本文選題：酶催化 + 反應(yīng)機(jī)理　； 參考：《山東大學(xué)》2016年碩士論文

【摘要】：酶催化反應(yīng)因具有催化效率高、反應(yīng)條件溫和等優(yōu)點(diǎn),在日常生活和工農(nóng)業(yè)業(yè)生產(chǎn)中被廣泛應(yīng)用。然而,由于酶促反應(yīng)體系的復(fù)雜性,目前從實(shí)驗(yàn)上檢測(cè)反應(yīng)過(guò)程中的中間體和過(guò)渡態(tài)的結(jié)構(gòu)還十分困難,對(duì)酶反應(yīng)機(jī)理的認(rèn)知主要是根據(jù)動(dòng)力學(xué)和突變?cè)囼?yàn)來(lái)推測(cè)。隨著量子化學(xué)理論方法和計(jì)算機(jī)技術(shù)的不斷發(fā)展,以量子化學(xué)為基礎(chǔ)的理論與計(jì)算化學(xué)可以從原子水平上研究化學(xué)反應(yīng)的過(guò)程,給出酶催化反應(yīng)的詳細(xì)機(jī)理、能量關(guān)系及決速步驟等信息,在研究生物大分子反應(yīng)機(jī)理方面具有突出優(yōu)勢(shì)。本論文以最新測(cè)得的三種生物降解酶的晶體結(jié)構(gòu)為基礎(chǔ),運(yùn)用量子力學(xué)與分子力學(xué)(QM/MM)相結(jié)合的方法對(duì)這些酶的催化機(jī)理進(jìn)行了較為系統(tǒng)的理論研究,在原子水平上給出了反應(yīng)的細(xì)節(jié),包括過(guò)渡態(tài)、中間體的構(gòu)型、能量關(guān)系、決速步驟等,闡明了一些活性殘基在催化中的不同作用,并對(duì)部分殘基進(jìn)行了突變計(jì)算,研究結(jié)果不僅彌補(bǔ)了實(shí)驗(yàn)研究的不足,而且為相關(guān)酶的實(shí)驗(yàn)研究及應(yīng)用開發(fā)提供了必要的基礎(chǔ)。主要研究?jī)?nèi)容包括：(1)N-酰基高絲氨酸內(nèi)酯酶催化機(jī)理的理論研究自然界中,許多致病的細(xì)菌通過(guò)群體感應(yīng)效應(yīng)使動(dòng)植物以及人類患病。N-酰基高絲氨酸內(nèi)酯(N-acyl-homoserine lactones, AHLs)作為一種群體感應(yīng)信號(hào)分子在革蘭氏陰性細(xì)菌中被廣泛利用。N-�；呓z氨酸內(nèi)酯酶通過(guò)降解AHLs分子,來(lái)阻止群體感應(yīng)發(fā)生,從而起到預(yù)防疾病的作用。實(shí)驗(yàn)上建議反應(yīng)過(guò)程內(nèi)酯環(huán)以分步的方式斷裂。本文利用QM/MM方法研究了N-酰基高絲氨酸內(nèi)酯酶的催化機(jī)理,計(jì)算結(jié)果表明反應(yīng)過(guò)程中的開環(huán)反應(yīng)是一個(gè)協(xié)同反應(yīng)而不是分步反應(yīng)。通過(guò)研究MM區(qū)中重要?dú)埢撵o電作用,確定了周圍殘基對(duì)催化反應(yīng)的影響,為進(jìn)一步進(jìn)行突變實(shí)驗(yàn)提供了理論指導(dǎo)。我們的研究對(duì)實(shí)驗(yàn)上提出的反應(yīng)機(jī)理進(jìn)行了部分修改,確定了詳細(xì)的反應(yīng)機(jī)理及其能量學(xué)信息,有助于理解高絲氨酸類內(nèi)酯酶的降解機(jī)理,為治療因高絲氨酸信號(hào)分子引起的疾病提供了理論指導(dǎo)。(2)2-吡喃酮-4,6-二羧酸水解酶催化機(jī)理的理論研究2-吡喃酮-4,6-二羧酸(PDC)是木質(zhì)素降解過(guò)程中的一種中間體。木質(zhì)素的降解對(duì)自然界中碳循環(huán)具有重要意義。2-吡喃酮-4,6-二羧酸(PDC)水解酶催化PDC水解生成兩種水解產(chǎn)物,分別為烯醇式產(chǎn)物4-羧基-2-羥基粘康酸(CHM)和酮式產(chǎn)物4-草酰中康酸(OMA)。本文利用QM/MM方法研究了PDC水解酶的催化機(jī)理。根據(jù)我們的計(jì)算結(jié)果可得到如下信息：整個(gè)水解反應(yīng)包括三個(gè)基元反應(yīng),由于第三步(氫轉(zhuǎn)移)反應(yīng)有兩種可能的途徑,因而可以得到兩種水解產(chǎn)物；通過(guò)突變研究,確定了三個(gè)組氨酸(His31、His33和His180)在反應(yīng)過(guò)程中的作用；反應(yīng)過(guò)程中反應(yīng)物、過(guò)渡態(tài)和中間體的構(gòu)型；整個(gè)反應(yīng)過(guò)程的勢(shì)能面。本論文對(duì)研究PDC聚合物的生物降解具有理論指導(dǎo)意義。(3)2,4'-二羥基苯乙酮加雙氧酶催化機(jī)理的理論研究2,4'-二羥基苯乙酮(DHAP)是木質(zhì)素的一種降解產(chǎn)物,2,4'-二羥基苯乙酮加雙氧酶(DAD)可以把DHAP進(jìn)一步降解成對(duì)羥基苯甲酸和甲酸。對(duì)于DAD的催化機(jī)理,實(shí)驗(yàn)學(xué)家通過(guò)研究該酶的仿生模型給出了一條涉及一個(gè)四元環(huán)中間體的生成與斷裂的機(jī)理。本文利用QM/MM方法研究了2,4'-二羥基苯乙酮加雙氧酶的催化機(jī)理。根據(jù)我們的計(jì)算結(jié)果涉及四元環(huán)的路徑能壘過(guò)高,于是我們對(duì)其他可能的機(jī)理進(jìn)行了研究。結(jié)果表明,DAD采用一種新的反應(yīng)機(jī)理催化2,4'-二羥基苯乙酮的降解,總反應(yīng)包含八步基元反應(yīng),其中前兩步機(jī)理與實(shí)驗(yàn)上建議的機(jī)理相同,最后一步基元反應(yīng)是決速步。因?yàn)槿貞B(tài)的氧氣與五重態(tài)的鐵作用可得到三種可能的自旋多重度(三重態(tài)、五重態(tài)和七重態(tài)),所以我們對(duì)一些關(guān)鍵步驟分別在三重態(tài)、五重態(tài)和七重態(tài)條件下進(jìn)行了計(jì)算。結(jié)果表明,反應(yīng)首先經(jīng)歷一個(gè)從三重態(tài)到五重態(tài)的轉(zhuǎn)變,隨后反應(yīng)主要在五重態(tài)勢(shì)能面上進(jìn)行。計(jì)算結(jié)果為研究金屬酶催化的脂肪族類碳碳鍵的斷裂反應(yīng)提供了理論指導(dǎo)。
