去卤化酶催化作用机制的理论研究
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摘要
去卤化酶可以催化碳卤键的水解断裂,产生相应的醇和卤离子。去卤化酶对含卤环境污染物具有重要的生物降解作用,长期以来一直是人们关注的热点。
目前研究的去卤化酶主要有五种:烷基卤去卤化酶、卤代酸去卤化酶、4-氯苯甲酰-辅酶A去卤化酶、卤代醇去卤化酶和3-卤丙烯酸去卤化酶。它们以不同的催化机制作用于多种有机卤化物,使碳卤键断裂。前三种酶催化时都是取代机制,经历一个酯酶中间体。后两者虽与前三种是类似的酶,但在不同的化学环境中催化机制不同。这些去卤化酶的结构相似,却具有底物特异性。另外,由于去卤化酶的种类很多,它的多样性使得底物范围大大拓宽,包括卤代烷烃、卤代环烷烃、卤代醇、卤代氨基化合物和卤代烯烃等。
其中,烷基卤去卤化酶是去卤化酶中一种典型且应用非常广泛的生物降解酶。1993年烷基卤去卤化酶(DhlA)晶体结构的确定,使得它的催化作用机制引起国内外科学家的广泛关注。目前对这种去卤化酶的研究取得了一定进展,但在研究烷基卤去卤化酶催化去卤的两步反应机制时,SN2亲核取代反应和酯酶中间体的水解反应的机理一直是人们争论的焦点。为了进一步说明去卤化酶催化动力的来源,本文使用量子化学中的密度泛函理论对SN2亲核取代反应和酯酶中间体的水解反应的机理进行了研究,为实验上研究去卤化酶的进化,提高去卤化酶的生物催化活性和拓宽底物范围提供了理论基础。
本论文的主要内容为:
1、我们用密度泛函理论对DhlA酶的SN2亲核取代反应进行了研究。研究表明,在DhlA酶的催化反应中,Asp124的碳酸基团以SN2亲核取代的方式进攻连接在底物上离去氯离子的碳上,得到酯酶中间体和氯离子。氧离子空穴和卤稳定残基上的不同的氢键相互作用在酶催化反应中意义重大。氧离子空穴上氢键的存在使得Asp124的羧酸基团更加靠近底物DCE,使得反应部位活性很高。在反应复合物中,Trp125起主要的稳定作用,而Trp125和Trp175在过渡态中都起非常重要的稳定作用。研究酶催化反应的溶剂效应发现,酶的催化作用主要在于酶中的反应物相对于非酶催化反应的反应物的不稳定作用。总之,酶催化主要是反应物相对不稳定和过渡态相对稳定的共同作用,使得能垒降低6.12 kcal/mol。
DhlA和LinB为同源酶。活化势垒分析表明,在它们的催化反应过程中都发生了SN2亲核取代反应。然而,这些酶的催化残基和活性中心是不同的。活性中心的DCE的构象自由。底物的两种邻位交叉式构象对反应的进行非常重要。DhlA酶催化时,底物的邻位交叉式构象(D (Cl1–C1–C2–Cl2) = -60°)容易发生去卤反应;而LinB酶催化反应时,另一邻位交叉式构象(D (Cl1–C1–C2–Cl2) = +60°)易于发生去卤化反应。
2、我们使用密度泛函方法研究了DhlA酶催化的酯酶中间体的水解反应。结果表明,酯酶中间体的水解反应涉及到His289活化的水分子与酯基的的亲核加成反应,同时伴随着水亲核试剂的质子迁移反应。酯酶中间体的水解经历了一个四面体中间体结构。然后消除和质子迁移反应导致四面体中间体的分解,最后得到相应的醇、卤离子和Asp124。在这两个反应途径中,第一步AdN反应都是决速步骤。气相中,质子化His289的质子迁移途径的势垒比脱质子水的质子迁移途径的低0.13 kcal/mol。因此,质子化His289的质子迁移途径是优势通道。苯中它的势垒比脱质子水的质子迁移途径的低0.67 kcal/mol。
研究酯酶中间体水解反应时发现,水促进的水解反应与质子化His289的质子迁移途径的三步反应机制是有差异的。水促进的水解反应涉及两步反应:第一步为AdN反应,第二步消除反应和质子迁移反应协同进行。其中,第一步AdN反应为决速步骤。水促进的水解反应可降低势垒3.35 kcal/mol。另外,疏水环境的溶剂苯也可以使势垒降低1.79 kcal/mol,加速水解反应的发生。我们在苯中得到的反应势垒为18.65 kcal/mol,这与最新报道的第一步AdN反应的势垒(19.5±2.1 kcal /mol)非常一致。因此,第二个水分子和酶的疏水环境对促进酶的水解去卤具有非常重要的作用。
Dehalogenases comprise such a group of microbial enzymes that catalyze the cleavage of carbon–halogen bonds into the corresponding alcohols and halide anions. There is a growing interest in the application of these enzymes as industrial biocatalysts. Recently, the catalytic prosperities of these enzymes in bioremediation applications have therefore been subjected to detailed investigations.
