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松针鞘瘿蚊气味结合蛋白TjapOBP1的同源模建及活性气味分子的筛选

朱蕊 焦继鹏 孙慧敏 武海卫 陶静

朱蕊, 焦继鹏, 孙慧敏, 武海卫, 陶静. 松针鞘瘿蚊气味结合蛋白TjapOBP1的同源模建及活性气味分子的筛选[J]. 北京林业大学学报. doi: 10.12171/j.1000-1522.20210188
引用本文: 朱蕊, 焦继鹏, 孙慧敏, 武海卫, 陶静. 松针鞘瘿蚊气味结合蛋白TjapOBP1的同源模建及活性气味分子的筛选[J]. 北京林业大学学报. doi: 10.12171/j.1000-1522.20210188
Zhu Rui, Jiao Jipeng, Sun Huimin, Wu Haiwei, Tao Jing. Homology modeling of the odorant binding protein TjapOBP1 of Thecodiplosis japonensis and screening of active odorant molecules[J]. Journal of Beijing Forestry University. doi: 10.12171/j.1000-1522.20210188
Citation: Zhu Rui, Jiao Jipeng, Sun Huimin, Wu Haiwei, Tao Jing. Homology modeling of the odorant binding protein TjapOBP1 of Thecodiplosis japonensis and screening of active odorant molecules[J]. Journal of Beijing Forestry University. doi: 10.12171/j.1000-1522.20210188

松针鞘瘿蚊气味结合蛋白TjapOBP1的同源模建及活性气味分子的筛选

doi: 10.12171/j.1000-1522.20210188
基金项目: 森林重要生物危害因子的监测预警和检疫技术与产品研发(2018YFC1200404)
详细信息
    作者简介:

    朱蕊。主要研究方向:森林保护。Email:zhurui0311@sina.com 地址:100083 北京市海淀区清华东路35号北京林业大学林学院

    责任作者:

    陶静,副教授。主要研究方向:森林保护。Email:taojing1029@hotmail.com 地址:同上

  • 中图分类号: S718.7

Homology modeling of the odorant binding protein TjapOBP1 of Thecodiplosis japonensis and screening of active odorant molecules

  • 摘要:   目的  松针鞘瘿蚊是近几年新发现入侵我国的林业有害生物,已经在山东省青岛市黄岛区造成了以黑松为主的沿海防护林大面积衰弱枯死。作为新入侵种对于松针鞘瘿蚊的防控基础研究极为薄弱,为了研发有效的防控技术,尽快遏制该虫的严重危害,避免进一步扩散,本文从松针鞘瘿蚊的寄主识别机制出发,以期开发针对性的引诱剂来进行监测诱杀。  方法  本研究基于松针鞘瘿蚊触角转录组数据筛选到的气味结合蛋白TjapOBP1的序列,通过同源模建的方法,得到了蛋白三维结构模型,利用Procheck、Verify_3D和ERRAT程序评估模型的可靠性。通过AutoDock软件将TjapOBP1与黑松针叶挥发物中测得的67种气味分子进行分子对接。  结果  同源模建结果显示,模建蛋白的氨基酸有95.5%落在最佳合理区,83.3%的氨基酸评分大于0.2,模建结构的误差值在73.2%,综上表明此次构建的松针鞘瘿蚊气味结合蛋白TjapOBP1三维模型有很高的可靠性。分子对接结果显示,β-月桂烯与TjapOBP1的结合效果最好,结合能为−5.26,另外,2,6-二甲基辛-1,5,7-三烯-3-醇、乙酸橙花酯、桧烯、乙酸薰衣草酯和1-异丙基-4-亚甲基二环[3.1.0]己-2-烯,这5种化合物与TjapOBP1的结合能依次升高,但均在−5.0以下,上述6种化学物质均有可能是能够被松针鞘瘿蚊TjapOBP1识别并结合的气味物质。  结论  三维结构模型的构建,为进一步研究松针鞘瘿蚊OBP的功能奠定基础。分子对接初步筛选了可能与TjapOBP1特异性结合的寄主挥发物,从而为引诱剂的开发提供支撑。

     

  • 图  1  松针鞘瘿蚊TjapOBP1与模板冈比亚按蚊AgamOBP20(ID:3VB1_A)的序列比对

    完全相同的残基以黄色背景显示,6个半胱氨酸位点以红色字体显示,连接符表示此位氨基酸在对齐比较中不存在。Strictly identical residues are highlighted with yellow background;six cysteine sites are indicated with red color;the hyphen indicates that the amino acid does not exist in alignment comparison.

