非血红素铁酶及分子间相互作用力场的研究
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摘要
本论文的研究工作分为两个方面,一是单核非红素酶的结构和催化性能的研究。单核非血红素酶是能够活化分子氧的铁氧化酶的一种,在生物、环境以及医学领域具有广泛的应用和重要的价值。非血红素酶中的一个常见的保守结构单元是2-组氨酸-1-羰基(2-His-l-carboxylate)三元组。我们通过分子动力学模拟和QM/MM计算从分子水平和电子水平上研究了羟乙基膦酸双加氧酶(HEPD)酶的结构及催化反应机理,分析了酶催化反应的影响因素。二是分子间弱相互作用的研究。分子间弱相互作用(比如卤键,氢键,硫键,磷键,cation-π等)在化学,生命科学和材料科学中占有重要地位。用分子动力学方法研究生物大分子和功能材料大分子的结构,形貌和性能时需要能恰当描述分子间弱相互作用的力场。但目前已有的分子力场不能合理描述分子间弱相互作用。为此我们设计了可极化椭球力场(PEff),用来描述具有方向性的分子川弱相互作用,并用我们所建造的力场研究了生物大分子中的卤键相互作用。我们的研究结果也为设计具有方向性的配位相互作用(比如Zn酶,Fe酶中配位相互作用)的力场提供了重要思路。
本论文的主要研究内容和结论如下
1.HEPD(?)(?)是一种典型的非血红索铁酶,它可以催化草铵膦(PTT)和磷霉素(Fosfomycin)等生物合成中的关键步骤。我们采用QM/MM方法,研究了HEPD酶的催化反应机理。QM/MM的计算模拟结果表明,HFPD酶中存在着不同的反应路径,整个反应过程分为四个步骤,包括氢转移,O-O键的断裂,C-C键的断裂,和产物HMP的生成。我们的研究结果表明,谷氨酸残基Glu176可以在一定程度上通过质子转移过程参与催化反应。对于整个反应过程来说,不同的反应路径具有一定的可调节性,并且它们与蛋白质环境有明显的相关性。我们提出的反应机理在很大程度上解释一些实验上观察到的比较矛盾的现象,修正了己有的羟基过氧化机理(hydroperoxylation)和羟基化机理(hydroxylation),这些结果为进一步理解和调节非血红素铁酶中的催化反应机理提供了一定的指导。
2.目前的一些实验研究表明,水分子在HEPD的催化反应过程中扮演着非常重要的角色。分子动力学模拟结果也表明,活性口袋附近存在一些运动受限的水分子。我们通过QM/MM方法研究了水分子参与的催化反应机理,水分子可以把羟基自由基(·OH)束缚在活性口袋中,并且可以把羟基自由基通过特定的反应转换成铁的氢氧化物(Fe-OH)。这个反应路径对于防止羟基自由基对酶的活性损伤有一定的意义。我们还发现,水分子可以作为非血红素铁酶活性中心的氧原子的一个来源,我们的计算结果表明,最终产物HMP中的氧无素大约有40%来自水分子,因此,我们提出的反应机理可以定量地解释O18同位素标记的实验结果。
3我们设计了一个新的力场函数,称之为可极化椭球力场(Polarizable Ellipsoidal force field, PEff)用来描述方向性较强的分子间弱相互作用。卤键是一种非常重要的弱键相互作用,而目前大部分经典力场都不能正确地模拟卤键作用,鉴于这种情况,我们首先将PEff力场用于卤键研究。静电势分布的各向异性和短程作用是卤键的两个基本特征,PEff力场较好地描述了这两个特征。在PEff力场中,共价卤原子的各向异性电荷分布采用一个球形的负电荷分布和一个椭球形的正电荷电荷分布的组合来描述,而极化能的贡献则通过一个诱导偶极模型来描述。通过模拟卤键势能面获得了PEff力场参数,最后得到的力场中包含一些有确定物理意义的组成部分,包括静电作用,排斥/色散作用以及极化相互作用等。我们的研究结果表明,PEff模型基本上可以正确地再现MP2水平计算得到的卤键势能面特点。
4.可极化椭球力场PEff与现在广泛应用的分子动力学模拟软件包在很大程度上兼容,因此很容易整合到现有的程序中。我们拟合得到的参数具有一定的可迁移性,同时这些参数与AMBER通用力场(GAFF)的参数是基本上兼容的。进一步地,我们采用PEff模型预测了人类组织蛋白酶L(hcatL)的卤键结构,所得结果与该蛋白酶的晶体结构非常吻合。这些结果表明,我们提出的PEff力场可以作为设计配位相互作用(比如Zn酶,Fe酶的活性中心)力场的重要基础。
The researches mainly includes two aspects, one is about the structural and catalytic properties of the mononuclear non-heme enzyme. The mononuclear non-heme enzyme is a kind of iron dependent oxygenases, which is important in biological, environmental and medical applications. A common structural motif of these non-heme enzymes is the2-His-1-carboxylate facial triad binding the divalent iron. Molecular dynamic simulations and QM/MM methods were used to study the catalytic reaction mechanism of Hydroxyethylphosphonate dioxygenase (HEPD) enzyme. The conditions that may ailed the enzymatic reaction were analyzed and the tunability of the reaction pathway was discussed Intermolecular interactions(such as halogen bonds and cation-π et al) and the coordinated interactions are usually highly directional, which cannot properly be described in classic force field. We designed a polarizable ellipsoidal force field (PEff) to improve the description of intermolecular interactions in classic force fields. And the PEff model has been attempted to study the halogen bonding in biomolecules. The PEff model is also useful to derive the force field of coordinated interactions (such as zinc and iron enzymes).