To date, there are five bacterial dehalogenases, including haloalkane dehalogenases, haloacid dehalogenases, 4-chlorobenzoyl-coenzyme A (CoA) dehalogenase, haloalcohol dehalogenase and a trans-3-chloroacrylic acid dehalogenase. These enzymes make use of a variety of distinctly different catalytic mechanisms to cleave carbon–halogen bonds. It is demonstrated the power of substitution mechanisms of the first three enzymes that proceed via a covalent aspartyl intermediate. For the latter two homologous ones, it is exploited that their catalytic mechanisms are different in different chemical environments. Although the five dehalogenases are very similar, they have some difference in the geometry and size of the active site cavity and differences in the way in which the leaving group is stabilized. Comparison of them is important for explaining the molecular evolution and enhancing the enzyme catalysis by mutations. There are so many kinds of bacterial dehalogenases that together they cover a broad range of substrates, halogenated compounds.
Haloalkane dehalogenases (EC 3.8.1.5) are a typical and widely-used bacterial dehalogenases. The mechanism of haloalkane dehalogenases became apparent when the structure of the Xanthobacter autotrophicus enzyme (DhlA) was solved by X-ray crystallography. Many studies have demonstrated that the enzymatic hydrolysis follows a two-step process with the formation of a covalent alkyl-enzyme ester intermediate. However, mechanistic issues about the first SN2 nucleophilic displacement reaction and the ester-enzyme hydrolysis reaction are still uncertain. In this paper, the first SN2 nucleophilic displacement reactions catalyzed by enzyme DhlA and LinB and the ester-enzyme hydrolysis reaction were investigated in detail by using density functional theory to explain the origin of enzyme catalysis. The mechanism investigations play an important role in explaining the origin of enzyme catalysis aimed at improving the enzyme activity and enhancing the substrate specificity.
The most important results are as follows:
(1) The SN2 nucleophilic displacement reaction catalyzed by enzyme DhlA was investigated in detail by using density functional theory. In enzyme DhlA catalysis, the carbon atom attached to the leaving halogen of the substrate is attacked by the carboxylate group of Asp124 in the SN2 fashion, yielding an alkyl-enzyme intermediate and a chlorine ion. Different hydrogen bonds patterns of the oxyanion hole and the halide-stabilizing residues, Trp125 and Trp175 play an important role in the dehalogenation reaction. The hydrogen bonds of the oxyanion hole make the carboxylate oxygen of Asp124 closer to DCE so that the reacting fragment is more reactive. Trp125 has a major stabilization effect on the reactant complex. The oxyanion hole and the halide-stabilizing residues concertedly cause an earlier TS with the activation barrier of 16.60 kcal/mol. The stabilization effect of Trp125 and Trp175 on Cl1 atom in TS1 is larger than that of RC1 by 15.67 kcal/mol so that they make contribution to the stabilization of the transition state. Moreover, analysis of the solvent effect on the reaction shows that enzyme catalysis is due to reactant-state destabilization relative to water solution. So the enzymatic action can be attributed to a combination of reactant-state destabilization and TS electrostatic stabilization. They lower the energy barrier by 6.12 kcal/mol.
