基于同源建模与分子对接的小菜蛾PxylOBP31广谱性配体识别分析

郭振平; 郑贞荧; 汪跃航; 徐凌; 杨广; 金文松; 蔡立君

基于同源建模与分子对接的小菜蛾PxylOBP31广谱性配体识别分析

Application of Homology Modeling and Molecular Docking for Studying Ligand Recognition of PxylOBP31 in Diamondback Moth

摘要

摘要:
目的在原子水平探讨小菜蛾气味结合蛋白PxylOBP31的配体识别机制，以期从结构层面揭示其识别特性。
方法以小菜蛾Plutella xylostella触角特异性表达的PxylOBP31为研究对象，采用同源建模与分子对接技术进行系统性分析。首先，基于Swiss-Model构建PxylOBP31的三维结构模型，并利用Procheck、Verify3D和ERRAT进行评估；进而采用AutoDock对PxylOBP31与39种挥发物进行分子对接，计算结合自由能并分析关键残基。
结果评估显示，拉氏构象图中98.0%的氨基酸残基位于最合理区，Verify3D评分中76.52%的残基得分大于0.1，ERRAT值高达99.07%，表明模型质量可靠。分子对接表明PxylOPB31与不同配体的结合自由能从−7.28 kcal·mol⁻¹（β-石竹烯）到−3.48 kcal·mol⁻¹（正己醇）不等。关键结合残基如Gln101、Asn108、Phe113等可能通过氢键和疏水作用构成结合口袋核心。
结论本研究不仅为阐明PxylOBP31的广谱配体识别机制提供原子层面的见解，也为后续基于该蛋白关键结合口袋精准设计小菜蛾嗅觉行为调控剂提供具体的结构依据和靶点信息。

Abstract:
Objective Ligand recognition of the odorant-binding protein PxylOBP31 in Plutella xylostella was investigated to decipher the olfactory mechanism of the pest.
Methods Homology modeling and molecular docking were applied to analyze PxylOBP31, the olfactory sensing-related protein specifically expressed in the antennae of P. xylostella. The Swiss model was used to construct the 3D structure of the protein to be evaluated by Procheck, Verify3D, and ERRAT. AutoDock was employed to examine the molecular docking, calculate the binding free energy, and analyze the key residues of the protein with 39 volatiles.
Results The applied model displayed a high reliability by 98.0% of the amino acid residues appearing in the highly optimal zones on the Ramachandran conformation diagram, 76.52% of them carrying a Verify 3D score greater than 0.1, and as high as 99.07% on ERRAT. The binding free energy of PxylOBP31 with the 39 ligands ranged from −7.28 kcal·mol⁻¹ on β-caryophyllene to −3.48 kcal·mol⁻¹ on 1-hexanol. The key binding residues, such as Gln101, Asn108, and Phe113, formed core pockets with the ligands possibly through hydrogen bonds or hydrophobic interactions.
Conclusion The molecular information revealed by this study on the mechanism of the broad-spectrum ligand recognition of PxylOBP31 provided a basis for the development of targeted olfactory regulators with precise binding pockets in the protein of P. xylostella.

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