The conclusions are summarized in the following section:
1. Hydroxyethylphosphonate dioxygenase (HEPD) is a typical mononuclear non-heme enzyme, which catalyzes a critical step in phosphinothricin (PT) biosynthetic pathway. HEPD activates O2by the divalent iron and catalyzes the conversion of2-HEP to HMP. By employing ab initio quantum mechanical/molecular mechanical (QM/MM) and molecular dynamics simulations(MD), we have provided further evidence against the previously proposed hydroperoxylation or hydroxylation mechanism of hydroxyethylphosphonate dioxygenase (HEPD). HEPD employs an interesting catalytic cycle based on concatenated bifurcations. This enzymatic reaction occurs in four major steps on the basis of our QM/MM calculations. The first step is the abstraction of hydrogen atom from the substrate, which leads to a distal or proximal hydroperoxo species (Fe(Ⅲ)-OOH). The second step is the cleavage of the O-O bond, and in the third step, the carbon-carbon bond is broken subsequently. Finally,2-HEP is converted to HMP The residue Glu176could take part in the catalytic reaction via a proton assisted mechanism. The reaction directions seem to be tunable and show significant environment dependence. These conclusions may provide insight to the development of biochemistry and material sciences.
2. The experimental studies suggest that water molecules play an important role in the catalytic reaction process of HEPD. Molecular dynamic (MD) simulations also point out that the trapped water at the active site is important in the active site.This work proposes a water involved reaction mechanism, where water molecules serve as an oxygen source in the generation of mononuclear non-heme iron oxo complexes. Meanwhile, water molecules seem to be responsible for converting the reactive hydroxyl radical group ('OH) to the ferric hydroxide (Fe(Ⅲ)-OH) in a specific way. This converting reaction may prevent the enzyme from damages caused by the hydroxyl radical groups. This work could provide a better interpretation on how the intermediates interact with water molecules and a quantitatively understanding on the018label experimental evidences in which only a relatively smaller ratio of oxygen atoms in water molecules (about40%) are incorporated into the final product HMP.
3. The current research reports a polarizable ellipsoidal force field (PEff) for the directional intermolecular interactions. Since widely applications of halogen bonds and the difficulty of modeling them in classical force fields, the PEff model was used to study the halogen bonds. The anisotropic effects and short-range quantum effects are two essential characters in the formation of halogen bonds. The anisotropic charge distribution was represented with the combination of a negative charged sphere and a positively charged ellipsoid. The polarization energy was incorporated by the induced dipole model. The resulting force field is "physically motivated", which includes separate, explicit terms to account for the electrostatic, repulsion/dispersion and polarization interaction.
