidae).Chinese Journal of Applied Entomology,54(1):45?55.[王菁桢,胡平,骆有庆,陶静,2017.光肩星天牛性信息素结合蛋白AglaPBP1和AglaPBP2基因鉴定和表达分析.应用昆虫学报,54(1):45?55.]
Wang ZW,Xu HC,Zhang WW,Wang PX,2016.Anoplophora glabripennis host plant selection with main host plant volatile chemical component analysis.Journal of Zhejiang A&FUniversity,33(4):558?563.[王紫薇,徐华潮,张娓娓,王佩星,2016.光肩星天牛对寄主的选择及主要寄主挥发物的化学成分分析.浙江农林大学学报,33(4):558?563.]
Zhang AJ,Oliver JE,Chauhan K,Zhao BG,Xia LQ,Xu ZC,2003.Evidence for contact sex recognition pheromone of the Asian longhorned beetle,Anoplophora glabripennis(Coleoptera:Cerambycidae).Naturwissenschaften,90(9):410?413.
Zhou JJ,Zhang GA,Huang W,Birkett MA,Field LM,Pickett JA,Pelosi P,2004.Revisiting the odorant-binding protein LUSH of Drosophila melanogaster:Evidence for odour recognition and discrimination.FEBS Letters,558(1):23?26.
Zhu N,Zhang DY,Wu LP,Hu Q,Fan JT,2017.Attractiveness of aggregation pheromones and host plant volatiles to Anoplophora glabripennis and A.chinensis(Coleoptera:Cerambycidae).Acta Entomologica Sinica,60(4):421?430.[朱宁,张冬勇,吴利平,胡琴,樊建庭,2017.聚集信息素和寄主植物挥发物对光肩星天牛和星天牛的引诱作用.昆虫学报,60(4):421?430.]
Ziemba BP,Murphy EJ,Edlin HT,Jones DN,2013.A novel mechanism of ligand binding and release in the odorant binding protein 20 from the malaria mosquito Anopheles gambiae.Protein Science,22(1):11?21.
Ahmed T,Hang T,Wang Z,He K,Bai S,2017.Molecular cloning,expression profile,odorant affinity,and stability of two odorant binding proteins in Macrocentrus cingulum Brischke(Hymenoptera:Braconidae).Archives of Insect Biochemistry and Physiology,92(2):e21347.
Baker D,Sali A,2001.Protein structure prediction and structural genomics.Science,294(5540):93?96.
Benkert P,Biasin M,Schwede T,2011.Toward the estimation of the absolute quality of individual protein structure models.Bioinformatics,27(3):343?350.
Benkert P,Tosatto SCE,Schomburg D,2008.QMEAN:Acomprehensive scoring function for model quality assessment.Proteins,71(1):261?277.
Biessmann H,Andronopoulou E,Biessmann MR,Douris V,Dimitratos SD,Eliopoulos E,2010.The Anopheles gambiae odorant binding protein 1(AgamOBP1)mediates indole recognition in the antennae of female mosquitoes.PLoS ONE,5(3):e9471.
Brito NF,Moreira MF,Melo AC,2016.A look inside odorantbinding proteins in insect chemoreception.Journal of Insect Physiology,95:51?65.
Damberger FF,Ishida Y,Leal WS,Wüthrich K,2007.Structural basis of ligand binding and release in insect pheromone-binding proteins:NMR structure of Antheraea polyphemus PBP1 at pH 4.5.Journal of Molecular Biology,373(4):811?819.
Du HF,Wang PX,Xu HC,Zhang WW,Wang ZW,2016.EAGresponses of Asian longhorn beetle Anoplophora glabripennis(Coleoptera:Cerambycidae)to volatiles of hickory.Journal of Zhejiang A&F University,33(1):166?171.[杜和芬,王佩星,徐华潮,张娓娓,王紫薇,2016.光肩星天牛对山核桃挥发物组分的触角电位分析.浙江农林大学学报,33(1):166?171.]
Eisenberg D,Luthy R,Bowie JU,1997.VERIFY3D:assessment of protein models with three-dimensional profiles.Methods in Enzymology,277:396?404.
Gong DP,Zhang HJ,Zhao P,Liu Y,Xia QY,Xiang ZH,2007.Identification and expression pattern of the chemosensory protein gene family in the silkworm,Bombyx mori.Insect Biochemistry and Molecular Biology,37(3):266?277.
Hu P,Wang JZ,Cui MM,Tao J,Luo YQ,2016.Antennal transcriptome analysis of the Asian longhorned beetle Anoplophora glabripennis.Scientific Reports,6:26652.
Lautenschlager C,Leal WS,Clardy J,2005.Coil-to-helix transition and ligand release of Bombyx mori pheromone-binding protein.Biochemical and Biophysical Research Communications,335(4):1044?1050.
Leal WS,2013.Odorant reception in insects:roles of receptors,binding proteins,and degrading enzymes.Annual Review of Entomology,58(1):373?391.
Leal WS,Chen AM,Ishida Y,2005.Kinetics and molecular properties of pheromone binding and release.Proceedings of the National Academy of Sciences of the United States of America,102(15):5386?5391.