    Figure  1.  Sequence alignment of TjapOBP1 with AgamOBP20 (PDB ID: 3VB1_A) from Anopholes gambiae

    图  2  松针鞘瘿蚊气味结合蛋白TjapOBP1三维结构图

    Figure  2.  3D structures of odorant binding protein TjapOBP1 of Thecodiplosis japonensis

    图  3  松针鞘瘿蚊气味结合蛋白模建结构的拉式构象图分析

    红色:最佳合理区,A、B、L区域;高亮黄色:较合适区,a、b、l、p区域;浅黄色:勉强接受区,~a、~b、~l、~p区域;白色:不合理区。Red, the best region, including A, B and L areas; bright yellow, the appropriate region, including a, b, l, p areas; pale yellow, the barely permitted region, including ~a, ~b, ~l, ~p areas; white, the disallowed region.

    Figure  3.  Ramachandran plot analysis of modeled Thecodiplosis japonensis OBP structure

    图  4  松针鞘瘿蚊气味结合蛋白模建结构的Verify_3D打分结果

    Figure  4.  Scoring of modeled Thecodiplosis japonensis OBP structure by Verify_3D

    图  5  ERRAT计算的松针鞘瘿蚊气味结合蛋白模建结构残基误差值

    图中白色表示误差值 < 95%,灰色表示95% ≤ 误差值 < 99%,黑色表示误差值 ≥ 99%。In the figure, white color indicates the error value < 95%; gray color indicates 95% ≤ the error value < 99%,and black color indicates the error value ≥ 99%.

    Figure  5.  Error value of ERRAT calculation of modeled Thecodiplosis japonensis OBP structure

    图  6  松针鞘瘿蚊TjapOBP1与β-月桂烯的结合模式

    A1:TjapOBP1(螺旋模型)与β-月桂烯(灰色模型)结合的三维结构;B1,C1:β-月桂烯(灰色模型)与蛋白末端口袋的详细结合模式。A1, 3D structure of the combined model between TjapOBP1 (the spiral model) and β-myrcene (the gray model);B1,C1:detailed binding mode of β-myrcene (the gray model) with the protein distal pocket.

    Figure  6.  Binding pattern of TjapOBP1 and β-myrcene

    图  7  松针鞘瘿蚊TjapOBP1与2,6-二甲基辛-1,5,7-三烯-3-醇的结合模式

    A2:TjapOBP1(螺旋模型)与2,6-二甲基辛-1,5,7-三烯-3-醇(灰色模型)结合的三维结构;B2,C2:2,6-二甲基辛-1,5,7-三烯-3-醇(灰色模型)与蛋白末端口袋的详细结合模式。A2, 3D structure of the combined model between TjapOBP1 (the spiral model) and 2,6-dimethylocta-1,5,7-trien-3-ol (the gray model); B2, C2, detailed binding mode of 2,6-dimethylocta-1,5,7-trien-3-ol (the gray model) with the protein distal pocket.

    Figure  7.  Binding pattern of TjapOBP1 and 2,6-dimethylocta-1,5,7-trien-3-ol

    图  8  松针鞘瘿蚊TjapOBP1与乙酸橙花酯的结合模式

    A3:TjapOBP1(螺旋模型)与乙酸橙花酯(灰色模型)结合的三维结构;B3, C3:乙酸橙花酯(灰色模型)与蛋白末端口袋的详细结合模式。A3, 3D structure of the combined model between TjapOBP1 (the spiral model) and neryl acetate (the gray model);B3,C3, detailed binding mode of neryl acetate (the gray model) with the protein distal pocket.

    Figure  8.  Binding pattern of TjapOBP1 and neryl acetate

    图  9  松针鞘瘿蚊TjapOBP1与桧烯的结合模式

    A4:TjapOBP1(螺旋模型)与桧烯(灰色模型)结合的三维结构;B4, C4:桧烯(灰色模型)与蛋白末端口袋的详细结合模式。A4, 3D structure of the combined model between TjapOBP1 (the spiral model) and sabinene (the gray model);B4, C4, detailed binding mode of sabinene (the gray model) with the protein distal pocket.

    Figure  9.  Binding pattern of TjapOBP1 and sabinene

    图  10  松针鞘瘿蚊TjapOBP1与乙酸薰衣草酯的结合模式

    A5:TjapOBP1(螺旋模型)与乙酸薰衣草酯(灰色模型)结合的三维结构;B5, C5:乙酸薰衣草酯(灰色模型)与蛋白末端口袋的详细结合模式。A5, 3D structure of the combined model between TjapOBP1 (the spiral model) and lavandulyl acetate (the gray model);B5, C5, detailed binding mode of lavandulyl acetate (the gray model) with the protein distal pocket.

