几类重要酶的催化反应机理的理论研究
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摘要
酶是由活细胞产生的具有催化功能的蛋白质。它属于生物大分子，但只有很小的部分起到结合底物或催化反应的作用，称为酶的活性中心。在酶催化过程中，底物或底物类似物在酶的活性中心瞬间生成酶-底物复合物，这个复合物具有较高的能量，是一种极为不稳定的状态。这种瞬间的状态很难通过实验方法来捕获。计算机模拟的出现有力的弥补了实验上的不足，能够从原子水平上获得整个反应历程的详细信息。通过分析酶催化反应的中间体和过渡态的结构，并结合动力学方法确定反应的限速步骤，就能够推知整个反应的催化机理。
本文主要利用量子化学计算方法，基于从蛋白质晶体结构中截取的团簇模型，对N~5-羧基氨基咪唑核苷酸变位酶、α－甲酰基辅酶A消旋酶和谷胱甘肽硫转移酶这三个体系进行了催化机理的理论研究。主要结果如下：
1.N~5-羧基氨基咪唑核苷酸变位酶催化的重排反应
对于除原生动物外的所有生命体来说，从头合成嘌呤这一过程都至关重要。在Class I PurE催化下生成5-氨基-4-羧基咪唑核苷酸(CAIR)这一反应是整个嘌呤合成过程中的关键步骤。遗传研究表明，Class I PurE对微生物的生长必不可少。这种酶的缺失会导致嘌呤缺陷体，在人类和鼠的血清中，这种缺陷体不具备繁殖能力，也没有抵御疾病的能力。
本文利用密度泛函理论B3LYP方法对N~5-羧基氨基咪唑核苷酸变位酶催化的重排反应机理进行了理论研究。基于EcPuE的晶体结构，我们构建了包含93个原子的理论模型来研究其催化机理，并利用自然键轨道理论(NBO)方法进行了电荷布居分析，进一步验证推测机理的正确性。结果表明，此重排反应分脱羧和羧化两个步骤进行。His45是一个既能起到广义酸作用又能起到广义碱作用的催化残基。在计算过程中，我们得到一个具有四面体结构的中间体（iso.CAIR），从理论上证实了之前实验上对该结构的预测。根据对每个优化结构的能量计算，绘制出总反应的势能面曲线，通过比较，AIR的羧化反应步骤为整个反应的限速步骤。同时，我们也考察了其它重要氨基酸残基（Ser43,Ala44, His45, Gly71, His75和Leu76等）对催化反应的影响。
2.α－甲酰基辅酶A消旋酶催化机理的理论研究
支链脂肪酸是人类日常饮食中的重要成分，也被用于非类固醇抗炎药物，如布洛芬。在代谢过程中，只有S构型底物能够通过支链脂酰辅酶A氧化酶发生代谢作用。α－甲酰基辅酶A消旋酶(AMACR)能够使各种α-甲酰基辅酶A衍生物发生S、R异构互变。因此，AMACR的这一功能使其成为必需酶。研究发现它在乳腺癌、直肠癌和卵巢癌中存在过表达现象。此外，AMACR是前列腺癌的高度敏感及特异的标志物，在前列腺癌的早期诊断中具有十分重要的临床应用价值。
在本文中，我们对来源于结核分枝杆菌的α－甲酰基辅酶A消旋酶(MCR)进行了深入研究。它与人类的氨基酸序列有着高达43%的同源性。计算选用B3LYP方法，结构的优化和单点能的计算分别在6-31G(d)和6-311++G(2d,2p)两个基组水平上完成。计算结果阐明了MCR催化反应的机理，支持Prasenjit Bhaumik等人通过实验方法预测的结果。在1,1-质子转移反应中，His126和Asp156作为广义碱和广义酸催化反应的进行。从优化的结构中可以看出，去质子反应后产生的中间体为平面烯醇负离子式，因此烯醇式或烯酮式的中间体构型被排除。通过对能垒的比较，我们认为在从S-异构体向R-异构体转变的过程中，去质子化步骤是整个消旋反应的限速步骤。应用理论方法详细地描述酶促反应的路径，将对基于过渡态结构设计和研发抗癌药物提供有力的帮助。
3.谷胱甘肽（GSH）激活机理的理论研究
谷胱甘肽硫转移酶（GSTs）能够引起亲电类毒性物质的代谢，因此谷胱甘肽硫转移酶具有重要的解毒作用。GSTs是通过催化谷胱甘肽（GSH）与一系列亲电类的毒性物质发生反应，生成无毒的可溶性物质，之后被排除细胞外以达到解毒目的。但是，它对药物的代谢会产生抗药性问题，导致临床治疗的失败。GSH在与亲电试剂反应之前首先要被激活为硫醇离子的形式。关于典型的GSTs—GSTA1-1, GSTP1-1和GSTM1-1中GSH的激活机理已经有了广泛的研究。而非典型的GSTs—Gtt2的激活机理研究尚未见报道。
本文应用Gaussian 03程序，采用B3LYP方法完成所有的几何构型优化、频率分析和能量计算，推测出新型谷胱甘肽硫转移酶Gtt2中谷胱甘肽（GSH）的激活机理。本文提出的GSH激活机理与实验假设相一致,并且从能量角度证明了该机理的合理性。在反应过程中，His133作为广义碱、水分子作为助催化剂。通过与典型GSTs的比较，分析了产物具有较高能量的原因。我们在计算过程中选取了两个模型，分别含有不同数量的水分子，考察了体系中水分子对GSH激活机理的影响。
Enzymes are catalysts that produced by living cells. Virtually all of themare protein. Enzymes belong to the biological macromolecule, but the regionthat binds the substrate and converts it into product is a relatively small part.This region is known as the active center. The enzyme combines with itssubstrate to form an enzyme-substrate complex. It is an extremely unstablestate and has the highest free energy in the reaction pathway. This transientspecie is difficult to capture by the experimental techniques. Computersimulation can make up the shortfall and give the detailed information of thecatalytic reaction on the atomic level. By analysis of the intermediates andtransition states, and binding the kinetic method to determine the rate-limitingstep, we can infer the catalytic mechanism of the enzymes.
1. The mechanism of rearrangement reaction catalyzed byN5-carboxyaminoimidazole ribonucleotide mutase
In this paper, quantum chemistry calculation methods were used. Thecluster model for the simulations was constructed on the basis of crystal structure. We have studied the catalytic mechanism ofN5-carboxyaminoimidazole ribonucleotide mutase, glutathione transferaseGtt2 andα-Methylacyl-CoA racemase using theoretical method. The mainresults are summarized as follows:
De novo purine biosynthesis is central to all life forms except protozoa.In this process, the carboxylationof 5-aminoimidazole ribonucleotide (AIR) isconverted to 4-carboxyaminoimidazole ribonucleotide (CAIR) catalyzed byClass I PurE. The necessity of Class I PurE for the growth of microbe hasbeen shown by genetic studies. Deletion of this enzyme will result in a purineauxotroph that is unable to propagate in human or mouse serum and is notviable in animal models predictive of disease.
In the present study, the complete reaction mechanism of PurE has beeninvestigated by using the density functional theory with the hybrid B3LYPfunctional. The model containing 93 atoms was constructed on the basis ofthe X-ray structure of PurE from Escherichia coli. Additionally, we hadpreceded the charge population analysis with the method of the Natural BondOrbital (NBO) to verify the soundness of the proposed mechanism. Theresults show that this rearrangement reaction is carried out in two steps, one isdecarboxylation and the other is carboxylation. The conserved residue His45plays an essential catalytic role as both general aicd and general base. Atetrahedral intermediate iso.CAIR is observed during the carboxylationreaction and it is a plausible construction proved in experiment. The potential energy curves are drawn in terms of single-point energies. By comparing theenergy barriers, we could consider the carboxylation step as the rate-limitingstep. Furthermore, other residues including Ser43, Ala44, His45, Gly71,His75 and Leu76 also play important roles via the strong hydrogen-bondinteractions.
2. Reaction mechanism ofα-Methylacyl-CoA racemase: Atheoretical investigation
The branched-chain fatty acids are important component in the humandiet. Also, they are used for non-steroidal anti-inflammatory drugs such asibuprofen. In their metabolic process, only the (S)-substrate can bemetabolized through the branched-chain acyl-coA oxidases.α-Methylacyl-CoA racemase (AMACR) catalyzes the conversion fromR-enantiomer to S-enantiomer at the 2-position of fatty acyl-CoA esters.Therefore, AMACR is the essential enzyme in the metabolic process. Inaddition, AMACR can be used as highly sensitive and specific marker forprostate cancer. It has very important clinical value in the early diagnosis ofprostate cancer. Subsequently, the over-expression has also been found inbreast, colorectal and ovarian cancer.
In this paper, amethylacyl-CoA racemase from Mycobacteriumtuberculosis (MCR) were studied. The amino acid sequence identity betweenMCR and human is up to 43%. The calculation was completed by using thedensity functional theory (DFT) B3LYP method. The geometry optimizations were done with 6-31G (d) basis set and the single-point energy calculationswere done with 6-311 + + G (2d, 2p) basis set. Our calculation resultsillustrate the catalytic mechanism of MCR, and support the experimentalresults proposed by Prasenjit Bhaumik. His126 and Asp156 function as thegeneral base and the general acid respectively in the 1, 1 - proton transferreaction. It can be seen from the optimized structure, the intermediate is aplane enolate anion type, so the type of the enol or ketene is excluded. Bycomparing the energy barrier, we consider that the conversion from theS-enantiomer to the R- enantiomer is the rate-limiting step during theracemization. The theoretical studies on the mechanism of 1, 1 - protontransfer reaction catalyzed by MCR will be helpful to synthetize theanti-cancer drugs which designed based on the transition state structure.
3．The theoretical study on the GSH activation mechanism
Glutathione S-transferase (GSTs) can cause the metabolism ofelectrophilic toxic substances. So it has an important role in detoxification.Glutathione (GSH) can react with a range of electrophilic toxic substances,and generate the non-toxic soluble substances, then the products are excludedfrom the cell. However, the drug metabolism will result in drug resistance,even the failure of clinical treatment. Before it reacting with the electrophilicsubstrates, GSH should be activated into the thiolate form. Recently, the GSHactivation mechanism catalyzed by typical GSTs (GSTA1-1, GSTP1-1 andGSTM1-1) has been proposed. How about the GSH activation mechanism catalyzed by the atypical GST (Gtt2)?
In the present study, all geometry optimizations, single-point calculationsand frequency analysis were performed using density functional theory (DFT)with the B3LYP functional and the basis set 6-31G (d) as implemented inGaussian03. The GSH activation mechanism of Gtt2 has been investigatedand the results are consistent with the experimental data available. The protontransfer mediated by a water molecule is energetically feasible. Theimportance of water molecule as promoter is unequivocal. His133 functionsas general base in the reaction. The reason why the product has a higherenergy has been analyzed by comparing with the typical GSTs. In addition,another model that including a smaller amount of water molecules wasselected. The effects of water molecules in the system were investigated. Itproved that different model does not cause the changes of the pathway, but theenergy and configuration will be affected.