[Abstract]:The enzyme catalyzed reaction has been widely used in daily life and industrial and agricultural production because of its high catalytic efficiency and mild reaction conditions. However, because of the complexity of the enzymatic reaction system, it is difficult to detect the structure of intermediate and transition state in the reaction process at present, and the cognition of the mechanism of the enzyme reaction is mainly based on the fact that the enzyme catalyzed reaction system is complex. With the continuous development of quantum chemical theory and computer technology, the theoretical and computational chemistry based on quantum chemistry and computational chemistry can study the process of chemical reactions from the atomic level, give information on the detailed mechanism, energy relations and the rate of determination of the enzyme in the study of biological macromolecules. Based on the crystal structure of the latest three biodegradable enzymes, this paper systematically studies the catalytic mechanism of these enzymes by combining the method of quantum mechanics and molecular mechanics (QM/MM), and gives the details of the reaction at the atomic level, including the transition state and the intermediate. The structure, the energy relation, the quick step and so on, clarify the different effects of some active residues in the catalysis, and calculate the mutation of some residues. The results not only make up the shortage of the experimental research, but also provide the necessary foundation for the experimental research and application development of the related enzymes. The main contents include: (1) the high acyl group of N- The theoretical study of the catalytic mechanism of the serine lactone enzyme in nature, many pathogenic bacteria are widely used as a kind of N-acyl-homoserine lactones (AHLs), the.N- acyl high serine lactone (lactones, AHLs), in gram - acyl high serine lactone in gram - negative bacteria through the quorum induction effect By degrading AHLs molecules to prevent the occurrence of quorum induction, the enzyme plays a role in preventing disease. In the experiment, it is suggested that the ester ring breaks in a stepwise way. In this paper, the catalytic mechanism of N- acyl hserine lactone enzyme was studied by QM/MM method. The results show that the ring opening reaction in the reaction process is a synergistic reaction. It is not a step reaction. Through the study of the electrostatic action of the important residues in the MM region, the influence of the surrounding residues on the catalytic reaction is determined, and the theoretical guidance is provided for the further mutation experiment. Our research has made some modifications to the reaction mechanism proposed in the experiment, determined the detailed reaction mechanism and the energy information, which is helpful to the theory of the reaction. The degradation mechanism of high serine lactone enzyme can provide theoretical guidance for the treatment of diseases caused