    Figure  10.  Binding pattern of TjapOBP1 and lavandulyl acetate

    图  11  松针鞘瘿蚊TjapOBP1与1-异丙基-4-亚甲基二环[3.1.0]己-2-烯的结合模式

    A6:TjapOBP1(螺旋模型)与1-异丙基-4-亚甲基二环[3.1.0]己-2-烯(灰色模型)结合的三维结构;B6, C6:1-异丙基-4-亚甲基二环[3.1.0]己-2-烯(灰色模型)与蛋白末端口袋的详细结合模式。A6, 3D structure of the combined model between TjapOBP1 (the spiral model) and 1-isopropyl-4-methylenebicyclo[3.1.0]hex-2-ene (the gray model);B6,C6, detailed binding mode of 1-isopropyl-4-methylenebicyclo[3.1.0]hex-2-ene (the gray model) with the protein distal pocket.

    Figure  11.  Binding pattern of TjapOBP1 and 1-isopropyl-4-methylenebicyclo[3.1.0]hex-2-ene

    表  1  分子对接结果

    Table  1.   Molecular docking results

    序号
    No.
    化合物名称
    Compound name
    CAS号
    CAS No.
    化学式
    Chemical formula
    结合能
    Binding energy
    1 β-月桂烯 β-myrcene 123-35-3 C10H16 −5.26
    2 2,6-二甲基辛-1,5,7-三烯-3-醇 2,6-dimethylocta-1,5,7-trien-3-ol 29414-56-0 C10H16O −5.24
    3 乙酸橙花酯 Neryl acetate 141-12-8 C12H20O2 −5.21
    4 桧烯 Sabinene 3387-41-5 C10H16 −5.14
    5 乙酸薰衣草酯 Lavandulyl acetate 25905-14-0 C12H20O2 −5.05
    6 1-异丙基-4-亚甲基二环[3.1.0]己-2-烯 1-isopropyl-4-methylenebicyclo[3.1.0]hex-2-ene 36262-09-6 C10H14 −5.04
    7 橙花醇 Nerol 106-25-2 C10H18O −4.93
    8 萜品油烯 Terpinolene
    586-62-9 C10H16 −4.72
    9 1-氯-5-甲基己烷 1-chloro-5-methylhexane 33240-56-1 C7H15Cl −4.67
    10 β-苧烯 β-thujene 28634-89-1 C10H16 −4.65
    11 α-蒎烯 α-pinene 80-56-8 C10H16 −4.58
    12 α-萜烯 α-terpinene 99-86-5 C10H16 −4.58
    13 1-亚甲基-4-(1-甲基乙烯基)环己烷 1-methylene-4-(1-methylvinyl)cyclohexane 499-97-8 C10H16 −4.51
    14 β-萜烯 β-terpinene 99-84-3 C10H16 −4.49
    15 β-水芹烯 β-phellandrene 555-10-2 C10H16 −4.46
    16 (-)-β-蒎烯 (-)-β-pinene 18172-67-3 C10H16 −4.44
    17 α-水芹烯 α-phellandrene 99-83-2 C10H16 −4.44
    18 香叶基丙酸 Geranyl propionate 105-90-8 C13H22O2 −4.41
    19 M-甲异丙苯 M-cymene 535-77-3 C10H14 −4.37
    20 (E)-2-己烯醛 (E)-2-hexenal 6728-26-3 C6H10O −4.30
    21 2-己烯醛 2-hexenal 505-57-7 C6H10O −4.28
    22 莰烯 Camphene 79-92-5 C10H16 −4.24
    23 d-柠檬烯 d-limonene 5989-27-5 C10H16 −4.20
    24 己醛 Hexanal 66-25-1 C6H12O −4.12
    25 对伞花烃 p-cymene 99-87-6 C10H14 −3.96
    26 荜澄茄油烯 Cubenene 29837-12-5 C15H24 −3.91
    27 三环烯 Tricyclene 508-32-7 C10H16 −3.89
    28 松香芹酮 Pinocarvone 30460-92-5 C10H14O −3.88
    29 γ-萜品烯 γ-terpinene 99-85-4 C10H16 −3.68
    30 环戊烯 Cyclofenchene 488-97-1 C10H16 −3.55
    31 3-蒈烯 3-carene 13466-78-9 C10H16 −3.18
    32 桃金娘烯醇 Myrtenol 515-00-4 C10H16O −3.11
    33 α-香柠檬烯 α-bergamotene 17699-05-7 C15H24 −2.59