本文主要利用量子化学计算方法，基于从蛋白质晶体结构中截取的团簇模型，对N~5-羧基氨基咪唑核苷酸变位酶、α－甲酰基辅酶A消旋酶和谷胱甘肽硫转移酶这三个体系进行了催化机理的理论研究。主要结果如下：
1.N~5-羧基氨基咪唑核苷酸变位酶催化的重排反应
对于除原生动物外的所有生命体来说，从头合成嘌呤这一过程都至关重要。在Class I PurE催化下生成5-氨基-4-羧基咪唑核苷酸(CAIR)这一反应是整个嘌呤合成过程中的关键步骤。遗传研究表明，Class I PurE对微生物的生长必不可少。这种酶的缺失会导致嘌呤缺陷体，在人类和鼠的血清中，这种缺陷体不具备繁殖能力，也没有抵御疾病的能力。
本文利用密度泛函理论B3LYP方法对N~5-羧基氨基咪唑核苷酸变位酶催化的重排反应机理进行了理论研究。基于EcPuE的晶体结构，我们构建了包含93个原子的理论模型来研究其催化机理，并利用自然键轨道理论(NBO)方法进行了电荷布居分析，进一步验证推测机理的正确性。结果表明，此重排反应分脱羧和羧化两个步骤进行。His45是一个既能起到广义酸作用又能起到广义碱作用的催化残基。在计算过程中，我们得到一个具有四面体结构的中间体（iso.CAIR），从理论上证实了之前实验上对该结构的预测。根据对每个优化结构的能量计算，绘制出总反应的势能面曲线，通过比较，AIR的羧化反应步骤为整个反应的限速步骤。同时，我们也考察了其它重要氨基酸残基（Ser43,Ala44, His45, Gly71, His75和Leu76等）对催化反应的影响。
2.α－甲酰基辅酶A消旋酶催化机理的理论研究
支链脂肪酸是人类日常饮食中的重要成分，也被用于非类固醇抗炎药物，如布洛芬。在代谢过程中，只有S构型底物能够通过支链脂酰辅酶A氧化酶发生代谢作用。α－甲酰基辅酶A消旋酶(AMACR)能够使各种α-甲酰基辅酶A衍生物发生S、R异构互变。因此，AMACR的这一功能使其成为必需酶。研究发现它在乳腺癌、直肠癌和卵巢癌中存在过表达现象。此外，AMACR是前列腺癌的高度敏感及特异的标志物，在前列腺癌的早期诊断中具有十分重要的临床应用价值。
在本文中，我们对来源于结核分枝杆菌的α－甲酰基辅酶A消旋酶(MCR)进行了深入研究。它与人类的氨基酸序列有着高达43%的同源性。计算选用B3LYP方法，结构的优化和单点能的计算分别在6-31G(d)和6-311++G(2d,2p)两个基组水平上完成。计算结果阐明了MCR催化反应的机理，支持Prasenjit Bhaumik等人通过实验方法预测的结果。在1,1-质子转移反应中，His126和Asp156作为广义碱和广义酸催化反应的进行。从优化的结构中可以看出，去质子反应后产生的中间体为平面烯醇负离子式，因此烯醇式或烯酮式的中间体构型被排除。通过对能垒的比较，我们认为在从S-异构体向R-异构体转变的过程中，去质子化步骤是整个消旋反应的限速步骤。应用理论方法详细地描述酶促反应的路径，将对基于过渡态结构设计和研发抗癌药物提供有力的帮助。
3.谷胱甘肽（GSH）激活机理的理论研究
谷胱甘肽硫转移酶（GSTs）能够引起亲电类毒性物质的代谢，因此谷胱甘肽硫转移酶具有重要的解毒作用。GSTs是通过催化谷胱甘肽（GSH）与一系列亲电类的毒性物质发生反应，生成无毒的可溶性物质，之后被排除细胞外以达到解毒目的。但是，它对药物的代谢会产生抗药性问题，导致临床治疗的失败。GSH在与亲电试剂反应之前首先要被激活为硫醇离子的形式。关于典型的GSTs—GSTA1-1, GSTP1-1和GSTM1-1中GSH的激活机理已经有了广泛的研究。而非典型的GSTs—Gtt2的激活机理研究尚未见报道。
本文应用Gaussian 03程序，采用B3LYP方法完成所有的几何构型优化、频率分析和能量计算，推测出新型谷胱甘肽硫转移酶Gtt2中谷胱甘肽（GSH）的激活机理。本文提出的GSH激活机理与实验假设相一致,并且从能量角度证明了该机理的合理性。在反应过程中，His133作为广义碱、水分子作为助催化剂。通过与典型GSTs的比较，分析了产物具有较高能量的原因。我们在计算过程中选取了两个模型，分别含有不同数量的水分子，考察了体系中水分子对GSH激活机理的影响。
Enzymes are catalysts that produced by living cells. Virtually all of themare protein. Enzymes belong to the biological macromolecule, but the regionthat binds the substrate and converts it into product is a relatively small part.This region is known as the active center. The enzyme combines with itssubstrate to form an enzyme-substrate complex. It is an extremely unstablestate and has the highest free energy in the reaction pathway. This transientspecie is difficult to capture by the experimental techniques. Computersimulation can make up the shortfall and give the detailed information of thecatalytic reaction on the atomic level. By analysis of the intermediates andtransition states, and binding the kinetic method to determine the rate-limitingstep, we can infer the catalytic mechanism of the enzymes.
1. The mechanism of rearrangement reaction catalyzed byN5-carboxyaminoimidazole ribonucleotide mutase
In this paper, quantum chemistry calculation methods were used. Thecluster model for the simulations was constructed on the basis of crystal structure. We have studied the catalytic mechanism ofN5-carboxyaminoimidazole ribonucleotide mutase, glutathione transferaseGtt2 andα-Methylacyl-CoA racemase using theoretical method. The mainresults are summarized as follows:
De novo purine biosynthesis is central to all life forms except protozoa.In this process, the carboxylationof 5-aminoimidazole ribonucleotide (AIR) isconverted to 4-carboxyaminoimidazole ribonucleotide (CAIR) catalyzed byClass I PurE. The necessity of Class I PurE for the growth of microbe hasbeen shown by genetic studies. Deletion of this enzyme will result in a purineauxotroph that is unable to propagate in human or mouse serum and is notviable in animal models predictive of disease.
In the present study, the complete reaction mechanism of PurE has beeninvestigated by using the density functional theory with the hybrid B3LYPfunctional. The model containing 93 atoms was constructed on the basis ofthe X-ray structure of PurE from Escherichia coli. Additionally, we hadpreceded the charge population analysis with the method of the Natural BondOrbital (NBO) to verify the soundness of the proposed mechanism. Theresults show that this rearrangement reaction is carried out in two steps, one isdecarboxylation and the other is carboxylation. The conserved residue His45plays an essential catalytic role as both general aicd and general base. Atetrahedral intermediate iso.CAIR is observed during the carboxylationreaction and it is a plausible construction proved in experiment. The potential energy curves are drawn in terms of single-point energies. By comparing theenergy barriers, we could consider the carboxylation step as the rate-limitingstep. Furthermore, other residues including Ser43, Ala44, His45, Gly71,His75 and Leu76 also play important roles via the strong hydrogen-bondinteractions.
2. Reaction mechanism ofα-Methylacyl-CoA racemase: Atheoretical investigation
The branched-chain fatty acids are important component in the humandiet. Also, they are used for non-steroidal anti-inflammatory drugs such asibuprofen. In their metabolic process, only the (S)-substrate can bemetabolized through the branched-chain acyl-coA oxidases.α-Methylacyl-CoA racemase (AMACR) catalyzes the conversion fromR-enantiomer to S-enantiomer at the 2-position of fatty acyl-CoA esters.Therefore, AMACR is the essential enzyme in the metabolic process. Inaddition, AMACR can be used as highly sensitive and specific marker forprostate cancer. It has very important clinical value in the early diagnosis ofprostate cancer. Subsequently, the over-expression has also been found inbreast, colorectal and ovarian cancer.
In this paper, amethylacyl-CoA racemase from Mycobacteriumtuberculosis (MCR) were studied. The amino acid sequence identity betweenMCR and human is up to 43%. The calculation was completed by using thedensity functional theory (DFT) B3LYP method. The geometry optimizations were done with 6-31G (d) basis set and the single-point energy calculationswere done with 6-311 + + G (2d, 2p) basis set. Our calculation resultsillustrate the catalytic mechanism of MCR, and support the experimentalresults proposed by Prasenjit Bhaumik. His126 and Asp156 function as thegeneral base and the general acid respectively in the 1, 1 - proton transferreaction. It can be seen from the optimized structure, the intermediate is aplane enolate anion type, so the type of the enol or ketene is excluded. Bycomparing the energy barrier, we consider that the conversion from theS-enantiomer to the R- enantiomer is the rate-limiting step during theracemization. The theoretical studies on the mechanism of 1, 1 - protontransfer reaction catalyzed by MCR will be helpful to synthetize theanti-cancer drugs which designed based on the transition state structure.
3．The theoretical study on the GSH activation mechanism
Glutathione S-transferase (GSTs) can cause the metabolism ofelectrophilic toxic substances. So it has an important role in detoxification.Glutathione (GSH) can react with a range of electrophilic toxic substances,and generate the non-toxic soluble substances, then the products are excludedfrom the cell. However, the drug metabolism will result in drug resistance,even the failure of clinical treatment. Before it reacting with the electrophilicsubstrates, GSH should be activated into the thiolate form. Recently, the GSHactivation mechanism catalyzed by typical GSTs (GSTA1-1, GSTP1-1 andGSTM1-1) has been proposed. How about the GSH activation mechanism catalyzed by the atypical GST (Gtt2)?
In the present study, all geometry optimizations, single-point calculationsand frequency analysis were performed using density functional theory (DFT)with the B3LYP functional and the basis set 6-31G (d) as implemented inGaussian03. The GSH activation mechanism of Gtt2 has been investigatedand the results are consistent with the experimental data available. The protontransfer mediated by a water molecule is energetically feasible. Theimportance of water molecule as promoter is unequivocal. His133 functionsas general base in the reaction. The reason why the product has a higherenergy has been analyzed by comparing with the typical GSTs. In addition,another model that including a smaller amount of water molecules wasselected. The effects of water molecules in the system were investigated. Itproved that different model does not cause the changes of the pathway, but theenergy and configuration will be affected.
引文
[1]李巍.生物信息学导论[M].郑州大学出版社. 2004.
[2] Benton D. Bioinformatics—principles and potential of a new multidisciplinary tool[J]. Trends in biotechnology, 1996, 14(8):261-272.
[3]纪兆华,裴志利,管仁初,梁艳春.生物信息学在新兴学科群中崛起[J].电脑知识与技术, 2008(22):1094-1096.
[4]张春霆.生物信息学的现状与展望[J].世界科技研究与发展, 2000,22(006):17-20.
[5] Littlejohn K.A., P. Hooley, P.W. Cox. Bioinformatics predicts diverse< i>Aspergillus hydrophobins with novel properties [J]. Food Hydrocolloids, 2011.
[6] Yu W., Y. Zhang, L. Xu, S. Sun, X. Jiang, F. Zhang. Microarray-based bioinformaticsanalysis of osteoblasts on TiO< sub> 2 nanotube layers [J]. Colloids andSurfaces B: Biointerfaces, 2011.
[7] Uzun A., S. Sharma, J. Padbury. A Bioinformatics Approach to Preterm Birth [J].American Journal of Reproductive Immunology, 2012.
[8] Fu-Jun L., W. Hai-Yan, L. Jian-Yuan. A new analysis of testicular proteins throughintegrative bioinformatics [J]. Molecular Biology Reports, 2011:1-6.
[9] Durrant C., M.A. Swertz, R. Alberts, D. Arends, S. M ller, R. Mott, P. Prins, K.J. VanDer Velde, R.C. Jansen, K. Schughart. Bioinformatics tools and database resourcesfor systems genetics analysis in mice—a short review and an evaluation of futureneeds [J]. Briefings in Bioinformatics, 2011.
[10] Holst A.G., S. Saber, M. Houshmand, E.V. Zaklyazminskaya, Y. Wang, H.K. Jensen, L.Refsgaard, S. Hauns , J.H. Svendsen, M.S. Olesen. Sodium Current and PotassiumTransient Outward Current Genes in Brugada Syndrome: Screening andBioinformatics [J]. Canadian Journal of Cardiology, 2012.
[11]孙有平,王正华,王勇献.后基因组时代生物信息学的新进展[J].国防科技大学学报, 2003, 25(001):1-6.
[12] Linderstr m-Lang K. Deuterium exchange between peptides and water [J]. Chem SocSpec Publ, 1955, 2:1-20.
[13] Feynman R.P., R.B. Leighton, M. Sands, Lectures on physics, vol. 1. 1963,Addison-Wesley, Reading, Massachusetts.
[14] Frauenfelder H., G.A. Petsko, D. Tsernoglou. Temperature-dependent X-raydiffraction as a probe of protein structural dynamics [J]. 1979.
[15] Artymiuk Pj, Ccf Blake, Dep Grace, Sj Oatley, Dc Phillips, Mje Sternberg.Crystallographic studies of the dynamic properties of lysozyme [J]. 1979.
[16] Ichiye T., M. Karplus. Fluorescence depolarization of tryptophan residues in proteins:a molecular dynamics study [J]. Biochemistry, 1983, 22(12):2884-2893.
[17] Dobson Cm, M. Karplus. [18] Internal motion of proteins: Nuclear magneticresonance measurements and dynamic simulations [J]. Methods in enzymology, 1986,131:362-389.
[18] B hm H.J., G. Klebe. What Can We Learn from Molecular Recognition inProtein–Ligand Complexes for the Design of New Drugs? [J]. Angewandte ChemieInternational Edition in English, 1996, 35(22):2588-2614.
[19]钟扬,生物学,张亮,生物信息学,赵琼,马坚.简明生物信息学[M].高等教育出版社. 2001.