4.The PF.ff modelis largelycompatible with existing,standard simulation packages The fitted parameters are transferable and compatible with the general AMBER force field (GAFF). This PEff model could correctly reproduces the potential energy surface of halogen bonds at MP2level. Finally, the prediction of the halogen bond properties of human Cathcpsin L (hcatL) has been found to be in excellent qualitative agreement with the co-crystal structures. Judging from the notably improved accuracy in comparison with the fixed charge models, the PEff model is expected to form the foundation for developing high quality force field of coordinated complex.
本论文的主要研究内容和结论如下
1.HEPD(?)(?)是一种典型的非血红索铁酶,它可以催化草铵膦(PTT)和磷霉素(Fosfomycin)等生物合成中的关键步骤。我们采用QM/MM方法,研究了HEPD酶的催化反应机理。QM/MM的计算模拟结果表明,HFPD酶中存在着不同的反应路径,整个反应过程分为四个步骤,包括氢转移,O-O键的断裂,C-C键的断裂,和产物HMP的生成。我们的研究结果表明,谷氨酸残基Glu176可以在一定程度上通过质子转移过程参与催化反应。对于整个反应过程来说,不同的反应路径具有一定的可调节性,并且它们与蛋白质环境有明显的相关性。我们提出的反应机理在很大程度上解释一些实验上观察到的比较矛盾的现象,修正了己有的羟基过氧化机理(hydroperoxylation)和羟基化机理(hydroxylation),这些结果为进一步理解和调节非血红素铁酶中的催化反应机理提供了一定的指导。
2.目前的一些实验研究表明,水分子在HEPD的催化反应过程中扮演着非常重要的角色。分子动力学模拟结果也表明,活性口袋附近存在一些运动受限的水分子。我们通过QM/MM方法研究了水分子参与的催化反应机理,水分子可以把羟基自由基(·OH)束缚在活性口袋中,并且可以把羟基自由基通过特定的反应转换成铁的氢氧化物(Fe-OH)。这个反应路径对于防止羟基自由基对酶的活性损伤有一定的意义。我们还发现,水分子可以作为非血红素铁酶活性中心的氧原子的一个来源,我们的计算结果表明,最终产物HMP中的氧无素大约有40%来自水分子,因此,我们提出的反应机理可以定量地解释O18同位素标记的实验结果。
3我们设计了一个新的力场函数,称之为可极化椭球力场(Polarizable Ellipsoidal force field, PEff)用来描述方向性较强的分子间弱相互作用。卤键是一种非常重要的弱键相互作用,而目前大部分经典力场都不能正确地模拟卤键作用,鉴于这种情况,我们首先将PEff力场用于卤键研究。静电势分布的各向异性和短程作用是卤键的两个基本特征,PEff力场较好地描述了这两个特征。在PEff力场中,共价卤原子的各向异性电荷分布采用一个球形的负电荷分布和一个椭球形的正电荷电荷分布的组合来描述,而极化能的贡献则通过一个诱导偶极模型来描述。通过模拟卤键势能面获得了PEff力场参数,最后得到的力场中包含一些有确定物理意义的组成部分,包括静电作用,排斥/色散作用以及极化相互作用等。我们的研究结果表明,PEff模型基本上可以正确地再现MP2水平计算得到的卤键势能面特点。
4.可极化椭球力场PEff与现在广泛应用的分子动力学模拟软件包在很大程度上兼容,因此很容易整合到现有的程序中。我们拟合得到的参数具有一定的可迁移性,同时这些参数与AMBER通用力场(GAFF)的参数是基本上兼容的。进一步地,我们采用PEff模型预测了人类组织蛋白酶L(hcatL)的卤键结构,所得结果与该蛋白酶的晶体结构非常吻合。这些结果表明,我们提出的PEff力场可以作为设计配位相互作用(比如Zn酶,Fe酶的活性中心)力场的重要基础。
The researches mainly includes two aspects, one is about the structural and catalytic properties of the mononuclear non-heme enzyme. The mononuclear non-heme enzyme is a kind of iron dependent oxygenases, which is important in biological, environmental and medical applications. A common structural motif of these non-heme enzymes is the2-His-1-carboxylate facial triad binding the divalent iron. Molecular dynamic simulations and QM/MM methods were used to study the catalytic reaction mechanism of Hydroxyethylphosphonate dioxygenase (HEPD) enzyme. The conditions that may ailed the enzymatic reaction were analyzed and the tunability of the reaction pathway was discussed Intermolecular interactions(such as halogen bonds and cation-π et al) and the coordinated interactions are usually highly directional, which cannot properly be described in classic force field. We designed a polarizable ellipsoidal force field (PEff) to improve the description of intermolecular interactions in classic force fields. And the PEff model has been attempted to study the halogen bonding in biomolecules. The PEff model is also useful to derive the force field of coordinated interactions (such as zinc and iron enzymes).