Li GH,Gao RT,Smith MT,Kong LC,2010.Study on dispersal of Anoplophora glabripennis(Motsch.)(Coleoptera:Cerambycidae)population.Forest Research,23(5):678?684.[李国宏,高瑞桐,Smith MT,孔令才,2010.光肩星天牛种群扩散规律的研究.林业科学研究,23(5):678?684.]
Li GW,Chen XL,Shang TC,2017a.Identification and tissue distribution of odorant binding proteins of female antennae Anoplophora nobilis Ganglbauer(Coleoptera:Cerambycidae).Chinese Journal of Ecology,36(6):1678?1689.[李广伟,陈秀琳,尚天翠,2017a黄斑星天牛雌虫触角气味结合蛋白基因的鉴定及组织分布.生态学杂志,36(6):1678?1689.]
Li GW,Lu YM,Chen XL,Shang TC,2017b.c DNA cloning,expression and ligand binding properties of the odorant binding protein AglaOBP12 in the Asian longhorned beetle,Anoplophora glabripennis(Coleoptera:Cerambycidae).Acta Entomologica Sinica,60(10):1141?1154.[李广伟,陈秀琳,尚天翠,2017b.光肩星天牛气味结合蛋白AglaOBP12的基因克隆、表达及配体结合特征.昆虫学报,60(10):1141?1154.]
Li GW,Lu Y,Chen XL,Shang TC,2017c.Extraction and identification of host-plant volatiles of Acer mono and EAGresponses of Anoplophora nobilis to the primary compounds of A.mono volatiles.Journal of Henan Normal University(Nature Science Edition),45(2):53?59.[李广伟,芦屹,陈秀琳,尚天翠,2017c.五角枫挥发物的提取鉴定及黄斑星天牛对主要组分的触角电位反应.河南师范大学学报(自然科学版),45(2):53?59.]
Maiti R,Van Domselaar GH,Zhang H,Wishart DS,2004.SuperPose:a simple server for sophisticated structural superposition.Nucleic Acids Research,32(Suppl.2):590?594.
Mao Y,Xu XZ,Xu W,Ishida Y,Leal WS,Ames JB,Clardy J,2010.Crystal and solution structures of an odorant-binding protein from the southern house mosquito complexed with an oviposition pheromone.Proceedings of the National Academy of Sciences of the United States of America,107(44):19102?19107.
Ramachandran GN,Ramakrishnan C,Sasisekharan V,1963.Stereochemistry of polypeptide chain configurations.Journal of Molecular Biology,7:95?99.
Thomsen R,Christensen MH,2006.MolDock:a new technique for high-accuracy molecular docking.Journal of Medicinal Chemistry,49(11):3315?3321.
Tzotzos G,Iley JN,Moore EA,2018.New insights on repellent recognition by Anopheles gambiae odorant-binding protein 1.PLoS ONE,13(4):e0194724.
Wang JZ,Hu P,Luo YQ,Tao J,2017.Identification and expression patterns of the pheromone binding protein genes AglaPBP1 and AglaPBP2 in Anoplophora glabripennis(Coleoptera:Cerambycidae).Chinese Journal of Applied Entomology,54(1):45?55.[王菁桢,胡平,骆有庆,陶静,2017.光肩星天牛性信息素结合蛋白AglaPBP1和AglaPBP2基因鉴定和表达分析.应用昆虫学报,54(1):45?55.]
Wang ZW,Xu HC,Zhang WW,Wang PX,2016.Anoplophora glabripennis host plant selection with main host plant volatile chemical component analysis.Journal of Zhejiang A&FUniversity,33(4):558?563.[王紫薇,徐华潮,张娓娓,王佩星,2016.光肩星天牛对寄主的选择及主要寄主挥发物的化学成分分析.浙江农林大学学报,33(4):558?563.]
Zhang AJ,Oliver JE,Chauhan K,Zhao BG,Xia LQ,Xu ZC,2003.Evidence for contact sex recognition pheromone of the Asian longhorned beetle,Anoplophora glabripennis(Coleoptera:Cerambycidae).Naturwissenschaften,90(9):410?413.
Zhou JJ,Zhang GA,Huang W,Birkett MA,Field LM,Pickett JA,Pelosi P,2004.Revisiting the odorant-binding protein LUSH of Drosophila melanogaster:Evidence for odour recognition and discrimination.FEBS Letters,558(1):23?26.
Zhu N,Zhang DY,Wu LP,Hu Q,Fan JT,2017.Attractiveness of aggregation pheromones and host plant volatiles to Anoplophora glabripennis and A.chinensis(Coleoptera:Cerambycidae).Acta Entomologica Sinica,60(4):421?430.[朱宁,张冬勇,吴利平,胡琴,樊建庭,2017.聚集信息素和寄主植物挥发物对光肩星天牛和星天牛的引诱作用.昆虫学报,60(4):421?430.]
Ziemba BP,Murphy EJ,Edlin HT,Jones DN,2013.A novel mechanism of ligand binding and release in the odorant binding protein 20 from the malaria mosquito Anopheles gambiae.Protein Science,22(1):11?21.