[20]赵国屏.生物信息学[M].科学出版社. 2002.
[21]鲁卫平,周元国.生物信息学的现状和展望[J].国外医学:临床生物化学与检验学分册, 2002, 23(005):254-255.
[22]陈润生.生物信息学及其研究进展[J].医学研究通讯, 2002, 31(12).
[23]王发生,毛君莲.生命科学时代的生物信息学[J].中国现代医学杂志, 2000,10(12):108-109.
[24]沈同,王镜岩.生物化学(上册) [J].北京:人民教育出版社, 1990, 1(9):8.
[25] Tsou C.L. The role of active site flexibility in enzyme catalysis [J]. Biochemistry.Biokhimii a, 1998, 63(3):253.
[26] Toth M.J., M.S. Miller, K.A. Ward, P.A. Ades. SKELETAL MUSCLEMITOCHONDRIAL DENSITY, GENE EXPRESSION AND ENZYMEACTIVITIES IN HUMAN HEART FAILURE: MINIMAL EFFECTS OF THEDISEASE AND RESISTANCE TRAINING [J]. Journal of Applied Physiology, 2012.
[27] Chien Y.H., N.C. Lee, S.C. Chiang, R.J. Desnick, W.L. Hwu. Fabry Disease:Incidence of the Common Later-Onsetα-Galactosidase A IVS4+ 919G> A Mutationin Taiwanese Newborns--Superiority of DNA-Based to Enzyme-Based NewbornScreening for Common Mutations [J]. Molecular medicine (Cambridge, Mass.), 2012.
[28] Macedo M.F., R. Quinta, C.S. Pereira, M.C. Sa Miranda. Enzyme replacement therapypartially prevents invariant Natural Killer T cell deficiency in the Fabry diseasemouse model [J]. Molecular Genetics and Metabolism, 2012.
[29] Ayebazibwe C., F.N. Mwiine, S.N. Balinda, K. Tj rneh j, S. Alexandersen.Application of the Ceditest FMDV type O and FMDV-NS enzyme-linkedimmunosorbent assays for detection of antibodies against Foot-and-mouth diseasevirus in selected livestock and wildlife species in Uganda [J]. Journal of VeterinaryDiagnostic Investigation, 2012, 24(2):270-276.
[30] Vassar R. BACE1, the Alzheimer's beta-secretase enzyme, in health and disease [J].Molecular Neurodegeneration, 2012, 7:1-1.
[31] Banugaria S.G., T.T. Patel, J. Mackey, S. Das, A. Amalfitano, A.S. Rosenberg, J.Charrow, Y.T. Chen, P.S. Kishnani. Persistence of high sustained antibodies toenzyme replacement therapy despite extensive immunomodulatory therapy in aninfant with Pompe disease: Need for agents to target antibody-secreting plasma cells[J]. Molecular Genetics and Metabolism, 2012.
[32] Allen M.P., D.J. Tildesley. Computer simulation of liquids [M]. Vol. 18: Oxforduniversity press. 1989.
[33] Becker O.M., A.D. Mackerell Jr, B. Roux, M. Watanabe. Computational biochemistryand biophysics [M]. CRC Press. 2001.
[34] Frenkel D., B. Smit. Understanding molecular simulation: from algorithms toapplications [M]. Academic Press, Inc. 1996.
[35] Kohn W. Nobel Lecture: Electronic structure of matter-wave functions and densityfunctionals [J]. Reviews of Modern Physics, 1999, 71(5):1253-1266.
[36] Warshel A. Computer simulations of enzyme catalysis: methods, progress, andinsights [J]. Annual review of biophysics and biomolecular structure, 2003,32(1):425-443.
[37] Friesner R.A., V. Guallar. Ab initio quantum chemical and mixed quantummechanics/molecular mechanics (QM/MM) methods for studying enzymaticcatalysis [J]. Annu. Rev. Phys. Chem., 2005, 56:389-427.
[38] Bruice T.C., K. Kahn. Computational enzymology [J]. Current Opinion in ChemicalBiology, 2000, 4(5):540-544.
[39] MartíS., M. Roca, J. Andrés, V. Moliner, E. Silla, I. Tuón, J. Bertrán. Theoreticalinsights in enzyme catalysis [J]. Chem. Soc. Rev., 2004, 33(2):98-107.
[40] Himo F. Quantum chemical modeling of enzyme active sites and reaction mechanisms[J]. Theoretical Chemistry Accounts: Theory, Computation, and Modeling(Theoretica Chimica Acta), 2006, 116(1):232-240.
[41] Senn H., W. Thiel. QM/MM methods for biological systems [J]. Atomistic approachesin modern biology, 2007:173-290.
[42] Siegbahn P.E.M., T. Borowski. Modeling enzymatic reactions involving transitionmetals [J]. Accounts of chemical research, 2006, 39(10):729-738.
[43] Kundu A., A. Bayya. Speech recognition using hybrid hidden Markov model and NNclassifier [J]. International journal of speech technology, 1998, 2(3):227-240.
[44]张阳德.生物信息学(5):药物设计与生物信息学[J].外科理论与实践, 2007,12(1):I0009-I0012.
[45]陈凯先,药物,蒋华良,嵇汝运.计算机辅助药物设计:原理,方法及应用[M].上海科学技术出版社. 2000.
[46]李亮助,孙强明.生物信息学在药物设计中的应用[J].生命的化学, 2003,23(5):364-366.
[47]郑彦,吕莉.计算机辅助药物设计在药物合成中的应用[J].齐鲁药事, 2008,27(10):614-616.
[48]赵金城,王庆莉,毕秀玲.计算机辅助直接药物分子设计[J].大连大学学报,2002, 23(006):22-30.
[49]梁桂兆,梅虎,周原,李志良.计算机辅助药物设计中的多维定量构效关系模型化方法[J].化学进展, 2006, 18(1):120-127.
[50]郑珩,王非.药物生物信息学[M].化学工业出版社. 2004.
[51]孙之荣,后基因组信息学. 2002,北京:清华大学出版社.
[52] Roos D.S. Bioinformatics--trying to swim in a sea of data [J]. Science, 2001,291(5507):1260-1261.
[53] Spengler S.J. Bioinformatics in the information age [J]. 2000.
[54]陈竺,强伯勤,方福德.基因组科学与人类疾病[M].科学出版社. 2001.
[55] Barnett C.B., K.J. Naidoo. Ring puckering: A metric for evaluating the accuracy ofAM1, PM3, PM3CARB-1, and SCC-DFTB carbohydrate QM/MM simulations [J].The Journal of Physical Chemistry B, 2010.
[56] Ramraj A., R.K. Raju, Q. Wang, I.H. Hillier, R.A. Bryce, M.A. Vincent. An evaluationof the GLYCAM06 and MM3 force fields, and the PM3-D* molecular orbitalmethod for modelling prototype carbohydrate-aromatic interactions [J]. Journal ofMolecular Graphics and Modelling, 2010, 29(3):321-325.
[57] Sattelle B.M., A. Almond. Less is more when simulating unsulfatedglycosaminoglycan 3D‐structure: Comparison of GLYCAM06/TIP3P,PM3‐CARB1/TIP3P, and SCC‐DFTB‐D /TIP3P predictions with experiment [J].Journal of computational chemistry, 2010, 31(16):2932-2947.
[58] Jensen F., Myilibrary. Introduction to computational chemistry [M]. Vol. 2: WileyNew York. 1999.
[59] Young D.C. Computational chemistry: a practical guide for applying techniques toreal world problems [M]. Wiley-Interscience. 2001.
[60] Re S., Y. Sugita. Modeling the Transition State of Enzyme-catalyzed PhosphorylTransfer Reaction Using QM/MM Method [J]. Yakugaku zasshi: Journal of thePharmaceutical Society of Japan, 2011, 131(8):1171.
[61] MartíS., J. Andrés, V. Moliner, E. Silla, I. Tuón, J. Bertrán. Theoretical QM/MMstudies of enzymatic pericyclic reactions [J]. Interdisciplinary Sciences:Computational Life Sciences, 2010, 2(1):115-131.
[62] Guallar V., F.H. Wallrapp. QM/MM methods: Looking inside heme proteinsbiochemisty [J]. Biophysical chemistry, 2010, 149(1):1-11.
[63] Barberet P., F. Vianna, M. Karamitros, T. Brun, N. Gordillo, P. Moretto, S. Incerti, H.Seznec. Monte-Carlo dosimetry on a realistic cell monolayer geometry exposed toalpha particles [J]. Physics in Medicine and Biology, 2012, 57:2189.
[64] Rai N., E.J. Maginn. Critical behaviour and vapour-liquid coexistence of1-alkyl-3-methylimidazolium bis (trifluoromethylsulfonyl) amide ionic liquids viaMonte Carlo simulations [J]. Faraday Discuss., 2011, 154(0):53-69.
[65] Premuda M., E. Palazzi, F. Ravegnani, D. Bortoli, S. Masieri, G. Giovanelli. MOCRA:a Monte Carlo code for the simulation of radiative transfer in the atmosphere [J].Optics Express, 2012, 20(7):7973-7993.
[66] Li Y., Y. Ma, J. Li, X. Jiang, W. Hu. Dynamic Monte Carlo simulations of doublecrystallization accelerated in microdomains of diblock copolymers [J]. Journal ofChemical Physics, 2012, 136(10):104906.
[67] Weiner P.K., P.A. Kollman. AMBER: Assisted model building with energy refinement.A general program for modeling molecules and their interactions [J]. Journal ofcomputational chemistry, 1981, 2(3):287-303.
[68] Scott W.R.P., P.H. Hünenberger, I.G. Tironi, A.E. Mark, S.R. Billeter, J. Fennen, A.E.Torda, T. Huber, P. Krüger, W.F. Van Gunsteren. The GROMOS biomolecularsimulation program package [J]. The Journal of Physical Chemistry A, 1999,103(19):3596-3607.
[69] Van Gunsteren W.F. Computer simulation of biomolecular systems: theoretical andexperimental applications [M]. Vol. 3: Springer. 1997.
[70] Tuckerman M.E., G.J. Martyna. Understanding modern molecular dynamics:techniques and applications [J]. The Journal of Physical Chemistry B, 2000,104(2):159-178.
[71] Karplus M., J.A. Mccammon. Molecular dynamics simulations of biomolecules [J].Nature Structural & Molecular Biology, 2002, 9(9):646-652.
[72] Fersht A. Structure and mechanism in protein science: a guide to enzyme catalysis andprotein folding [M]. WH Freeman. 1999.
[73] Garcia-Viloca M., J. Gao, M. Karplus, D.G. Truhlar. How enzymes work: analysis bymodern rate theory and computer simulations [J]. Science, 2004, 303(5655):186-195.
[74] Mulholland A.J. Modelling enzyme reaction mechanisms, specificity and catalysis [J].Drug Discovery Today, 2005, 10(20):1393-1402.
[75] Warshel A. Computer modeling of chemical reactions in enzymes and solutions [J].1991.
[76] Warshel A., P.K. Sharma, M. Kato, Y. Xiang, H. Liu, M.H.M. Olsson. Electrostaticbasis for enzyme catalysis [J]. Chemical reviews, 2006, 106(8):3210.
[77] Zhang X., Kn Houk. Why enzymes are proficient catalysts: beyond the Paulingparadigm [J]. Accounts of chemical research, 2005, 38(5):379-385.
[1]谈国霞,吴磊磊.量子化学发展综述[J]. _高校理科研究, 2007.
[2]常进.量子化学方法在计算化合物物理,化学,生物学性质中的应用[J].
[3]刘文剑.新一代相对论量子化学方法[J].中国基础科学, 2007(002):10-11.
[4] Jug K. Quantum chemical methods and their applications to chemical reactions [J].Theoretical Chemistry Accounts: Theory, Computation, and Modeling (TheoreticaChimica Acta), 1980, 54(4):263-300.
[5]陈光巨,黄元河.量子化学[M].华东理工大学出版社. 2008.
[6] Small D.W., M. Head-Gordon. Post-modern valence bond theory for stronglycorrelated electron spins [J]. Phys. Chem. Chem. Phys., 2011, 13(43):19285-19297.
[7] De Marco G., P. Várnai. Molecular simulation of conformational transitions inbiomolecules using a combination of structure-based potential and empirical valencebond theory [J]. Phys. Chem. Chem. Phys., 2009, 11(45):10694-10700.
[8] Truhlar D.G. Valence bond theory for chemical dynamics [J]. Journal of computationalchemistry, 2007, 28(1):73-86.
