生物酶在生命活动中起着至关重要的作用，和我们的生活也密切相关。无论在实验测定还是理论计算领域，对酶催化反应机理的研究都存在着诸多挑战。本报告即是采用分子动力学模拟结合QM/MM组合方法，分别计算了8-氧鸟嘌呤脱氨酶、异黄蝶呤脱氨酶和烟酰胺酶的反应机理，并为这三个体系的定点突变实验提供了有用的建议。总体来说，本报告的主要工作可以概括为：

In biochemistry field, biological enzymes play a key role in life activities. But the investigation on their reaction mechanisms is still a challenging in both experimental and theoretical fields. The work of this report was the simulations of 8-oxoguanine deaminase (8-oxoGD), isoxanthopterin deaminase and nicotinamidase in QM/MM MD level, and the results can give some useful suggestions to site-directed mutagenesis studies. The main work of this dissertation can be summarized as follows:(1)The deamination reaction of 8-oxoguanine (8-oxoG) catalyzed by 8-oxoguanine deaminase (8-oxoGD) plays a critically important role in the DNA repair activity for oxidative damage. In order to elucidate the enzymatic catalysis mechanisms from the perspective of the 8-oxoguanine binding, departure of 2-hydroxy-1H-purine-6,8 (7H,9H)-dione from active site, and formation of 8-oxoxanthine processes, a combined QM(PM3)/MM molecular dynamics simulation has been performed, which suggested that the rate-limiting step corresponds to the nucleophilic attack from zinc-coordinate hydroxide group to free 8-oxoguanine. Through conformational analyses, we are able to show that Trp115, Trp123 and Leu119 connect O8@8-oxoguanine with hydrogen bonds respectively, and mutations to histidine or phenylalanine for tryptophan and alanine for leucine could potentially lead to a mutant with enhanced activity. On this ground, the proton transfer mechanism for 8-oxoxanthine forming was further discussed. Both Glu218 and water molecule could be used as proton shuttle, and water molecule plays a major role in proton transfer from OW to N1 in substrate. On the other hand, comparative simulations on the deamination of guanine and isocytosine reveal that, for the helping of hydrogen bonds between O8@8-oxoguanine and enzyme, O8@8-oxoguanine is the fastest to be deaminated among the three substrates which are also supported by the experimental kinetic constants.(2)The deaminasion process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this dissertation, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to active site. The simulations which change the substrate to pterin 6-carboxylate was also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.(3)The deaminasion process of nicotinamide to nicotinic acid by nicotinamidase simulated by using combined QM(PM3)/MM molecular dynamics method. Calculated results show that, nucleophilic attack by sulfur group is the rate-limiting step of the whole reaction process. High energy consumption mainly because the nucleophilic attack needs to break the hydrogen bond between substate and Ala155. So we considered to mutate the loop of Ala155 to make Ala155 far from nicotinamide, which could weaken the hydrogen bond and increase the reactivity of nicotinamidase. Release of ammonia process and nucleophilic attack by sulfur group process are concerted. Similarly, release of Cys159 process and nucleophilic attack by hydroxyl group process are concerted too. Proton transfer from Asp16 to Cys159 includes two steps. The first one is HW6 transfer from OD3@Asp16 to O9, the second one is HW5 transfer from O9 to S@Cys159.