DhlA and LinB are homologous enzymes. Analysis of the activation barriers reveals that the reaction process catalyzed by LinB is very similar to that of DhlA. However, their catalytic triad and active sites are different. DCE is able to benefit from substantial conformational freedom within the active site. The preponderant conformer is important for the reaction to proceed. For DhlA catalysis, the gauche conformer (D (Cl1–C1–C2–Cl2) = -60°) of the substrate is easier to take place, whereas the same conformer of the substrate is difficult to dehalogenate in LinB.
(2) The ester-enzyme hydrolysis reaction catalyzed by enzyme DhlA was investigated in detail using density functional theory. The ester-enzyme hydrolysis reaction involves a nucleophilic addition of a water molecule to the carbonyl group, which is catalyzed by the general base His289 and is accompanied by a proton transfer from the nucleophilic water. The ester is hydrolyzed via a TI and it splits to a corresponding alcohol and acid (Asp124). After TI, elimination and another proton transfer process take place. Herein whether the transferred proton is from protonated His289 or deprotonated water nucleophile was elucidated. In both of the two pathways, the first AdN step is rate-limiting. In the gas phase, the barrier for the pathway with the transferred proton from protonated His289 is lower than that of the pathway with the transferred proton from deprotonated water molecular by 0.13 kcal/mol. Thus the former is the preponderant process. In benzene, the barrier for the dominant pathway is lower than that of the inferior pathway by 0.67 kcal/mol.
When a second water molecule involved in the X-ray structure of DhlA was also selected, the hydrolysis mechanism is different. Unlike three steps in the pathway with the transferred proton from protonated His289, only two steps were involved in the water assisted hydrolysis. The first AdN step is followed by the concerted step of elimination and the second proton transfer. The overall reaction is also dominated by the first AdN step. In the gas phase, the hydrolysis can be accelerated by lowering the barrier, 3.35 kcal/mol. Moreover, benzene can make an effect on promoting ester hydrolysis, lowering the barrier by 1.79 kcal/mol. The obtained activation barrier in benzene, 18.65 kcal/mol is in fairly good agreement with the recently reported barrier of the AdN step, 19.5±2.1 kcal /mol. Therefore both the second water molecule and the protein environment play an important role in hydrolytic dehalogenation.
目前研究的去卤化酶主要有五种:烷基卤去卤化酶、卤代酸去卤化酶、4-氯苯甲酰-辅酶A去卤化酶、卤代醇去卤化酶和3-卤丙烯酸去卤化酶。它们以不同的催化机制作用于多种有机卤化物,使碳卤键断裂。前三种酶催化时都是取代机制,经历一个酯酶中间体。后两者虽与前三种是类似的酶,但在不同的化学环境中催化机制不同。这些去卤化酶的结构相似,却具有底物特异性。另外,由于去卤化酶的种类很多,它的多样性使得底物范围大大拓宽,包括卤代烷烃、卤代环烷烃、卤代醇、卤代氨基化合物和卤代烯烃等。