[9] Raimondi M., M. Simonetta, G. Tantardini. AB initio valence bond theory [J].Computer Physics Reports, 1985, 2:171-216.
[10] Balint-Kurti Gg. Reply to``Ab initio valence-bond theory'' [J]. Physical Review A,1986, 34:674.
[11] Nakai H., M. Hoshino, K. Miyamoto, S. Hyodo. Elimination of translational androtational motions in nuclear orbital plus molecular orbital theory [J]. The Journal ofchemical physics, 2005, 122:164101.
[12] Mohr M., J.P. Mcnamara, H. Wang, S.A. Rajeev, J. Ge, C.A. Morgado, I.H. Hillier.The use of methods involving semi-empirical molecular orbital theory to study thestructure and reactivity of transition metal complexes [J]. Faraday Discuss., 2003,124(0):413-428.
[13] Maranón J., J.L. Pousa. Path integral, collective coordinates, and molecular-orbitaltheory [J]. Physical Review A, 1987, 36(12):5530.
[14] Hagiwara Y., M. Tateno. Recent advances in jointed quantum mechanics andmolecular mechanics calculations of biological macromolecules: schemes andapplications coupled to ab initio calculations [J]. Journal of Physics: CondensedMatter, 2010, 22:413101.
[15] Picardi E., G. Pesole. Computational methods for ab initio and comparative genefinding [J]. Methods in Molecular Biology, 2010, 609:269-284.
[16] Mulder F.A.A., M. Filatov. NMR chemical shift data and ab initio shieldingcalculations: emerging tools for protein structure determination [J]. Chem. Soc. Rev.,2010, 39(2):578-590.
[17] Liu L.A., J.S. Bader. Structure-based ab initio prediction of transcriptionfactor-binding sites [J]. Methods Mol. Biol, 2009, 541:1-19.
[18] Friesner R.A., V. Guallar. Ab initio quantum chemical and mixed quantummechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis[J]. Annu. Rev. Phys. Chem., 2005, 56:389-427.
[19] Chivian D., T. Robertson, R. Bonneau, D. Baker. Ab initio methods [J]. Structuralbioinformatics, 2003:547-557.
[20] Ghosh A., P.R. Taylor. High-level ab initio calculations on the energetics of low-lyingspin states of biologically relevant transition metal complexes: a first progress report[J]. Current Opinion in Chemical Biology, 2003, 7(1):113-124.
[21] Bailey W.C. B3LYP calculation of deuterium quadrupole coupling constants inmolecules [J]. Journal of molecular spectroscopy, 1998, 190(2):318-323.
[22] Carbonniere P., T. Lucca, C. Pouchan, N. Rega, V. Barone. Vibrational computationsbeyond the harmonic approximation: Performances of the B3LYP density functionalfor semirigid molecules [J]. Journal of computational chemistry, 2005, 26(4):384-388.
[23] Kolboe S., S. Svelle. Does an ethene/benzenium ion complex exist? A discrepancybetween B3LYP and MP2 predictions [J]. The Journal of Physical Chemistry A, 2008,112(29):6399-6400.
[24] Payne P.W. Analytic construction of Hartree-Fock density matrices [J]. Proceedings ofthe National Academy of Sciences, 1980, 77(11):6293.
[25] Goldman Sp, A. Dalgarno. Finite-basis-set approach to the Dirac-Hartree-Fockequations [J]. Physical review letters, 1986, 57(4):408-411.
[26] Bushmaker A.W., V.V. Deshpande, S. Hsieh, M.W. Bockrath, S.B. Cronin. DirectObservation of Born Oppenheimer Approximation Breakdown in Carbon Nanotubes[J]. Nano letters, 2009, 9(2):607-611.
[27] Hijikata Y., H. Nakashima, H. Nakatsuji. Solving non-Born–OppenheimerSchr dinger equation for hydrogen molecular ion and its isotopomers using the freecomplement method [J]. The Journal of chemical physics, 2009, 130:024102.
[28] Lemus R., A. Frank. Constrained calculations in the electron-vibron model and theBorn-Oppenheimer approximation [J]. Physical review. A, 1993, 47(6A):4920-4933.
[29] Blümel R., B. Esser. Quantum chaos in the Born-Oppenheimer approximation [J].Physical review letters, 1994, 72(23):3658-3661.
[30] Rozsnyai Bf, F. Martino, J. Ladik. Calculation of the Energy Band Structures ofComplicated Periodic DNA Models in the SemiempiricalSCF–LCAO–Crystal‐O rbital Approximation [J]. The Journal of chemical physics,1970, 52:5708.
[31] De Andrada E Silva Ea, Ic Da Cunha Lima, A. Ferreira Da Silva. Two-dimensionalhydrogen molecule and the alternant-molecular-orbital approximation [J]. Phys. Rev.A;(United States), 1986, 33(4).
[32] Gross E.K.U., R.M. Dreizler. Density functional theory [M]. Vol. 337: Springer. 1995.
[33] Tse J.S. Ab initio molecular dynamics with density functional theory [J]. Annualreview of physical chemistry, 2002, 53(1):249-290.
[34]林梦海.量子化学计算方法与应用[M].科学出版社. 2004.
[35] Halpern A.M., E.D. Glendening. An intrinsic reaction coordinate calculation of thetorsion-internal rotation potential of hydrogen peroxide and its isotopomers [J]. TheJournal of chemical physics, 2004, 121:273.
[36] Riska E.B. On the solvent effect in experimental chemical skin carcinogenesis;lipophilic-hydrophilic (surface active) agents as solvents for carcinogens [J]. Actapathologica et microbiologica Scandinavica. Supplement, 1956, 39(Suppl 114):1.
[37] Peterson J.M., Wr Guild. A differential solvent effect on thermal stability of geneticmarkers in DNA [J]. Journal of Molecular Biology, 1966, 20(3):497-503.
[38] Barbara P.F., G.C. Walker, T.P. Smith. Vibrational modes and the dynamic solventeffect in electron and proton transfer [J]. Science, 1992, 256(5059):975-981.
[39] Ben‐Naim A., Kl Ting, Rl Jernigan. Solvent effect on binding thermodynamics ofbiopolymers [J]. Biopolymers, 1990, 29(6‐7 ):901-919.
[40] Hopmann E., W. Arlt, M. Minceva. Solvent system selection in counter-currentchromatography using conductor-like screening model for real solvents [J]. Journal ofChromatography A, 2011, 1218(2):242-250.
[41] Fu K.X., Q. Zhu, X.Y. Li, Z. Gong, J.Y. Ma, R.X. He. Continuous medium theory fornonequilibrium solvation: IV. Solvent reorganization energy of electron transfer basedon conductor‐l ike screening model [J]. Journal of computational chemistry, 2006,27(3):368-374.
[42] Oleszek‐Kudlak S., M. Grabda, E. Shibata, F. Eckert, T. Nakamura. Application ofthe conductor‐like screening model for real solvents for prediction of the aqueoussolubility of chlorobenzenes depending on temperature and salinity [J].Environmental toxicology and chemistry, 2005, 24(6):1368-1375.
[43] Yoshitake Y., H. Nakagawa, K. Harano. A Theoretical Study of Neighboring-GroupParticipation in Thione-to-Thiol Rearrangement of Xanthates. Molecular OrbitalCalculation Using a Conductor-Like Screening Model (COSMO) Approach [J].Chemical and pharmaceutical bulletin, 2001, 49(11):1433-1439.
[44]崔凤超.羟氰裂解酶及两类氧甲基转移酶催化机理的理论研究[D]. 2010.
[45]张继龙.几类重要蛋白质的分子动力学模拟及相关抑制剂的改良[D]. 2010.
[46]楚慧郢.蛋白质的分子动力学模拟和催化机理的理论研究[D]. 2009.
[47]赵勇山.几类重要蛋白的结构及其催化机理的理论研究[D]. 2009.
[48] Re S., Y. Sugita. Modeling the Transition State of Enzyme-catalyzed PhosphorylTransfer Reaction Using QM/MM Method [J]. Yakugaku zasshi: Journal of thePharmaceutical Society of Japan, 2011, 131(8):1171.
[49] MartíS., J. Andrés, V. Moliner, E. Silla, I. Tuón, J. Bertrán. Theoretical QM/MMstudies of enzymatic pericyclic reactions [J]. Interdisciplinary Sciences:Computational Life Sciences, 2010, 2(1):115-131.
[50] Menikarachchi L.C., J.A. Gascón. QM/MM approaches in medicinal chemistryresearch [J]. Current Topics in Medicinal Chemistry, 2010, 10(1):46-54.
[51] Senn H.M., W. Thiel. QM/MM methods for biomolecular systems [J]. AngewandteChemie International Edition, 2009, 48(7):1198-1229.
[52] Garcia-Viloca M., J. Gao, M. Karplus, D.G. Truhlar. How enzymes work: analysis bymodern rate theory and computer simulations [J]. Science, 2004, 303(5655):186-195.
[53] Mulholland A.J. Modelling enzyme reaction mechanisms, specificity and catalysis [J].Drug Discovery Today, 2005, 10(20):1393-1402.
[54] Warshel A., P.K. Sharma, M. Kato, Y. Xiang, H. Liu, M.H.M. Olsson. Electrostaticbasis for enzyme catalysis [J]. Chemical reviews, 2006, 106(8):3210.
[55] Bruice T.C., K. Kahn. Computational enzymology [J]. Current Opinion in ChemicalBiology, 2000, 4(5):540-544.
[56] Siegbahn P.E.M., T. Borowski. Modeling enzymatic reactions involving transitionmetals [J]. Accounts of chemical research, 2006, 39(10):729-738.
[57] Gao J., D.G. Truhlar. Quantum mechanical methods for enzyme kinetics [J]. Annualreview of physical chemistry, 2002, 53(1):467-505.
[58] Mulholland A.J. Computational enzymology: modelling the mechanisms of biologicalcatalysts [J]. Biochemical Society Transactions, 2008, 36(1):22-26.
[59] Ryde U. Combined quantum and molecular mechanics calculations on metalloproteins[J]. Current Opinion in Chemical Biology, 2003, 7(1):136-142.
[60] Senn H.M., W. Thiel. QM/MM studies of enzymes [J]. Current Opinion in ChemicalBiology, 2007, 11(2):182-187.
[61] Zhang Y. Pseudobond ab initio QM/MM approach and its applications to enzymereactions [J]. Theoretical Chemistry Accounts: Theory, Computation, and Modeling(Theoretica Chimica Acta), 2006, 116(1):43-50.
[1] Firestine S.M., S.W. Poon, E.J. Mueller, J.A. Stubbe, V.J. Davisson. ReactionsCatalyzed by 5-Aminoimidazole Ribonucleotide Carboxylases from Escherichia coliand Gallus gallus: A Case for Divergent Catalytic Mechanisms? [J]. Biochemistry,1994, 33(39):11927-11934.
[2] Mueller E.J., E. Meyer, J. Rudolph, V.J. Davisson, J.A. Stubbe.N5-carboxyaminoimidazole ribonucleotide: Evidence for a new intermediate and twonew enzymic activities in the de novo purine biosynthetic pathway of Escherichia coli[J]. Biochemistry, 1994, 33(8):2269-2278.
[3] Mathews I.I., T.J. Kappock, J.A. Stubbe, S.E. Ealick. Crystal structure of Escherichiacoli PurE, an unusual mutase in the purine biosynthetic pathway [J]. Structure, 1999,7(11):1395-1406.
[4] Meyer E., T.J. Kappock, C. Osuji, J.A. Stubbe. Evidence for the direct transfer of thecarboxylate of N 5-carboxyaminoimidazole ribonucleotide (N 5-CAIR) to generate4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutase [J]. Biochemistry, 1999, 38(10):3012-3018.
[5] Ivanovics G., E. Marjai, A. Dobozy. The growth of purine mutants of Bacillus anthracisin the body of the mouse [J]. Journal of general microbiology, 1968, 53(2):147-162.
[6] Samant S., H. Lee, M. Ghassemi, J. Chen, J.L. Cook, A.S. Mankin, A.A. Neyfakh.Nucleotide biosynthesis is critical for growth of bacteria in human blood [J]. PLoSpathogens, 2008, 4(2):e37.
[7] Donovan M., J.J. Schumuke, W.A. Fonzi, S.L. Bonar, K. Gheesling-Mullis, G.S. Jacob,V.J. Davisson, S.B. Dotson. Virulence of a PhosphoribosylaminoimidazoleCarboxylase-DeficientCandida albicans Strain in an Immunosuppressed Murine Modelof Systemic Candidiasis [J]. Infection and immunity, 2001, 69(4):2542-2548.