by high serine signal molecules. (2) theoretical study on the catalytic mechanism of 2- -4,6- two carboxylic acid hydrolase, 2- (PDC) is an intermediate in the degradation of lignin. The degradation of lignin in natural carbon cycle The.2- hydrolysis of pyruvone -4,6- two carboxylic acid (PDC) hydrolase catalyzes the hydrolysis of PDC to produce two kinds of hydrolysates, which are 4- carboxylic -2- hydroxyviscoacic acid (CHM) and 4- oxacylic acid (OMA) in the enol product, respectively. This paper studies the catalytic mechanism of PDC hydrolase by QM/MM method. The following information can be obtained according to our calculation results. The whole hydrolysis reaction includes three elemental reactions, and because there are two possible pathways in the third step (hydrogen transfer) reaction, two kinds of hydrolysates can be obtained. Through the mutation study, the role of three histidine (His31, His33 and His180) in the reaction process is determined; the configuration of the reactant, transition state and intermediate in the reaction process; The potential energy surface of the reaction process. This paper has theoretical guiding significance for the study of biodegradation of PDC polymers. (3) theoretical study on the catalytic mechanism of 2,4'- two hydroxybenzophenone plus dioxygen enzyme, 2,4'- two hydroxyacetophenone (DHAP) is a degradation product of lignin, and 2,4'- two hydroxyacetophenone plus dioxygen enzyme (DAD) can further degrade DHAP into DHAP In the catalytic mechanism of hydroxy benzoic acid and formic acid. By studying the bionic model of the enzyme, an experimenter gives a mechanism involving the formation and fracture of a four membered ring intermediate. In this paper, the catalytic mechanism of 2,4'- two hydroxyacetophenone plus dioxygenase is studied by QM/MM method. According to our calculation, the four membered ring is involved. The path energy barrier is too high, so we have studied other possible mechanisms. The results show that DAD uses a new reaction mechanism to catalyze the degradation of 2,4'- two hydroxy acetophenone. The total reaction contains eight steps of the basic reaction, of which the first two steps are the same as that suggested in the experiment, and the final step reaction is a quick step. Because of the three heavy state. The action of oxygen and iron in the five state can be obtained by three possible spin multiples (three, five, and seven heavy). So we calculate some of the key steps in three, five and seven states, respectively. The results show that the reaction first experienced a transition from three to five, then the reaction was mainly in five. The calculated results provide theoretical guidance for the study of the fracture reaction of fatty carbon carbon bonds catalyzed by metalloenzymes.

【學(xué)位授予單位】：山東大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2016
【分類號(hào)】：O629.8

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