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双条杉天牛OBP与其嗅觉相关化学物质的分子对接及分子动力学分析

引用本文：李涵,郝恩华,杨曦,孙漂,陆鹏飞,乔海莉.双条杉天牛OBP与其嗅觉相关化学物质的分子对接及分子动力学分析.植物保护学报,2023,50(4):991-1000

DOI：10.13802/j.cnki.zwbhxb.2023.2022047

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作者	单位	E-mail
李涵	北京林业大学林学院, 省部共建森林培育与保护教育部重点实验室, 北京 100083
郝恩华	北京林业大学林学院, 省部共建森林培育与保护教育部重点实验室, 北京 100083
杨曦	北京林业大学林学院, 省部共建森林培育与保护教育部重点实验室, 北京 100083
孙漂	北京林业大学林学院, 省部共建森林培育与保护教育部重点实验室, 北京 100083
陆鹏飞	北京林业大学林学院, 省部共建森林培育与保护教育部重点实验室, 北京 100083	lpengfei224@126.com
乔海莉	中国医学科学院北京协和医学院药用植物研究所, 北京 100193	qhl193314@sina.com

中文摘要:为探究双条杉天牛Semanotus bifasciatus气味结合蛋白（odorant binding protein，OBP）与信息化合物的识别结合机理，筛选出与OBP结合效果最佳的化学配体，选择在双条杉天牛触角中高表达的OBP2、OBP6、OBP7序列，通过Swiss-model在线软件对其进行同源模建，使用ERRAT程序、Procheck和Verify_3D进行建模质量评估；采用Autodock软件对OBP模型和相关化学物质进行分子对接分析，通过GROMACS 2019.6软件包进行目的OBP与结合效果最佳配体复合体的分子动力学模拟。结果显示，OBP2、OBP6和OBP7模型所得到的ERRAT值分别为97.03%、94.06%和97.39%，三维结构与一级结构的兼容性所得评分大于0.2的氨基酸百分比均大于80.00%，且拉氏构象图中氨基酸位于最佳合理区的数量均大于90.00%，说明所建模型合理；在11个化合物中，柏木醇与OBP2、OBP6和OBP7的结合性能最好，结合能分别为-7.04、-6.86和-6.62 kJ/mol，在结合过程中，疏水作用力和氢键作用力共同作用使蛋白与配体的结合更稳定；分子动力学模拟结果显示，OBP-配体复合物在100 ns时间内的均方根偏差均达到稳定，其中OBP2-配体和OBP7-配体稳定在0.3 nm附近，OBP6-配体稳定在0.35 nm附近；同时氨基酸残基的均方根波动曲线值普遍较低，3个复合物体系中最低值均降到了0.1 nm以下，进一步证明了对接结果的稳定性好。

中文关键词:双条杉天牛气味结合蛋白同源建模分子对接分子动力学模拟

Molecular docking and molecular dynamics analysis of odorant binding proteins of juniper bark borer Semanotus bifasciatus and its related semiochemicals

Author Name	Affiliation	E-mail
Li Han	Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
Hao Enhua	Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
Yang Xi	Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
Sun Piao	Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
Lu Pengfei	Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China	lpengfei224@126.com
Qiao Haili	Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China	qhl193314@sina.com

Abstract:In order to investigate the olfactory recognition of juniper bark borer Semanotus bifasciatus and the binding mechanisms of odorant binding proteins (OBPs) with semiochemicals, the chemical ligands with the best binding effect to OBPs were screened. Highly expressed OBP2, OBP6, and OBP7 in the antennae of S. bifasciatus were selected, and homology modeling was performed using the online Swiss-model software. The modeling quality was assessed using the ERRAT program, Procheck, and Verify_3D. Molecular docking analysis of the OBP models and related chemical substances was conducted using Autodock software, and molecular dynamics simulations of the target OBPs and the complexes with the best binding ligands were carried out using the GROMACS 2019.6 software package. The results showed that the ERRAT values for OBP2, OBP6, and OBP7 models were 97.03%, 94.06%, and 97.39%, respectively. The percentage of amino acids with a compatibility score greater than 0.2 for the three-dimensional structure and primary structure was more than 80.00%, and the number of amino acids in the most favorable and rational area of the Ramachandran plot was more than 90.00%, fully demonstrating the rationality of the modeling results. Among the 11 compounds, borneol exhibited the best binding performance with OBP2, OBP6, and OBP7, with a binding energy of -7.04, -6.86 and -6.62 kJ/mol, respectively. During the binding process, hydrophobic forces and hydrogen bonding interactions jointly contributed to the stability of protein-ligand binding. Molecular dynamics simulation results showed that the root mean square deviation (RMSD) values of OBP-ligand complexes reached conformational equilibrium within 100 ns, with OBP2-ligand and OBP7-ligand stabilizing at around 0.3 nm, and OBP6-ligand stabilizing at around 0.35 nm. Meanwhile, the root mean square fluctuation (RMSF) values of the amino acid residues were generally low, with the lowest values in all three complex systems reaching below 0.1 nm, further proving the good stability of the docking results.

keywords:Semanotus bifasciatus odorant binding protein homology modeling molecular docking molecular dynamics

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