[8] Thoden J.B., H.M. Holden, S.M. Firestine. Structural Analysis of the Active SiteGeometry of N 5-Carboxyaminoimidazole Ribonucleotide Synthetase fromEscherichia coli , [J]. Biochemistry, 2008, 47(50):13346-13353.
[9] Hoskins A.A., M. Morar, T.J. Kappock, I.I. Mathews, J.B. Zaugg, T.E. Barder, P. Peng,A. Okamoto, S.E. Ealick, J.A. Stubbe. N 5-CAIR Mutase: Role of a CO2 Binding Siteand Substrate Movement in Catalysis [J]. Biochemistry, 2007, 46(10):2842-2855.
[10] Becke A.D. Density‐functional thermochemistry. IV. A new dynamical correlationfunctional and implications for exact‐exchange mixing [J]. The Journal of chemicalphysics, 1996, 104:1040.
[11] Foresman Jb, A. Frisch, Exploring Chemistry with Electronic Structure Methods, ;Gaussian: Pittsburgh, PA, 1996, Chapter.
[12] Miehlich B., A. Savin, H. Stoll, H. Preuss. Chem Phys Lett 157: 200; c) Lee C [J].Yang W, Parr G (1988) Phys Rev B, 1989, 37:785.
[13] Trucks Gw, Hb Schlegel, Ge Scuseria, Ma Robb, Jr Cheeseman, Ja Montgomery Jr, T.Vreven, Kn Kudin, Jc Burant, Jm Millam. Gaussian 03, revision C. 02; Gaussian [J].Inc.: Wallingford, CT, 2004.
[14] Cammi R., B. Mennucci, J. Tomasi. Second-order M ller-Plesset analyticalderivatives for the polarizable continuum model using the relaxed density approach [J].The Journal of Physical Chemistry A, 1999, 103(45):9100-9108.
[15] Cammi R., B. Mennucci, J. Tomasi. An attempt to bridge the gap betweencomputation and experiment for nonlinear optical properties: macroscopicsusceptibilities in solution [J]. The Journal of Physical Chemistry A, 2000,104(20):4690-4698.
[16] Cossi M., V. Barone. Time-dependent density functional theory for molecules in liquidsolutions [J]. The Journal of chemical physics, 2001, 115:4708.
[17] Cossi M., G. Scalmani, N. Rega, V. Barone. New developments in the polarizablecontinuum model for quantum mechanical and classical calculations on molecules insolution [J]. The Journal of chemical physics, 2002, 117:43.
[18] Estroff L.A., A.D. Hamilton. Water gelation by small organic molecules [J].ChemInform, 2004, 35(20):no-no.
[19] Barreto P., H. Kim, B. Lynn, M. Scott. Efficient algorithms for pairing-basedcryptosystems [J]. Advances in Cryptology—CRYPTO 2002, 2002:354-369.
[20] Swaminathan S., N. Khanna. Dengue: recent advances in biology and current status oftranslational research [J]. Current molecular medicine, 2009, 9(2):152-173.
[21] Himo F. Quantum chemical modeling of enzyme active sites and reaction mechanisms[J]. Theoretical Chemistry Accounts: Theory, Computation, and Modeling (TheoreticaChimica Acta), 2006, 116(1):232-240.
[22] Georgieva P., F. Himo. Density functional theory study of the reaction mechanism ofthe DNA repairing enzyme alkylguanine alkyltransferase [J]. Chemical Physics Letters,2008, 463(1-3):214-218.
[23] Hopmann K.H., F. Himo. Theoretical study of the full reaction mechanism of humansoluble epoxide hydrolase [J]. Chemistry-A European Journal, 2006,12(26):6898-6909.
[24] Georgieva P., F. Himo. Quantum chemical modeling of enzymatic reactions: The caseof histone lysine methyltransferase [J]. Journal of computational chemistry, 2010,31(8):1707-1714.
[25] Velichkova P., F. Himo. Methyl transfer in glycine N-methyltransferase. A theoreticalstudy [J]. The Journal of Physical Chemistry B, 2005, 109(16):8216-8219.
[26] Lundberg M., P.E.M. Siegbahn, K. Morokuma. The mechanism for isopenicillin Nsynthase from density-functional modeling highlights the similarities with otherenzymes in the 2-his-1-carboxylate family [J]. Biochemistry, 2008, 47(3):1031-1042.
[27] Lucas A., J.L. Valverde, P. Sánchez, F. Dorado, M.J. Ramos. Hydroisomerization of n-octane over platinum catalysts with or without binder [J]. Applied Catalysis A:General, 2005, 282(1):15-24.
[28] Velichkova P., F. Himo. Theoretical study of the methyl transfer in guanidinoacetatemethyltransferase [J]. The Journal of Physical Chemistry B, 2006, 110(1):16-19.
[29] Sousa S.F., E.S. Carvalho, D.M. Ferreira, I.S. Tavares, P.A. Fernandes, M.J. Ramos,J. .A.N.F. Gomes. Comparative analysis of the performance of commonly availabledensity functionals in the determination of geometrical parameters for zinc complexes[J]. Journal of computational chemistry, 2009, 30(16):2752-2763.
[30] Dourado D.F.A.R., P.A. Fernandes, B. Mannervik, M.J. Ramos. Glutathionetransferase A1-1: catalytic importance of arginine 15 [J]. The Journal of PhysicalChemistry B, 2010, 114(4):1690-1697.
[31] Francois J.A., C.M. Starks, S. Sivanuntakorn, H. Jiang, A.E. Ransome, J.W. Nam, C.Z.Constantine, T.J. Kappock. Structure of a NADH-insensitive hexameric citratesynthase that resists acid inactivation [J]. Biochemistry, 2006, 45(45):13487-13499.
[32] Acevedo O., W.L. Jorgensen. Medium effects on the decarboxylation of a biotinmodel in pure and mixed solvents from QM/MM simulations [J]. The Journal oforganic chemistry, 2006, 71(13):4896-4902.
[33] Yu J., J. Wang, W. Lin, S. Li, H. Li, J. Zhou, P. Ni, W. Dong, S. Hu, C. Zeng. Thegenomes of Oryza sativa: a history of duplications [J]. PLoS biology, 2005, 3(2):e38.
[34] Mauser H., W.A. King, J.E. Gready, T.J. Andrews. CO2 fixation by RuBisCO:Computational dissection of the key steps of carboxylation, hydration, and CC bondcleavage [J]. Journal of the American Chemical Society, 2001, 123(44):10821-10829.
[35] Tranchimand S., C.M. Starks, I.I. Mathews, S.C. Hockings, T.J. Kappock. Treponemadenticola PurE Is a Bacterial AIR Carboxylase [J]. Biochemistry, 2011.
[1] Savolainen K., P. Bhaumik, W. Schmitz, T.J. Kotti, E. Conzelmann, R.K. Wierenga, J.K.Hiltunen.α-Methylacyl-CoA Racemase from Mycobacterium tuberculosis [J]. Journalof Biological Chemistry, 2005, 280(13):12611-12620.
[2] Schmitz W., R. Fingerhut, E. Conzelmann. Purification and properties of anα‐methylacyl‐CoA racemase from rat liver [J]. European Journal of Biochemistry,1994, 222(2):313-323.
[3] Russell D.W. The enzymes, regulation, and genetics of bile acid synthesis [J]. Annualreview of biochemistry, 2003, 72(1):137-174.
[4] Hiltunen J.K., Y.M. Qin. [beta]-Oxidation-strategies for the metabolism of a widevariety of acyl-CoA esters [J]. Biochimica et Biophysica Acta (BBA)-Molecular andCell Biology of Lipids, 2000, 1484(2-3):117-128.
[5] Wierzbicki A.S., M.D. Lloyd, C.J. Schofield, M.D. Feher, F.B. Gibberd. Refsum'sdisease: a peroxisomal disorder affecting phytanic acidα‐o xidation [J]. Journal ofneurochemistry, 2002, 80(5):727-735.
[6] Mukherji M., C.J. Schofield, A.S. Wierzbicki, G.A. Jansen, R.J.A. Wanders, M.D.Lloyd. The chemical biology of branched-chain lipid metabolism [J]. Progress in lipidresearch, 2003, 42(5):359-376.
[7] Lloyd M.D., D.J. Darley, A.S. Wierzbicki, M.D. Threadgill.α‐Methylacyl‐CoAracemase–an‘obscure’metabolic enzyme takes centre stage [J]. FEBS Journal, 2008,275(6):1089-1102.
[8] Qin Y.M., M.H. Poutanen, H.M. Helander, A.P. Kvist, K.M. Siivari, W. Schmitz, E.Conzelmann, U. Hellman, J.K. Hiltunen. Peroxisomal multifunctional enzyme ofbeta-oxidation metabolizing D-3-hydroxyacyl-CoA esters in rat liver: molecularcloning, expression and characterization [J]. Biochemical Journal, 1997, 321(Pt 1):21.
[9] Ferdinandusse S., H. Rusch, Aem Van Lint, G. Dacremont, Rja Wanders, P. Vreken.Stereochemistry of the peroxisomal branched-chain fatty acidα-andβ-oxidationsystems in patients suffering from different peroxisomal disorders [J]. Journal of lipidresearch, 2002, 43(3):438-444.
[10] Ogino S., T. Kawasaki, G.J. Kirkner, M. Loda, C.S. Fuchs. CpG island methylatorphenotype-low (CIMP-low) in colorectal cancer: possible associations with male sexand KRAS mutations [J]. The Journal of molecular diagnostics: JMD, 2006, 8(5):582.
[11] Lakis S., T. Papamitsou, C. Panagiotopoulou, R. Kotakidou, V. Kotoula. AMACR isassociated with advanced pathologic risk factors in sporadic colorectal adenomas [J].World journal of gastroenterology: WJG, 2010, 16(20):2476.
[12] Daugherty S.E., Y.Y. Shugart, E.A. Platz, M.D. Fallin, W.B. Isaacs, R.M. Pfeiffer, R.Welch, W.Y. Huang, D. Reding, R.B. Hayes. Polymorphic variants inα‐m ethylacyl‐CoA racemase and prostate cancer [J]. The Prostate, 2007,67(14):1487-1497.
[13] Bhaumik P., P. Kursula, V. Ratas, E. Conzelmann, J.K. Hiltunen, W. Schmitz, R.K.Wierenga. Crystallization and preliminary X-ray diffraction studies ofan-methylacyl-CoA racemase from Mycobacterium tuberculosis [J]. ActaCrystallographica Section D: Biological Crystallography, 2003, 59(2):353-355.
[14] Darley D.J., D.S. Butler, S.J. Prideaux, T.W. Thornton, A.D. Wilson, T.J. Woodman,M.D. Threadgill, M.D. Lloyd. Synthesis and use of isotope-labelled substrates for amechanistic study on humanα-methylacyl-CoA racemase 1A (AMACR; P504S) [J].Org. Biomol. Chem., 2009, 7(3):543-552.
[15] Bhaumik P., W. Schmitz, A. Hassinen, J.K. Hiltunen, E. Conzelmann, R.K. Wierenga.The catalysis of the 1, 1-proton transfer byα-methyl-acyl-CoA racemase is coupled toa movement of the fatty acyl moiety over a hydrophobic, methionine-rich surface [J].Journal of Molecular Biology, 2007, 367(4):1145-1161.
[16] Frisch Mj, Gw Trucks, Hb Schlegel, Ge Scuseria, Ma Robb, Jr Cheeseman, JaMontgomery Jr, T. Vreven, Kn Kudin, Jc Burant. Gaussian 03, Rev. C. 02. Gaussian[J]. Inc., Wallingford, CT, 2004.
[17] Cammi R., B. Mennucci, J. Tomasi. Second-order M ller-Plesset analyticalderivatives for the polarizable continuum model using the relaxed density approach [J].The Journal of Physical Chemistry A, 1999, 103(45):9100-9108.
[18] Cammi R., B. Mennucci, J. Tomasi. An attempt to bridge the gap betweencomputation and experiment for nonlinear optical properties: macroscopicsusceptibilities in solution [J]. The Journal of Physical Chemistry A, 2000,104(20):4690-4698.
[19] Cossi M., N. Rega, G. Scalmani, V. Barone. Polarizable dielectric model of solvationwith inclusion of charge penetration effects [J]. The Journal of chemical physics, 2001,114:5691.
[20] Cossi M., G. Scalmani, N. Rega, V. Barone. New developments in the polarizablecontinuum model for quantum mechanical and classical calculations on molecules insolution [J]. The Journal of chemical physics, 2002, 117:43.
