分子动力学模拟残基突变对芳香烃受体配体结合区的影响

Molecular Dynamics Studies on the Structure of Aryl Hydrocarbon Receptor Fragment Affected by Site-Directed Mutagenesis

芳香烃受体(Aryl hydrocarbon receptor,AhR)属于配体依赖性的转录因子蛋白。本文通过对AhR配体结合区域(Ligand binding domain,LBD)的结构功能及物种特异性分析,发现在其结合腔口有一些关键残基可能起到"门控"作用,进一步将野生型(WT)和3个突变模型(Phe289Ala、Tyr316Ala、Ile319Ala)进行分子动力学模拟,从蛋白稳定性、蛋白结构变化、蛋白结合腔变化及蛋白和配体结合能力4个方面分析3个残基的门控作用。研究发现,Phe289、Tyr316、Ile319氨基酸残基通过形成疏水作用为AhR LBD起到"门控"作用;而将这些氨基酸分别突变后,其蛋白稳定性降低,整体运动性增加,配体亲和力减弱,其中Tyr316、Ile319对腔内体积影响较大,Phe289使腔内环境稳定性降低。本研究可为基于芳香烃受体的药物设计提供相关理论指导。

The Aryl hydrocarbon receptor （AhR）, a ligand-actived nuclear transcription factor, regulates the expressions of a diverse group of genes when small molecules go into the pocket of its single ligand binding domain （LBD） . In this study, we found Phe289, Tyr316 and I1e319 play ＂gatekeeper＂ roles via comparing genus-species specific and structure analysis. The four mutation models （WT, Phe289Ala, Tyr316Ala, Ile319Ala） were performed using the Amber99sb force field of GROMACS software package. The complex stability, protein conformational change, active site volume and binding free energy of the binary complex were analyzed by ＂gatekeeper＂ residues function. The results indicated that Phe289, Tyr316 and Ile319 play ＂ gatekeeper＂ roles through hydrophobic interaction. The whole structure analyses demonstrate that mutagenesis comes from the pockets, which will destabilize cavity environment, causing obvious fluctuations and leading to low ligand-affinity and ligand escape. These simulation results interpret some experimental phenomena and provide further structural information that are useful in drug design based on aryl hydrocarbon receptor.