ABSTRACT Structural and dynamical properties of the autotransporter esterase EstA from bacterium Pseudomonas aeruginosa were studied using molecular dynamics (MD) simulations. Four different systems, including the full-length EstA enzyme inserted into a solvated 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) lipid bilayer, as well as the solvated isolated passenger domain of EstA were simulated without ligand and in complex with 4-hydroxyphenyloctanoate bound as tetrahedral intermediate. Detailed analysis of non-covalent interactions was performed based on 100 ns long MD simulations. It was found that active site interactions include not only the catalytic triad (Ser14, Asp286, His289), but also a three-residue oxyanion hole (backbone of Ser14, Gly92 and Asn147), hydrophobic residues involved in tetrahedral intermediate stabilisation, and residues participating in the active site hydrogen bond network. Moreover, interactions between protein domains were analysed and it was found that interacting residues are located on specific structures not usually found in GDSL hydrolases or autotransporter β barrels. In the case of full-length EstA enzyme, MD simulations point to specific interactions between the central and remote regions of the active site which are important for adequate intermediate stabilisation.

中文翻译：

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铜绿假单胞菌自转运体酯酶 ESTA 中功能相关域间和活性位点相互作用的分子动力学研究

摘要 使用分子动力学 (MD) 模拟研究了来自铜绿假单胞菌的自转运体酯酶 EstA 的结构和动力学特性。四种不同的系统，包括插入到溶剂化 1-棕榈酰-2-油酰-磷脂酰乙醇胺 (POPE) 脂质双层中的全长 EstA 酶，以及在没有配体的情况下与 4-羟基苯基辛酸酯结合为四面体中间体。基于 100 ns 长的 MD 模拟对非共价相互作用进行了详细分析。发现活性位点相互作用不仅包括催化三联体（Ser14、Asp286、His289），还包括三残基氧阴离子孔（Ser14、Gly92 和 Asn147 的骨架），参与四面体中间稳定的疏水残基，和参与活性位点氢键网络的残基。此外，分析了蛋白质结构域之间的相互作用，发现相互作用的残基位于 GDSL 水解酶或自动转运蛋白 β 桶中通常不存在的特定结构上。在全长 EstA 酶的情况下，MD 模拟指向活性位点中心和偏远区域之间的特定相互作用，这对于充分的中间稳定很重要。