    34 2-异丙基-5-甲基苯甲醚 2-isopropyl-5-methylanisole 1076-56-8 C11H16O −2.29
    35 顺-β-胡椒烯,立体异构体 cis-β-copaene, stereoisomer C15H24 −1.16
    36 顺-β-胡椒烯 cis-β-copaene 18252-44-3 C15H24 −1.14
    37 胡椒烯 Copaene 3856-25-5 C15H24 −0.58
    38 衣兰烯 Ylangene 14912-44-8 C15H24 −0.01
    39 乙酸龙脑酯 Bornyl acetate 76-49-3 C12H20O2 0.31
    40 (-)-冰片基乙酸酯 (-)-bornyl acetate 5655-61-8 C12H20O2 0.33
    41 β-甲基紫罗酮 β-methylionone 127-43-5 C14H22O 0.42
    42 1,2,3,4,4A,7-六氢-1,6-二甲基-4-(1-甲基乙基)-萘
    1,2,3,4,4A,7-hexahydro-1,6-dimethyl-4-(1-methylethyl)-naphthalene
    16728-99-7 C15H24 2.63
    43 α-荜澄茄油烯 α-cubebene 17699-14-8 C15H24 4.12
    44 γ-衣兰油烯 γ-muurolene 30021-74-0 C15H24 5.04
    45 α-衣兰油烯 α-muurolene 10208-80-7 C15H24 5.38
    46 (+)-epi-二环倍半水芹烯 (+)-epi-bicyclosesquiphellandrene C15H24 6.39
    47 (1R,4R)-4-甲基-7-甲亚基-1-丙烷-2-基-2,3,4,4a,5,6-六氢-1H-萘
    (1R,4R)-4-methyl-7-methylidene-1-propan-2-yl-2,3,4,4a,5,6-hexahydro-1H-naphthalene
    C15H24 6.42
    48 (+)-γ-古芸烯 (+)-γ-gurjunene 22567-17-5 C15H24 6.55
    49 3,8一卡达三烯 Cadala-1(10),3,8-triene C15H22 6.87
    50 β-杜松烯 β-cadinene 523-47-7 C15H24 6.96
    51 (+)-α-杜松烯 (+)-α-cadinene 24406-05-1 C15H24 9.10
    52 1-异丙基-4,7-二甲基-1,2,3,5,6,8a-六氢萘
    1-isopropyl-4,7-dimethyl-1,2,3,5,6,8a-hexahydronaphthalene
    16729-01-4 C15H24 9.21
    53 (+)-δ-杜松烯 (+)-δ-cadinene 483-76-1 C15H24 9.25
    54 香橙烯 Aromandendrene 489-39-4 C15H24 10.92
    55 (1S,4S,4aS)-1-异丙基-4,7-二甲基-1,2,3,4,4a,5-六氢萘
    (1S,4S,4aS)-1-isopropyl-4,7-dimethyl-1,2,3,4,4a,5-hexahydronaphthalene
    C15H24 11.71
    56 γ-杜松烯 γ-cadinene 39029-41-9 C15H24 12.53
    57 (S,1Z,6Z)-8-异丙基-1-甲基-5-亚甲基环癸-1,6-二烯
    (S,1Z,6Z)-8-isopropyl-1-methyl-5-methylenecyclodeca-1,6-diene
    317819-80-0 C15H24 12.95
    58 2-亚甲基-5-(1-甲基乙烯基)-8-甲基-二环[5.3.0]癸烷
    2-methylene-5-(1-methylvinyl)-8-methyl-bicyclo[5.3.0]decane
    C15H24 13.86
    59 顺-菖蒲烯 cis-calamenene 72937-55-4 C15H22 14.71
    60 β-愈创木烯 β-guaiene 88-84-6 C15H24 17.04
    61 石竹烯 Caryophyllene 87-44-5 C15H24 18.81
    62 大根香叶烯D Germacrene D 23986-74-5 C15H24 19.24
    63 长(松)叶烯 Longifolene 475-20-7 C15H24 24.28
    64 氧化石竹烯 Caryophyllene oxide 1139-30-6 C15H24O 28.37
    65 葎草烯 Humulene 6753-98-6 C15H24 27.39
    66 十二甲基环六硅氧烷 Cyclohexasiloxane-dodecamethyl 540-97-6 C12H36O6Si6
    67 十甲基环五硅氧烷 Cyclopentasiloxane-decamethyl 541-02-6 C10H30O5Si5
    下载: 导出CSV
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出版历程
  • 收稿日期:  2021-05-17
  • 修回日期:  2021-06-19
  • 网络出版日期:  2021-07-02

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