Homology modeling of the odorant binding protein TjapOBP1 of <i>Thecodiplosis japonensis</i> and screening of active odorant molecules

Zhu Rui; Jiao Jipeng; Sun Huimin; Wu Haiwei; Tao Jing

doi:10.12171/j.1000-1522.20210188

Journal of Beijing Forestry University > 2021 > 43(9): 77-86. > 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, 2021, 43(9): 77-86. DOI: 10.12171/j.1000-1522.20210188

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

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

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Received Date: May 16, 2021
Revised Date: June 18, 2021
Available Online: July 01, 2021
Published Date: October 14, 2021

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Abstract

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

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References

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

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