[21] Chen S.L., W.H. Fang, F. Himo. Theoretical study of the phosphotriesterase reactionmechanism [J]. The Journal of Physical Chemistry B, 2007, 111(6):1253-1255.
[22] Sevastik R., F. Himo. Quantum chemical modeling of enzymatic reactions: The caseof 4-oxalocrotonate tautomerase [J]. Bioorganic chemistry, 2007, 35(6):444-457.
[23] Hopmann K.H., J.D. Guo, F. Himo. Theoretical investigation of the first-shellmechanism of nitrile hydratase [J]. Inorganic chemistry, 2007, 46(12):4850-4856.
[24] Tanner M.E. Understanding nature's strategies for enzyme-catalyzed racemization andepimerization [J]. Accounts of chemical research, 2002, 35(4):237-246.
[25] Benning M.M., H. Shim, F.M. Raushel, H.M. Holden. High resolution X-raystructures of different metal-substituted forms of phosphotriesterase fromPseudomonas diminuta [J]. Biochemistry, 2001, 40(9):2712-2722.
[26] Georgieva P., F. Himo. Density functional theory study of the reaction mechanism ofthe DNA repairing enzyme alkylguanine alkyltransferase [J]. Chemical PhysicsLetters, 2008, 463(1-3):214-218.
[1] Armstrong R.N. Glutathione S-transferases: reaction mechanism, structure, andfunction [J]. Chemical research in toxicology, 1991, 4(2):131-140.
[2] Liu S., P. Zhang, X. Ji, Ww Johnson, Gl Gilliland, Rn Armstrong. Contribution oftyrosine 6 to the catalytic mechanism of isoenzyme 3-3 of glutathione S-transferase[J]. Journal of Biological Chemistry, 1992, 267(7):4296-4299.
[3] Graminski G.F., Y. Kubo, R.N. Armstrong. Spectroscopic and kinetic evidence for thethiolate anion of glutathione at the active site of glutathione S-transferase [J].Biochemistry, 1989, 28(8):3562-3568.
[4] Josephy P.D., B. Mannervik. Molecular toxicology [M]. Oxford University Press, USA.2006.
[5] Josephy Pd, B. Mannervik. Glutathione transferases [J]. Molecular Toxicology,2006:333-364.
[6] Mcilwain Cc, Dm Townsend, Kd Tew. Glutathione S-transferase polymorphisms:cancer incidence and therapy [J]. Oncogene, 2006, 25(11):1639-1648.
[7] Moyer A.M., O.E. Salavaggione, S.J. Hebbring, I. Moon, M.A.T. Hildebrandt, B.W.Eckloff, D.J. Schaid, E.D. Wieben, R.M. Weinshilboum. Glutathione S-transferase T1and M1: gene sequence variation and functional genomics [J]. Clinical CancerResearch, 2007, 13(23):7207-7216.
[8] Dourado D.F.A.R., P.A. Fernandes, M.J. Ramos. Mammalian cytosolic glutathionetransferases [J]. Current Protein and Peptide Science, 2008, 9(4):325-337.
[9] Dourado D.F.A.R., P.A. Fernandes, M.J. Ramos. Glutathione transferase A1-1: catalyticrole of water [J]. Theoretical Chemistry Accounts: Theory, Computation, andModeling (Theoretica Chimica Acta), 2009, 124(1):71-83.
[10] Habig W.H., M.J. Pabst, W.B. Jakoby. Glutathione S-transferases the first enzymaticstep in mercapturic acid formation [J]. Journal of Biological Chemistry, 1974,249(22):7130-7139.
[11] Armstrong R.N. Structure, catalytic mechanism, and evolution of the glutathionetransferases [J]. Chemical research in toxicology, 1997, 10(1):2-18.
[12] Sheehan D., G. Meade, V.M. Foley, C.A. Dowd. Structure, function and evolution ofglutathione transferases: implications for classification of non-mammalian membersof an ancient enzyme superfamily [J]. Biochemical Journal, 2001, 360(Pt 1):1.
[13] Di Ilio C., A. Aceto, R. Piccolomini, N. Allocati, A. Faraone, L. Cellini, G. Ravagnan,G. Federici. Purification and characterization of three forms of glutathione transferasefrom Proteus mirabilis [J]. Biochemical Journal, 1988, 255(3):971.
[14] Allocati N., L. Federici, M. Masulli, C. Di Ilio. Glutathione transferases in bacteria [J].FEBS Journal, 2009, 276(1):58-75.
[15] Dirr H., P. Reinemer, R. Huber. X‐ray crystal structures of cytosolic glutathioneS‐transferases [J]. European Journal of Biochemistry, 1994, 220(3):645-661.
[16] Ma X.X., Y.L. Jiang, Y.X. He, R. Bao, Y. Chen, C.Z. Zhou. Structures of yeastglutathione-S-transferase Gtt2 reveal a new catalytic type of GST family [J]. EMBOreports, 2009, 10(12):1320-1326.
[17] Adang Ae, J. Brussee, A. Van Der Gen, Gj Mulder. The glutathione-binding site inglutathione S-transferases. Investigation of the cysteinyl, glycyl and gamma-glutamyldomains [J]. Biochemical Journal, 1990, 269(1):47.
[18] Gustafsson A., P.L. Pettersson, L. Grehn, P. Jemth, B. Mannervik. Role of theglutamylα-carboxylate of the substrate glutathione in the catalytic mechanism ofhuman glutathione transferase A1-1 [J]. Biochemistry, 2001, 40(51):15835-15845.
[19] Caccuri A.M., M.L. Bello, M. Nuccetelli, M. Nicotra, P. Rossi, G. Antonini, G.Federici, G. Ricci. Proton release upon glutathione binding to glutathione transferaseP1-1: kinetic analysis of a multistep glutathione binding process [J]. Biochemistry,1998, 37(9):3028-3034.
[20] Párraga A., I. García-Sáez, S.B. Walsh, T.J. Mantle, M. Coll. The three-dimensionalstructure of a class-Pi glutathione S-transferase complexed with glutathione: theactive-site hydration provides insights into the reaction mechanism [J]. BiochemicalJournal, 1998, 333(Pt 3):811.
[21] Dourado D.F.A.R., P.A. Fernandes, B. Mannervik, M.J. Ramos. Glutathionetransferase: new model for glutathione activation [J]. Chemistry-A European Journal,2008, 14(31):9591-9598.
[22] Dourado D.F.A.R., P.A. Fernandes, B. Mannervik, M.J. Ramos. Glutathionetransferase A1-1: catalytic importance of arginine 15 [J]. The Journal of PhysicalChemistry B, 2010, 114(4):1690-1697.
[23] Dourado D.F.A.R., P.A. Fernandes, M.J. Ramos. Glutathione Transferase ClassesAlpha, Pi, and Mu: GSH Activation Mechanism [J]. The Journal of PhysicalChemistry B, 2010.
[24] Frisch M.J., Gw Trucks, Hb Schlegel, Ge Scuseria, Ma Robb, Jr Cheeseman, JaMontgomery Jr, T. Vreven, Kn Kudin, Jc Burant. Gaussian 03, revision B. 04 [J].Gaussian: Pittsburgh, PA, 2003.
[25] Li L., X. Lin, Z. Li. Hydroxylation Reaction Mechanism for Nitrosodimethylamine byOxygen Atom [J].
[26] Liu Y., H. Dong, H. Zhang, G. Wang, Z. Li, H. Chen. Prediction of RNA SecondaryStructure Based on Particle Swarm Optimization [J]. Chem. Res. Chinese Universities,2011, 27(1):108-112.
[27] Cammi R., B. Mennucci, J. Tomasi. Second-order M ller-Plesset analyticalderivatives for the polarizable continuum model using the relaxed density approach [J].The Journal of Physical Chemistry A, 1999, 103(45):9100-9108.
[28] Cossi M., V. Barone. Time-dependent density functional theory for molecules in liquidsolutions [J]. The Journal of chemical physics, 2001, 115:4708.
[29] Gonzalez C., H.B. Schlegel. An improved algorithm for reaction path following [J].The Journal of chemical physics, 1989, 90:2154.
[30] Gonzalez C., H.B. Schlegel. Reaction path following in mass-weighted internalcoordinates [J]. Journal of Physical Chemistry, 1990, 94(14):5523-5527.
[31] Chen S.L., W.H. Fang, F. Himo. Theoretical study of the phosphotriesterase reactionmechanism [J]. The Journal of Physical Chemistry B, 2007, 111(6):1253-1255.
[32] Sevastik R., F. Himo. Quantum chemical modeling of enzymatic reactions: The caseof 4-oxalocrotonate tautomerase [J]. Bioorganic chemistry, 2007, 35(6):444-457.
[33] Zhao Y., R. Hou, H. Zhang, Q. Zheng, C. Sun. Insight into Reaction Mechanism ofSirtuins via Molecular Simulation and Density Functional Theory Study [J].高等学校化学研究:英文版, 2010(005):833-837.
[34] Georgieva P., F. Himo. Density functional theory study of the reaction mechanism ofthe DNA repairing enzyme alkylguanine alkyltransferase [J]. Chemical PhysicsLetters, 2008, 463(1-3):214-218.
[35] Hopmann K.H., F. Himo. Theoretical study of the full reaction mechanism of humansoluble epoxide hydrolase [J]. Chemistry-A European Journal, 2006,12(26):6898-6909.
[36] Hu C.H., T. Brinck, K. Hult. Ab initio and density functional theory studies of thecatalytic mechanism for ester hydrolysis in serine hydrolases [J]. International journalof quantum chemistry, 1998, 69(1):89-103.
[37] Yao Y., Z. Li. Inhibition Mechanism of Cholinesterases by Carbamate: A TheoreticalStudy [J]. Chemical Research in Chinese Universities, 2008, 24(6):778-781.
[38] Bowman A.L., L. Ridder, I.M.C.M. Rietjens, J. Vervoort, A.J. Mulholland. Moleculardeterminants of xenobiotic metabolism: QM/MM simulation of the conversion of1-chloro-2, 4-dinitrobenzene catalyzed by M1-1 glutathione S-transferase [J].Biochemistry, 2007, 46(21):6353-6363.
[2] Benton D. Bioinformatics—principles and potential of a new multidisciplinary tool[J]. Trends in biotechnology, 1996, 14(8):261-272.
[3]纪兆华,裴志利,管仁初,梁艳春.生物信息学在新兴学科群中崛起[J].电脑知识与技术, 2008(22):1094-1096.
[4]张春霆.生物信息学的现状与展望[J].世界科技研究与发展, 2000,22(006):17-20.
[5] Littlejohn K.A., P. Hooley, P.W. Cox. Bioinformatics predicts diverse< i>Aspergillus hydrophobins with novel properties [J]. Food Hydrocolloids, 2011.
[6] Yu W., Y. Zhang, L. Xu, S. Sun, X. Jiang, F. Zhang. Microarray-based bioinformaticsanalysis of osteoblasts on TiO< sub> 2 nanotube layers [J]. Colloids andSurfaces B: Biointerfaces, 2011.
[7] Uzun A., S. Sharma, J. Padbury. A Bioinformatics Approach to Preterm Birth [J].American Journal of Reproductive Immunology, 2012.
[8] Fu-Jun L., W. Hai-Yan, L. Jian-Yuan. A new analysis of testicular proteins throughintegrative bioinformatics [J]. Molecular Biology Reports, 2011:1-6.
[9] Durrant C., M.A. Swertz, R. Alberts, D. Arends, S. M ller, R. Mott, P. Prins, K.J. VanDer Velde, R.C. Jansen, K. Schughart. Bioinformatics tools and database resourcesfor systems genetics analysis in mice—a short review and an evaluation of futureneeds [J]. Briefings in Bioinformatics, 2011.
[10] Holst A.G., S. Saber, M. Houshmand, E.V. Zaklyazminskaya, Y. Wang, H.K. Jensen, L.Refsgaard, S. Hauns , J.H. Svendsen, M.S. Olesen. Sodium Current and PotassiumTransient Outward Current Genes in Brugada Syndrome: Screening andBioinformatics [J]. Canadian Journal of Cardiology, 2012.
[11]孙有平,王正华,王勇献.后基因组时代生物信息学的新进展[J].国防科技大学学报, 2003, 25(001):1-6.
[12] Linderstr m-Lang K. Deuterium exchange between peptides and water [J]. Chem SocSpec Publ, 1955, 2:1-20.
[13] Feynman R.P., R.B. Leighton, M. Sands, Lectures on physics, vol. 1. 1963,Addison-Wesley, Reading, Massachusetts.