其中,烷基卤去卤化酶是去卤化酶中一种典型且应用非常广泛的生物降解酶。1993年烷基卤去卤化酶(DhlA)晶体结构的确定,使得它的催化作用机制引起国内外科学家的广泛关注。目前对这种去卤化酶的研究取得了一定进展,但在研究烷基卤去卤化酶催化去卤的两步反应机制时,SN2亲核取代反应和酯酶中间体的水解反应的机理一直是人们争论的焦点。为了进一步说明去卤化酶催化动力的来源,本文使用量子化学中的密度泛函理论对SN2亲核取代反应和酯酶中间体的水解反应的机理进行了研究,为实验上研究去卤化酶的进化,提高去卤化酶的生物催化活性和拓宽底物范围提供了理论基础。
本论文的主要内容为:
1、我们用密度泛函理论对DhlA酶的SN2亲核取代反应进行了研究。研究表明,在DhlA酶的催化反应中,Asp124的碳酸基团以SN2亲核取代的方式进攻连接在底物上离去氯离子的碳上,得到酯酶中间体和氯离子。氧离子空穴和卤稳定残基上的不同的氢键相互作用在酶催化反应中意义重大。氧离子空穴上氢键的存在使得Asp124的羧酸基团更加靠近底物DCE,使得反应部位活性很高。在反应复合物中,Trp125起主要的稳定作用,而Trp125和Trp175在过渡态中都起非常重要的稳定作用。研究酶催化反应的溶剂效应发现,酶的催化作用主要在于酶中的反应物相对于非酶催化反应的反应物的不稳定作用。总之,酶催化主要是反应物相对不稳定和过渡态相对稳定的共同作用,使得能垒降低6.12 kcal/mol。
DhlA和LinB为同源酶。活化势垒分析表明,在它们的催化反应过程中都发生了SN2亲核取代反应。然而,这些酶的催化残基和活性中心是不同的。活性中心的DCE的构象自由。底物的两种邻位交叉式构象对反应的进行非常重要。DhlA酶催化时,底物的邻位交叉式构象(D (Cl1–C1–C2–Cl2) = -60°)容易发生去卤反应;而LinB酶催化反应时,另一邻位交叉式构象(D (Cl1–C1–C2–Cl2) = +60°)易于发生去卤化反应。
2、我们使用密度泛函方法研究了DhlA酶催化的酯酶中间体的水解反应。结果表明,酯酶中间体的水解反应涉及到His289活化的水分子与酯基的的亲核加成反应,同时伴随着水亲核试剂的质子迁移反应。酯酶中间体的水解经历了一个四面体中间体结构。然后消除和质子迁移反应导致四面体中间体的分解,最后得到相应的醇、卤离子和Asp124。在这两个反应途径中,第一步AdN反应都是决速步骤。气相中,质子化His289的质子迁移途径的势垒比脱质子水的质子迁移途径的低0.13 kcal/mol。因此,质子化His289的质子迁移途径是优势通道。苯中它的势垒比脱质子水的质子迁移途径的低0.67 kcal/mol。
研究酯酶中间体水解反应时发现,水促进的水解反应与质子化His289的质子迁移途径的三步反应机制是有差异的。水促进的水解反应涉及两步反应:第一步为AdN反应,第二步消除反应和质子迁移反应协同进行。其中,第一步AdN反应为决速步骤。水促进的水解反应可降低势垒3.35 kcal/mol。另外,疏水环境的溶剂苯也可以使势垒降低1.79 kcal/mol,加速水解反应的发生。我们在苯中得到的反应势垒为18.65 kcal/mol,这与最新报道的第一步AdN反应的势垒(19.5±2.1 kcal /mol)非常一致。因此,第二个水分子和酶的疏水环境对促进酶的水解去卤具有非常重要的作用。
Dehalogenases comprise such a group of microbial enzymes that catalyze the cleavage of carbon–halogen bonds into the corresponding alcohols and halide anions. There is a growing interest in the application of these enzymes as industrial biocatalysts. Recently, the catalytic prosperities of these enzymes in bioremediation applications have therefore been subjected to detailed investigations.
To date, there are five bacterial dehalogenases, including haloalkane dehalogenases, haloacid dehalogenases, 4-chlorobenzoyl-coenzyme A (CoA) dehalogenase, haloalcohol dehalogenase and a trans-3-chloroacrylic acid dehalogenase. These enzymes make use of a variety of distinctly different catalytic mechanisms to cleave carbon–halogen bonds. It is demonstrated the power of substitution mechanisms of the first three enzymes that proceed via a covalent aspartyl intermediate. For the latter two homologous ones, it is exploited that their catalytic mechanisms are different in different chemical environments. Although the five dehalogenases are very similar, they have some difference in the geometry and size of the active site cavity and differences in the way in which the leaving group is stabilized. Comparison of them is important for explaining the molecular evolution and enhancing the enzyme catalysis by mutations. There are so many kinds of bacterial dehalogenases that together they cover a broad range of substrates, halogenated compounds.
