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

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

朱蕊^1,,
焦继鹏¹,
孙慧敏¹,
武海卫²,
陶静^1, ,

1.
北京林业大学林木有害生物防治北京市重点实验室，北京 100083
2.
山东省林业科学研究院，济南 250014

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
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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

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

Zhu Rui^1
,,
Jiao Jipeng¹,
Sun Huimin¹,
Wu Haiwei²,
Tao Jing^{1
, ,}

1.
Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing 100083, China
2.
Shandong Academy of Forestry, Jinan 250014, Shandong, China

摘要

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。
- 松针鞘瘿蚊 /
- 气味结合蛋白 /
- 同源模建 /
- 分子对接
Abstract: Objective Thecodiplosis japonensis is a newly discovered forest pest invading China in recent years. It has caused a large area of the weakening and dying of the coastal shelter forest of Pinus thunbergii in Huangdao District, Qingdao City, Shandong Province of eastern China. As a new invasive species, basic research on the prevention and control of Thecodiplosis japonensis is extremely weak. In order to develop effective prevention and control technologies to contain the serious harm of Thecodiplosis japonensis as soon as possible and avoid further spread, this paper starts from the host identification mechanism, so as to develop targeted attractants for monitoring and killing. Method In this study, the sequence of the odorant binding protein TjapOBP1 was screened from the antennal transcriptome data of Thecodiplosis japonensis, and the 3D structure model of the protein was obtained by homology modeling. We evaluated the reliability of the model with Procheck, Verify_3D and ERRAT. TjapOBP1 was docked with 67 ligand molecules measured in the volatiles of Pinus thunbergii by AutoDock software. Result Procheck analysis showed that 95.5% of the amino acids of TjapOBP1 fell in the optimal reasonable region. Verify_3D analysis showed that 83.3% of the amino acid score was greater than 0.2. The ERRAT values of TjapOBP1 were 73.2%. To sum up, the modeling results had high reliability. Molecular docking results showed that β-Myrcene had the best binding effect with TjapOBP1, and the binding energy was −5.26. In addition, the binding energies of 2,6-dimethylocta-1,5,7-trien-3-ol, neryl acetate, sabinene, lavandulyl acetate and 1-isopropyl-4-methylenebicyclo[3.1.0]hex-2-ene with TjapOBP1 increased successively, but were all below −5.0. All these 6 chemicals may be the odors that can be recognized and bound by TjapOBP1. Conclusion The establishment of 3D structural model laid a foundation for further study of the function of OBP in Thecodiplosis japonensis. Molecular docking screened the host volatiles that may bind specifically to this OBP, thus providing support for the development of attractants.
- Thecodiplosis japonensis /
- odorant binding protein /
- homology modeling /
- molecular docking

HTML全文

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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