[14] Frauenfelder H., G.A. Petsko, D. Tsernoglou. Temperature-dependent X-raydiffraction as a probe of protein structural dynamics [J]. 1979.
[15] Artymiuk Pj, Ccf Blake, Dep Grace, Sj Oatley, Dc Phillips, Mje Sternberg.Crystallographic studies of the dynamic properties of lysozyme [J]. 1979.
[16] Ichiye T., M. Karplus. Fluorescence depolarization of tryptophan residues in proteins:a molecular dynamics study [J]. Biochemistry, 1983, 22(12):2884-2893.
[17] Dobson Cm, M. Karplus. [18] Internal motion of proteins: Nuclear magneticresonance measurements and dynamic simulations [J]. Methods in enzymology, 1986,131:362-389.
[18] B hm H.J., G. Klebe. What Can We Learn from Molecular Recognition inProtein–Ligand Complexes for the Design of New Drugs? [J]. Angewandte ChemieInternational Edition in English, 1996, 35(22):2588-2614.
[19]钟扬,生物学,张亮,生物信息学,赵琼,马坚.简明生物信息学[M].高等教育出版社. 2001.
[20]赵国屏.生物信息学[M].科学出版社. 2002.
[21]鲁卫平,周元国.生物信息学的现状和展望[J].国外医学:临床生物化学与检验学分册, 2002, 23(005):254-255.
[22]陈润生.生物信息学及其研究进展[J].医学研究通讯, 2002, 31(12).
[23]王发生,毛君莲.生命科学时代的生物信息学[J].中国现代医学杂志, 2000,10(12):108-109.
[24]沈同,王镜岩.生物化学(上册) [J].北京:人民教育出版社, 1990, 1(9):8.
[25] Tsou C.L. The role of active site flexibility in enzyme catalysis [J]. Biochemistry.Biokhimii a, 1998, 63(3):253.
[26] Toth M.J., M.S. Miller, K.A. Ward, P.A. Ades. SKELETAL MUSCLEMITOCHONDRIAL DENSITY, GENE EXPRESSION AND ENZYMEACTIVITIES IN HUMAN HEART FAILURE: MINIMAL EFFECTS OF THEDISEASE AND RESISTANCE TRAINING [J]. Journal of Applied Physiology, 2012.
[27] Chien Y.H., N.C. Lee, S.C. Chiang, R.J. Desnick, W.L. Hwu. Fabry Disease:Incidence of the Common Later-Onsetα-Galactosidase A IVS4+ 919G> A Mutationin Taiwanese Newborns--Superiority of DNA-Based to Enzyme-Based NewbornScreening for Common Mutations [J]. Molecular medicine (Cambridge, Mass.), 2012.
[28] Macedo M.F., R. Quinta, C.S. Pereira, M.C. Sa Miranda. Enzyme replacement therapypartially prevents invariant Natural Killer T cell deficiency in the Fabry diseasemouse model [J]. Molecular Genetics and Metabolism, 2012.
[29] Ayebazibwe C., F.N. Mwiine, S.N. Balinda, K. Tj rneh j, S. Alexandersen.Application of the Ceditest FMDV type O and FMDV-NS enzyme-linkedimmunosorbent assays for detection of antibodies against Foot-and-mouth diseasevirus in selected livestock and wildlife species in Uganda [J]. Journal of VeterinaryDiagnostic Investigation, 2012, 24(2):270-276.
[30] Vassar R. BACE1, the Alzheimer's beta-secretase enzyme, in health and disease [J].Molecular Neurodegeneration, 2012, 7:1-1.
[31] Banugaria S.G., T.T. Patel, J. Mackey, S. Das, A. Amalfitano, A.S. Rosenberg, J.Charrow, Y.T. Chen, P.S. Kishnani. Persistence of high sustained antibodies toenzyme replacement therapy despite extensive immunomodulatory therapy in aninfant with Pompe disease: Need for agents to target antibody-secreting plasma cells[J]. Molecular Genetics and Metabolism, 2012.
[32] Allen M.P., D.J. Tildesley. Computer simulation of liquids [M]. Vol. 18: Oxforduniversity press. 1989.
[33] Becker O.M., A.D. Mackerell Jr, B. Roux, M. Watanabe. Computational biochemistryand biophysics [M]. CRC Press. 2001.
[34] Frenkel D., B. Smit. Understanding molecular simulation: from algorithms toapplications [M]. Academic Press, Inc. 1996.
[35] Kohn W. Nobel Lecture: Electronic structure of matter-wave functions and densityfunctionals [J]. Reviews of Modern Physics, 1999, 71(5):1253-1266.
[36] Warshel A. Computer simulations of enzyme catalysis: methods, progress, andinsights [J]. Annual review of biophysics and biomolecular structure, 2003,32(1):425-443.
[37] Friesner R.A., V. Guallar. Ab initio quantum chemical and mixed quantummechanics/molecular mechanics (QM/MM) methods for studying enzymaticcatalysis [J]. Annu. Rev. Phys. Chem., 2005, 56:389-427.
[38] Bruice T.C., K. Kahn. Computational enzymology [J]. Current Opinion in ChemicalBiology, 2000, 4(5):540-544.
[39] MartíS., M. Roca, J. Andrés, V. Moliner, E. Silla, I. Tuón, J. Bertrán. Theoreticalinsights in enzyme catalysis [J]. Chem. Soc. Rev., 2004, 33(2):98-107.
[40] Himo F. Quantum chemical modeling of enzyme active sites and reaction mechanisms[J]. Theoretical Chemistry Accounts: Theory, Computation, and Modeling(Theoretica Chimica Acta), 2006, 116(1):232-240.
[41] Senn H., W. Thiel. QM/MM methods for biological systems [J]. Atomistic approachesin modern biology, 2007:173-290.
[42] Siegbahn P.E.M., T. Borowski. Modeling enzymatic reactions involving transitionmetals [J]. Accounts of chemical research, 2006, 39(10):729-738.
[43] Kundu A., A. Bayya. Speech recognition using hybrid hidden Markov model and NNclassifier [J]. International journal of speech technology, 1998, 2(3):227-240.
[44]张阳德.生物信息学(5):药物设计与生物信息学[J].外科理论与实践, 2007,12(1):I0009-I0012.
[45]陈凯先,药物,蒋华良,嵇汝运.计算机辅助药物设计:原理,方法及应用[M].上海科学技术出版社. 2000.
[46]李亮助,孙强明.生物信息学在药物设计中的应用[J].生命的化学, 2003,23(5):364-366.
[47]郑彦,吕莉.计算机辅助药物设计在药物合成中的应用[J].齐鲁药事, 2008,27(10):614-616.
[48]赵金城,王庆莉,毕秀玲.计算机辅助直接药物分子设计[J].大连大学学报,2002, 23(006):22-30.
[49]梁桂兆,梅虎,周原,李志良.计算机辅助药物设计中的多维定量构效关系模型化方法[J].化学进展, 2006, 18(1):120-127.
[50]郑珩,王非.药物生物信息学[M].化学工业出版社. 2004.
[51]孙之荣,后基因组信息学. 2002,北京:清华大学出版社.
[52] Roos D.S. Bioinformatics--trying to swim in a sea of data [J]. Science, 2001,291(5507):1260-1261.
[53] Spengler S.J. Bioinformatics in the information age [J]. 2000.
[54]陈竺,强伯勤,方福德.基因组科学与人类疾病[M].科学出版社. 2001.
[55] Barnett C.B., K.J. Naidoo. Ring puckering: A metric for evaluating the accuracy ofAM1, PM3, PM3CARB-1, and SCC-DFTB carbohydrate QM/MM simulations [J].The Journal of Physical Chemistry B, 2010.
[56] Ramraj A., R.K. Raju, Q. Wang, I.H. Hillier, R.A. Bryce, M.A. Vincent. An evaluationof the GLYCAM06 and MM3 force fields, and the PM3-D* molecular orbitalmethod for modelling prototype carbohydrate-aromatic interactions [J]. Journal ofMolecular Graphics and Modelling, 2010, 29(3):321-325.
[57] Sattelle B.M., A. Almond. Less is more when simulating unsulfatedglycosaminoglycan 3D‐structure: Comparison of GLYCAM06/TIP3P,PM3‐CARB1/TIP3P, and SCC‐DFTB‐D /TIP3P predictions with experiment [J].Journal of computational chemistry, 2010, 31(16):2932-2947.
[58] Jensen F., Myilibrary. Introduction to computational chemistry [M]. Vol. 2: WileyNew York. 1999.
[59] Young D.C. Computational chemistry: a practical guide for applying techniques toreal world problems [M]. Wiley-Interscience. 2001.
[60] Re S., Y. Sugita. Modeling the Transition State of Enzyme-catalyzed PhosphorylTransfer Reaction Using QM/MM Method [J]. Yakugaku zasshi: Journal of thePharmaceutical Society of Japan, 2011, 131(8):1171.
[61] MartíS., J. Andrés, V. Moliner, E. Silla, I. Tuón, J. Bertrán. Theoretical QM/MMstudies of enzymatic pericyclic reactions [J]. Interdisciplinary Sciences:Computational Life Sciences, 2010, 2(1):115-131.
[62] Guallar V., F.H. Wallrapp. QM/MM methods: Looking inside heme proteinsbiochemisty [J]. Biophysical chemistry, 2010, 149(1):1-11.
[63] Barberet P., F. Vianna, M. Karamitros, T. Brun, N. Gordillo, P. Moretto, S. Incerti, H.Seznec. Monte-Carlo dosimetry on a realistic cell monolayer geometry exposed toalpha particles [J]. Physics in Medicine and Biology, 2012, 57:2189.
[64] Rai N., E.J. Maginn. Critical behaviour and vapour-liquid coexistence of1-alkyl-3-methylimidazolium bis (trifluoromethylsulfonyl) amide ionic liquids viaMonte Carlo simulations [J]. Faraday Discuss., 2011, 154(0):53-69.
[65] Premuda M., E. Palazzi, F. Ravegnani, D. Bortoli, S. Masieri, G. Giovanelli. MOCRA:a Monte Carlo code for the simulation of radiative transfer in the atmosphere [J].Optics Express, 2012, 20(7):7973-7993.
[66] Li Y., Y. Ma, J. Li, X. Jiang, W. Hu. Dynamic Monte Carlo simulations of doublecrystallization accelerated in microdomains of diblock copolymers [J]. Journal ofChemical Physics, 2012, 136(10):104906.
[67] Weiner P.K., P.A. Kollman. AMBER: Assisted model building with energy refinement.A general program for modeling molecules and their interactions [J]. Journal ofcomputational chemistry, 1981, 2(3):287-303.
[68] Scott W.R.P., P.H. Hünenberger, I.G. Tironi, A.E. Mark, S.R. Billeter, J. Fennen, A.E.Torda, T. Huber, P. Krüger, W.F. Van Gunsteren. The GROMOS biomolecularsimulation program package [J]. The Journal of Physical Chemistry A, 1999,103(19):3596-3607.
[69] Van Gunsteren W.F. Computer simulation of biomolecular systems: theoretical andexperimental applications [M]. Vol. 3: Springer. 1997.
[70] Tuckerman M.E., G.J. Martyna. Understanding modern molecular dynamics:techniques and applications [J]. The Journal of Physical Chemistry B, 2000,104(2):159-178.
[71] Karplus M., J.A. Mccammon. Molecular dynamics simulations of biomolecules [J].Nature Structural & Molecular Biology, 2002, 9(9):646-652.
[72] Fersht A. Structure and mechanism in protein science: a guide to enzyme catalysis andprotein folding [M]. WH Freeman. 1999.
[73] Garcia-Viloca M., J. Gao, M. Karplus, D.G. Truhlar. How enzymes work: analysis bymodern rate theory and computer simulations [J]. Science, 2004, 303(5655):186-195.
[74] Mulholland A.J. Modelling enzyme reaction mechanisms, specificity and catalysis [J].Drug Discovery Today, 2005, 10(20):1393-1402.
[75] Warshel A. Computer modeling of chemical reactions in enzymes and solutions [J].1991.
[76] Warshel A., P.K. Sharma, M. Kato, Y. Xiang, H. Liu, M.H.M. Olsson. Electrostaticbasis for enzyme catalysis [J]. Chemical reviews, 2006, 106(8):3210.
[77] Zhang X., Kn Houk. Why enzymes are proficient catalysts: beyond the Paulingparadigm [J]. Accounts of chemical research, 2005, 38(5):379-385.
[1]谈国霞,吴磊磊.量子化学发展综述[J]. _高校理科研究, 2007.