Haloalkane dehalogenases (EC 3.8.1.5) are a typical and widely-used bacterial dehalogenases. The mechanism of haloalkane dehalogenases became apparent when the structure of the Xanthobacter autotrophicus enzyme (DhlA) was solved by X-ray crystallography. Many studies have demonstrated that the enzymatic hydrolysis follows a two-step process with the formation of a covalent alkyl-enzyme ester intermediate. However, mechanistic issues about the first SN2 nucleophilic displacement reaction and the ester-enzyme hydrolysis reaction are still uncertain. In this paper, the first SN2 nucleophilic displacement reactions catalyzed by enzyme DhlA and LinB and the ester-enzyme hydrolysis reaction were investigated in detail by using density functional theory to explain the origin of enzyme catalysis. The mechanism investigations play an important role in explaining the origin of enzyme catalysis aimed at improving the enzyme activity and enhancing the substrate specificity.
The most important results are as follows:
(1) The SN2 nucleophilic displacement reaction catalyzed by enzyme DhlA was investigated in detail by using density functional theory. In enzyme DhlA catalysis, the carbon atom attached to the leaving halogen of the substrate is attacked by the carboxylate group of Asp124 in the SN2 fashion, yielding an alkyl-enzyme intermediate and a chlorine ion. Different hydrogen bonds patterns of the oxyanion hole and the halide-stabilizing residues, Trp125 and Trp175 play an important role in the dehalogenation reaction. The hydrogen bonds of the oxyanion hole make the carboxylate oxygen of Asp124 closer to DCE so that the reacting fragment is more reactive. Trp125 has a major stabilization effect on the reactant complex. The oxyanion hole and the halide-stabilizing residues concertedly cause an earlier TS with the activation barrier of 16.60 kcal/mol. The stabilization effect of Trp125 and Trp175 on Cl1 atom in TS1 is larger than that of RC1 by 15.67 kcal/mol so that they make contribution to the stabilization of the transition state. Moreover, analysis of the solvent effect on the reaction shows that enzyme catalysis is due to reactant-state destabilization relative to water solution. So the enzymatic action can be attributed to a combination of reactant-state destabilization and TS electrostatic stabilization. They lower the energy barrier by 6.12 kcal/mol.
DhlA and LinB are homologous enzymes. Analysis of the activation barriers reveals that the reaction process catalyzed by LinB is very similar to that of DhlA. However, their catalytic triad and active sites are different. DCE is able to benefit from substantial conformational freedom within the active site. The preponderant conformer is important for the reaction to proceed. For DhlA catalysis, the gauche conformer (D (Cl1–C1–C2–Cl2) = -60°) of the substrate is easier to take place, whereas the same conformer of the substrate is difficult to dehalogenate in LinB.
(2) The ester-enzyme hydrolysis reaction catalyzed by enzyme DhlA was investigated in detail using density functional theory. The ester-enzyme hydrolysis reaction involves a nucleophilic addition of a water molecule to the carbonyl group, which is catalyzed by the general base His289 and is accompanied by a proton transfer from the nucleophilic water. The ester is hydrolyzed via a TI and it splits to a corresponding alcohol and acid (Asp124). After TI, elimination and another proton transfer process take place. Herein whether the transferred proton is from protonated His289 or deprotonated water nucleophile was elucidated. In both of the two pathways, the first AdN step is rate-limiting. In the gas phase, the barrier for the pathway with the transferred proton from protonated His289 is lower than that of the pathway with the transferred proton from deprotonated water molecular by 0.13 kcal/mol. Thus the former is the preponderant process. In benzene, the barrier for the dominant pathway is lower than that of the inferior pathway by 0.67 kcal/mol.
When a second water molecule involved in the X-ray structure of DhlA was also selected, the hydrolysis mechanism is different. Unlike three steps in the pathway with the transferred proton from protonated His289, only two steps were involved in the water assisted hydrolysis. The first AdN step is followed by the concerted step of elimination and the second proton transfer. The overall reaction is also dominated by the first AdN step. In the gas phase, the hydrolysis can be accelerated by lowering the barrier, 3.35 kcal/mol. Moreover, benzene can make an effect on promoting ester hydrolysis, lowering the barrier by 1.79 kcal/mol. The obtained activation barrier in benzene, 18.65 kcal/mol is in fairly good agreement with the recently reported barrier of the AdN step, 19.5±2.1 kcal /mol. Therefore both the second water molecule and the protein environment play an important role in hydrolytic dehalogenation.
引文
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