水分子对乳清酸核苷单磷酸盐催化脱羧的影响
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摘要
乳清酸核苷-5′-单磷酸盐脱羧酶(ODCase)催化乳清酸核苷-5'-单磷酸盐(OMP)脱羧生成尿苷-5'-单磷酸盐(UMP)是核酸生物合成的一个关键步骤,ODCase是目前已知催化效率较高的酶之一,它可以使自发脱羧反应的催化效率提高17个数量级还多。ODCase是一种蛋白质单成分酶,不包含任何的金属离子和辅基,且有结果显示其高效的催化能力只是来源于非共价作用。这一特性是脱羧酶所不常见的。这为我们更深入地理解酶的催化机理提供了一个理想的研究模型。
1995年Wolfenden和Radzicka发现乳清酸核苷-5'-单磷酸盐脱羧酶是一种非常高效的脱羧酶,从此ODCase的催化机理成为人们关注的焦点。经过十几年的研究,ODCase的催化机理仍然没有公认的解释。
以往的研究主要提出了:过渡态稳定化机理,基态去稳定化机理,C-5位置直接质子化机理,O-2(OMP的2'位氧原子)质子化机理,O-4(OMP的4'位氧原子)质子化的机理,亲电取代机理等几种重要的机理,这些机理大部分只单独研究了OMP的O-2、O-4、C-5等几个特殊的部位,没有综合地研究各部位的作用。而且以前的研究中虽然部分地考虑了水分子的作用,但没有重点和全面的去研究水分子的作用。
本文在前人研究成果的基础上根据过渡态理论设计了各种模型,用密度泛函B3LYP方法计算了各模型的反应势垒和N-1位置的~(15)N动力学同位素效应及C-6位置羧基碳原子的~(13)C动力学同位素效应。结果显示反应势垒,~(15)N动力学同位素效应和~(13)C动力学同位素效应与实验值基本吻合,表明水分子在ODCase催化OMP生成UMP的过程中起重要作用。
本文主要研究内容和取得的结果为:
(一)采用混合泛函B3LYP的方法计算了质子化的水分子与OMP的O-2形成氢键对乳清酸核苷单磷酸盐脱羧酶(ODCase)催化作用的影响,得到OMP脱羧势垒为24.9kcal/mol。无水分子作用时势垒为39.6 kcal/mol,可看出水分子与O-2形成氢键后脱羧反应的势垒减小了。表明水分子在ODCase催化过程中起重要作用
(二)用密度泛函B3LYP方法计算了OMP的O-2、O-4与水分子同时作用对OMP催化脱羧势垒的影响,并与O-2、O-4和水分子单独作用的情况相比较,同时考虑了过渡态稳定化机理,基态去稳定化机理。结果表明带正电荷的氨基酸残基通过水分子链的桥梁作用与底物OMP的O-2、O-4形成低势垒氢键,能够使OMP的脱羧势垒显著降低,也表明ODCase巨大的催化能力是ODCase的各催化因素协同作用的结果。
(三)设计并优化了乳清酸核苷单磷酸盐催化脱羧的模型,计算了该模型的反应势垒、N-1位置的~(15)N动力学同位素效应和C-6位置羧基碳原子的~(13)C动力学同位素效应。结果显示~(15)N动力学同位素效应和~(13)C动力学同位素效应与实验值基本吻合,表明了水分子参与反应过程的可能性。
Orotidine 5`-phosphate decarboxylase (ODCase,) catalyzes the decarboxylation of orotidine 5`-phosphate (OMP) to form uridine 5`-phosphate in the crucial step of nucleic acid biosynthesis. ODCase is one of the most efficient enzymes. It can increase the rate of decarboxylation by 17 orders of magnitude. ODCase distinguishes itself from other enzymes by the fact that there is no direct participation of cofactors or metal ions, nor formation of a covalent intermediate with a group on the protein. Analyzing the mechanism of ODCase can therefore be an important step in understanding enzyme catalysis on a more general level.