The conclusions are summarized in the following section:
1. Hydroxyethylphosphonate dioxygenase (HEPD) is a typical mononuclear non-heme enzyme, which catalyzes a critical step in phosphinothricin (PT) biosynthetic pathway. HEPD activates O2by the divalent iron and catalyzes the conversion of2-HEP to HMP. By employing ab initio quantum mechanical/molecular mechanical (QM/MM) and molecular dynamics simulations(MD), we have provided further evidence against the previously proposed hydroperoxylation or hydroxylation mechanism of hydroxyethylphosphonate dioxygenase (HEPD). HEPD employs an interesting catalytic cycle based on concatenated bifurcations. This enzymatic reaction occurs in four major steps on the basis of our QM/MM calculations. The first step is the abstraction of hydrogen atom from the substrate, which leads to a distal or proximal hydroperoxo species (Fe(Ⅲ)-OOH). The second step is the cleavage of the O-O bond, and in the third step, the carbon-carbon bond is broken subsequently. Finally,2-HEP is converted to HMP The residue Glu176could take part in the catalytic reaction via a proton assisted mechanism. The reaction directions seem to be tunable and show significant environment dependence. These conclusions may provide insight to the development of biochemistry and material sciences.
2. The experimental studies suggest that water molecules play an important role in the catalytic reaction process of HEPD. Molecular dynamic (MD) simulations also point out that the trapped water at the active site is important in the active site.This work proposes a water involved reaction mechanism, where water molecules serve as an oxygen source in the generation of mononuclear non-heme iron oxo complexes. Meanwhile, water molecules seem to be responsible for converting the reactive hydroxyl radical group ('OH) to the ferric hydroxide (Fe(Ⅲ)-OH) in a specific way. This converting reaction may prevent the enzyme from damages caused by the hydroxyl radical groups. This work could provide a better interpretation on how the intermediates interact with water molecules and a quantitatively understanding on the018label experimental evidences in which only a relatively smaller ratio of oxygen atoms in water molecules (about40%) are incorporated into the final product HMP.
3. The current research reports a polarizable ellipsoidal force field (PEff) for the directional intermolecular interactions. Since widely applications of halogen bonds and the difficulty of modeling them in classical force fields, the PEff model was used to study the halogen bonds. The anisotropic effects and short-range quantum effects are two essential characters in the formation of halogen bonds. The anisotropic charge distribution was represented with the combination of a negative charged sphere and a positively charged ellipsoid. The polarization energy was incorporated by the induced dipole model. The resulting force field is "physically motivated", which includes separate, explicit terms to account for the electrostatic, repulsion/dispersion and polarization interaction.
4.The PF.ff modelis largelycompatible with existing,standard simulation packages The fitted parameters are transferable and compatible with the general AMBER force field (GAFF). This PEff model could correctly reproduces the potential energy surface of halogen bonds at MP2level. Finally, the prediction of the halogen bond properties of human Cathcpsin L (hcatL) has been found to be in excellent qualitative agreement with the co-crystal structures. Judging from the notably improved accuracy in comparison with the fixed charge models, the PEff model is expected to form the foundation for developing high quality force field of coordinated complex.
引文
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