In 1995, Wolfenden and Radzicka showed that orotidine 5'-monophosphate decarboxylase(ODCase) was the most proficient enzyme. Since then, the mechanism of catalysis has been widely debated although the study about it has been carrying out for decades.
During the past decades, some mechanistic proposals with novel features have been forwarded, such as: concerted O-2 protonation mechanism, C-5 protonation mechanism, concerted C-6 protonation/decarboxylation mechanism, electrostatic stabilization of transition state mechanism, electrostatic stress of the ground state mechanism, O-4 protonation mechanism. Most of these mechanisms are only about the partial functional factors such as O-2,O-4 and C-5 . In addition, the influence of water molecules were considered on the superficial level in the past study.
Based on the previous study, several models were designed. The effect of water molecules on the enzyme-catalyzed decarboxylation of Orotidine 5'–Monophosphate was investigated using density functional theory with the B3LYP functional. Barriers and ~(15)N kinetic isotope effect,~(13)C kinetic isotope effect of different models were calculated. Our results indicates that water molecules play an important role in TS stabilization.
The main results of this thesis are as follows:
Firstly, the model in which O-2 of OMP bond to a protonated water molecule were studied used hybrid Density Functional Theory (B3LYP functional) . The barrier of this model is 24.9kcal/mol. Compared with the barrier 39.6kcal/mol of the model just removing the protonated water molecular. The results showed that the indirect interactions between O-2 of the pyrimidine ring and the positive charged residues through chains of water molecules can lower the barrier height for decarboxylation significantly.
Secondly , the effect of water molecules bonding to the O-2 and O-4 of OMP in the same time on the enzyme-catalyzed decarboxylation of Orotidine 5'–Monophosphate were investigated using density functional theory in the same level. Barriers of different models have been calculated and results were compared with the case of water molecules bonding to O-2/O-4 respectively. Our computation indicates that water molecules play an important role in TS stabilization. Our computation also indicates that it is the collective actions of various catalytic factors that make ODCase such a proficient enzyme.
Thirdly, several models of the decarboxylation of OMP have been designed and optimized. ~(15)N kinetic isotope effect of N-1 and ~(13)C kinetic isotope effect of C-6 were calculated. The outcome of ~(13)C kinetic isotope effect and ~(15)N kinetic isotope effect consisting with the experimental result show that water molecules playing an important role in the decarboxylation of OMP.
1995年Wolfenden和Radzicka发现乳清酸核苷-5'-单磷酸盐脱羧酶是一种非常高效的脱羧酶,从此ODCase的催化机理成为人们关注的焦点。经过十几年的研究,ODCase的催化机理仍然没有公认的解释。
以往的研究主要提出了:过渡态稳定化机理,基态去稳定化机理,C-5位置直接质子化机理,O-2(OMP的2'位氧原子)质子化机理,O-4(OMP的4'位氧原子)质子化的机理,亲电取代机理等几种重要的机理,这些机理大部分只单独研究了OMP的O-2、O-4、C-5等几个特殊的部位,没有综合地研究各部位的作用。而且以前的研究中虽然部分地考虑了水分子的作用,但没有重点和全面的去研究水分子的作用。
本文在前人研究成果的基础上根据过渡态理论设计了各种模型,用密度泛函B3LYP方法计算了各模型的反应势垒和N-1位置的~(15)N动力学同位素效应及C-6位置羧基碳原子的~(13)C动力学同位素效应。结果显示反应势垒,~(15)N动力学同位素效应和~(13)C动力学同位素效应与实验值基本吻合,表明水分子在ODCase催化OMP生成UMP的过程中起重要作用。
本文主要研究内容和取得的结果为:
(一)采用混合泛函B3LYP的方法计算了质子化的水分子与OMP的O-2形成氢键对乳清酸核苷单磷酸盐脱羧酶(ODCase)催化作用的影响,得到OMP脱羧势垒为24.9kcal/mol。无水分子作用时势垒为39.6 kcal/mol,可看出水分子与O-2形成氢键后脱羧反应的势垒减小了。表明水分子在ODCase催化过程中起重要作用
(二)用密度泛函B3LYP方法计算了OMP的O-2、O-4与水分子同时作用对OMP催化脱羧势垒的影响,并与O-2、O-4和水分子单独作用的情况相比较,同时考虑了过渡态稳定化机理,基态去稳定化机理。结果表明带正电荷的氨基酸残基通过水分子链的桥梁作用与底物OMP的O-2、O-4形成低势垒氢键,能够使OMP的脱羧势垒显著降低,也表明ODCase巨大的催化能力是ODCase的各催化因素协同作用的结果。
(三)设计并优化了乳清酸核苷单磷酸盐催化脱羧的模型,计算了该模型的反应势垒、N-1位置的~(15)N动力学同位素效应和C-6位置羧基碳原子的~(13)C动力学同位素效应。结果显示~(15)N动力学同位素效应和~(13)C动力学同位素效应与实验值基本吻合,表明了水分子参与反应过程的可能性。
Orotidine 5`-phosphate decarboxylase (ODCase,) catalyzes the decarboxylation of orotidine 5`-phosphate (OMP) to form uridine 5`-phosphate in the crucial step of nucleic acid biosynthesis. ODCase is one of the most efficient enzymes. It can increase the rate of decarboxylation by 17 orders of magnitude. ODCase distinguishes itself from other enzymes by the fact that there is no direct participation of cofactors or metal ions, nor formation of a covalent intermediate with a group on the protein. Analyzing the mechanism of ODCase can therefore be an important step in understanding enzyme catalysis on a more general level.
In 1995, Wolfenden and Radzicka showed that orotidine 5'-monophosphate decarboxylase(ODCase) was the most proficient enzyme. Since then, the mechanism of catalysis has been widely debated although the study about it has been carrying out for decades.
During the past decades, some mechanistic proposals with novel features have been forwarded, such as: concerted O-2 protonation mechanism, C-5 protonation mechanism, concerted C-6 protonation/decarboxylation mechanism, electrostatic stabilization of transition state mechanism, electrostatic stress of the ground state mechanism, O-4 protonation mechanism. Most of these mechanisms are only about the partial functional factors such as O-2,O-4 and C-5 . In addition, the influence of water molecules were considered on the superficial level in the past study.
Based on the previous study, several models were designed. The effect of water molecules on the enzyme-catalyzed decarboxylation of Orotidine 5'–Monophosphate was investigated using density functional theory with the B3LYP functional. Barriers and ~(15)N kinetic isotope effect,~(13)C kinetic isotope effect of different models were calculated. Our results indicates that water molecules play an important role in TS stabilization.
The main results of this thesis are as follows:
Firstly, the model in which O-2 of OMP bond to a protonated water molecule were studied used hybrid Density Functional Theory (B3LYP functional) . The barrier of this model is 24.9kcal/mol. Compared with the barrier 39.6kcal/mol of the model just removing the protonated water molecular. The results showed that the indirect interactions between O-2 of the pyrimidine ring and the positive charged residues through chains of water molecules can lower the barrier height for decarboxylation significantly.
Secondly , the effect of water molecules bonding to the O-2 and O-4 of OMP in the same time on the enzyme-catalyzed decarboxylation of Orotidine 5'–Monophosphate were investigated using density functional theory in the same level. Barriers of different models have been calculated and results were compared with the case of water molecules bonding to O-2/O-4 respectively. Our computation indicates that water molecules play an important role in TS stabilization. Our computation also indicates that it is the collective actions of various catalytic factors that make ODCase such a proficient enzyme.
Thirdly, several models of the decarboxylation of OMP have been designed and optimized. ~(15)N kinetic isotope effect of N-1 and ~(13)C kinetic isotope effect of C-6 were calculated. The outcome of ~(13)C kinetic isotope effect and ~(15)N kinetic isotope effect consisting with the experimental result show that water molecules playing an important role in the decarboxylation of OMP.
引文
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