[2]常进.量子化学方法在计算化合物物理,化学,生物学性质中的应用[J].
[3]刘文剑.新一代相对论量子化学方法[J].中国基础科学, 2007(002):10-11.
[4] Jug K. Quantum chemical methods and their applications to chemical reactions [J].Theoretical Chemistry Accounts: Theory, Computation, and Modeling (TheoreticaChimica Acta), 1980, 54(4):263-300.
[5]陈光巨,黄元河.量子化学[M].华东理工大学出版社. 2008.
[6] Small D.W., M. Head-Gordon. Post-modern valence bond theory for stronglycorrelated electron spins [J]. Phys. Chem. Chem. Phys., 2011, 13(43):19285-19297.
[7] De Marco G., P. Várnai. Molecular simulation of conformational transitions inbiomolecules using a combination of structure-based potential and empirical valencebond theory [J]. Phys. Chem. Chem. Phys., 2009, 11(45):10694-10700.
[8] Truhlar D.G. Valence bond theory for chemical dynamics [J]. Journal of computationalchemistry, 2007, 28(1):73-86.
[9] Raimondi M., M. Simonetta, G. Tantardini. AB initio valence bond theory [J].Computer Physics Reports, 1985, 2:171-216.
[10] Balint-Kurti Gg. Reply to``Ab initio valence-bond theory'' [J]. Physical Review A,1986, 34:674.
[11] Nakai H., M. Hoshino, K. Miyamoto, S. Hyodo. Elimination of translational androtational motions in nuclear orbital plus molecular orbital theory [J]. The Journal ofchemical physics, 2005, 122:164101.
[12] Mohr M., J.P. Mcnamara, H. Wang, S.A. Rajeev, J. Ge, C.A. Morgado, I.H. Hillier.The use of methods involving semi-empirical molecular orbital theory to study thestructure and reactivity of transition metal complexes [J]. Faraday Discuss., 2003,124(0):413-428.
[13] Maranón J., J.L. Pousa. Path integral, collective coordinates, and molecular-orbitaltheory [J]. Physical Review A, 1987, 36(12):5530.
[14] Hagiwara Y., M. Tateno. Recent advances in jointed quantum mechanics andmolecular mechanics calculations of biological macromolecules: schemes andapplications coupled to ab initio calculations [J]. Journal of Physics: CondensedMatter, 2010, 22:413101.
[15] Picardi E., G. Pesole. Computational methods for ab initio and comparative genefinding [J]. Methods in Molecular Biology, 2010, 609:269-284.
[16] Mulder F.A.A., M. Filatov. NMR chemical shift data and ab initio shieldingcalculations: emerging tools for protein structure determination [J]. Chem. Soc. Rev.,2010, 39(2):578-590.
[17] Liu L.A., J.S. Bader. Structure-based ab initio prediction of transcriptionfactor-binding sites [J]. Methods Mol. Biol, 2009, 541:1-19.
[18] Friesner R.A., V. Guallar. Ab initio quantum chemical and mixed quantummechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis[J]. Annu. Rev. Phys. Chem., 2005, 56:389-427.
[19] Chivian D., T. Robertson, R. Bonneau, D. Baker. Ab initio methods [J]. Structuralbioinformatics, 2003:547-557.
[20] Ghosh A., P.R. Taylor. High-level ab initio calculations on the energetics of low-lyingspin states of biologically relevant transition metal complexes: a first progress report[J]. Current Opinion in Chemical Biology, 2003, 7(1):113-124.
[21] Bailey W.C. B3LYP calculation of deuterium quadrupole coupling constants inmolecules [J]. Journal of molecular spectroscopy, 1998, 190(2):318-323.
[22] Carbonniere P., T. Lucca, C. Pouchan, N. Rega, V. Barone. Vibrational computationsbeyond the harmonic approximation: Performances of the B3LYP density functionalfor semirigid molecules [J]. Journal of computational chemistry, 2005, 26(4):384-388.
[23] Kolboe S., S. Svelle. Does an ethene/benzenium ion complex exist? A discrepancybetween B3LYP and MP2 predictions [J]. The Journal of Physical Chemistry A, 2008,112(29):6399-6400.
[24] Payne P.W. Analytic construction of Hartree-Fock density matrices [J]. Proceedings ofthe National Academy of Sciences, 1980, 77(11):6293.
[25] Goldman Sp, A. Dalgarno. Finite-basis-set approach to the Dirac-Hartree-Fockequations [J]. Physical review letters, 1986, 57(4):408-411.
[26] Bushmaker A.W., V.V. Deshpande, S. Hsieh, M.W. Bockrath, S.B. Cronin. DirectObservation of Born Oppenheimer Approximation Breakdown in Carbon Nanotubes[J]. Nano letters, 2009, 9(2):607-611.
[27] Hijikata Y., H. Nakashima, H. Nakatsuji. Solving non-Born–OppenheimerSchr dinger equation for hydrogen molecular ion and its isotopomers using the freecomplement method [J]. The Journal of chemical physics, 2009, 130:024102.
[28] Lemus R., A. Frank. Constrained calculations in the electron-vibron model and theBorn-Oppenheimer approximation [J]. Physical review. A, 1993, 47(6A):4920-4933.
[29] Blümel R., B. Esser. Quantum chaos in the Born-Oppenheimer approximation [J].Physical review letters, 1994, 72(23):3658-3661.
[30] Rozsnyai Bf, F. Martino, J. Ladik. Calculation of the Energy Band Structures ofComplicated Periodic DNA Models in the SemiempiricalSCF–LCAO–Crystal‐O rbital Approximation [J]. The Journal of chemical physics,1970, 52:5708.
[31] De Andrada E Silva Ea, Ic Da Cunha Lima, A. Ferreira Da Silva. Two-dimensionalhydrogen molecule and the alternant-molecular-orbital approximation [J]. Phys. Rev.A;(United States), 1986, 33(4).
[32] Gross E.K.U., R.M. Dreizler. Density functional theory [M]. Vol. 337: Springer. 1995.
[33] Tse J.S. Ab initio molecular dynamics with density functional theory [J]. Annualreview of physical chemistry, 2002, 53(1):249-290.
[34]林梦海.量子化学计算方法与应用[M].科学出版社. 2004.
[35] Halpern A.M., E.D. Glendening. An intrinsic reaction coordinate calculation of thetorsion-internal rotation potential of hydrogen peroxide and its isotopomers [J]. TheJournal of chemical physics, 2004, 121:273.
[36] Riska E.B. On the solvent effect in experimental chemical skin carcinogenesis;lipophilic-hydrophilic (surface active) agents as solvents for carcinogens [J]. Actapathologica et microbiologica Scandinavica. Supplement, 1956, 39(Suppl 114):1.
[37] Peterson J.M., Wr Guild. A differential solvent effect on thermal stability of geneticmarkers in DNA [J]. Journal of Molecular Biology, 1966, 20(3):497-503.
[38] Barbara P.F., G.C. Walker, T.P. Smith. Vibrational modes and the dynamic solventeffect in electron and proton transfer [J]. Science, 1992, 256(5059):975-981.
[39] Ben‐Naim A., Kl Ting, Rl Jernigan. Solvent effect on binding thermodynamics ofbiopolymers [J]. Biopolymers, 1990, 29(6‐7 ):901-919.
[40] Hopmann E., W. Arlt, M. Minceva. Solvent system selection in counter-currentchromatography using conductor-like screening model for real solvents [J]. Journal ofChromatography A, 2011, 1218(2):242-250.
[41] Fu K.X., Q. Zhu, X.Y. Li, Z. Gong, J.Y. Ma, R.X. He. Continuous medium theory fornonequilibrium solvation: IV. Solvent reorganization energy of electron transfer basedon conductor‐l ike screening model [J]. Journal of computational chemistry, 2006,27(3):368-374.
[42] Oleszek‐Kudlak S., M. Grabda, E. Shibata, F. Eckert, T. Nakamura. Application ofthe conductor‐like screening model for real solvents for prediction of the aqueoussolubility of chlorobenzenes depending on temperature and salinity [J].Environmental toxicology and chemistry, 2005, 24(6):1368-1375.
[43] Yoshitake Y., H. Nakagawa, K. Harano. A Theoretical Study of Neighboring-GroupParticipation in Thione-to-Thiol Rearrangement of Xanthates. Molecular OrbitalCalculation Using a Conductor-Like Screening Model (COSMO) Approach [J].Chemical and pharmaceutical bulletin, 2001, 49(11):1433-1439.
[44]崔凤超.羟氰裂解酶及两类氧甲基转移酶催化机理的理论研究[D]. 2010.
[45]张继龙.几类重要蛋白质的分子动力学模拟及相关抑制剂的改良[D]. 2010.
[46]楚慧郢.蛋白质的分子动力学模拟和催化机理的理论研究[D]. 2009.
[47]赵勇山.几类重要蛋白的结构及其催化机理的理论研究[D]. 2009.
[48] Re S., Y. Sugita. Modeling the Transition State of Enzyme-catalyzed PhosphorylTransfer Reaction Using QM/MM Method [J]. Yakugaku zasshi: Journal of thePharmaceutical Society of Japan, 2011, 131(8):1171.
[49] MartíS., J. Andrés, V. Moliner, E. Silla, I. Tuón, J. Bertrán. Theoretical QM/MMstudies of enzymatic pericyclic reactions [J]. Interdisciplinary Sciences:Computational Life Sciences, 2010, 2(1):115-131.
[50] Menikarachchi L.C., J.A. Gascón. QM/MM approaches in medicinal chemistryresearch [J]. Current Topics in Medicinal Chemistry, 2010, 10(1):46-54.
[51] Senn H.M., W. Thiel. QM/MM methods for biomolecular systems [J]. AngewandteChemie International Edition, 2009, 48(7):1198-1229.
[52] Garcia-Viloca M., J. Gao, M. Karplus, D.G. Truhlar. How enzymes work: analysis bymodern rate theory and computer simulations [J]. Science, 2004, 303(5655):186-195.
[53] Mulholland A.J. Modelling enzyme reaction mechanisms, specificity and catalysis [J].Drug Discovery Today, 2005, 10(20):1393-1402.
[54] Warshel A., P.K. Sharma, M. Kato, Y. Xiang, H. Liu, M.H.M. Olsson. Electrostaticbasis for enzyme catalysis [J]. Chemical reviews, 2006, 106(8):3210.
[55] Bruice T.C., K. Kahn. Computational enzymology [J]. Current Opinion in ChemicalBiology, 2000, 4(5):540-544.
[56] Siegbahn P.E.M., T. Borowski. Modeling enzymatic reactions involving transitionmetals [J]. Accounts of chemical research, 2006, 39(10):729-738.
[57] Gao J., D.G. Truhlar. Quantum mechanical methods for enzyme kinetics [J]. Annualreview of physical chemistry, 2002, 53(1):467-505.
[58] Mulholland A.J. Computational enzymology: modelling the mechanisms of biologicalcatalysts [J]. Biochemical Society Transactions, 2008, 36(1):22-26.
[59] Ryde U. Combined quantum and molecular mechanics calculations on metalloproteins[J]. Current Opinion in Chemical Biology, 2003, 7(1):136-142.
[60] Senn H.M., W. Thiel. QM/MM studies of enzymes [J]. Current Opinion in ChemicalBiology, 2007, 11(2):182-187.
[61] Zhang Y. Pseudobond ab initio QM/MM approach and its applications to enzymereactions [J]. Theoretical Chemistry Accounts: Theory, Computation, and Modeling(Theoretica Chimica Acta), 2006, 116(1):43-50.
[1] Firestine S.M., S.W. Poon, E.J. Mueller, J.A. Stubbe, V.J. Davisson. ReactionsCatalyzed by 5-Aminoimidazole Ribonucleotide Carboxylases from Escherichia coliand Gallus gallus: A Case for Divergent Catalytic Mechanisms? [J]. Biochemistry,1994, 33(39):11927-11934.
[2] Mueller E.J., E. Meyer, J. Rudolph, V.J. Davisson, J.A. Stubbe.N5-carboxyaminoimidazole ribonucleotide: Evidence for a new intermediate and twonew enzymic activities in the de novo purine biosynthetic pathway of Escherichia coli[J]. Biochemistry, 1994, 33(8):2269-2278.
[3] Mathews I.I., T.J. Kappock, J.A. Stubbe, S.E. Ealick. Crystal structure of Escherichiacoli PurE, an unusual mutase in the purine biosynthetic pathway [J]. Structure, 1999,7(11):1395-1406.
[4] Meyer E., T.J. Kappock, C. Osuji, J.A. Stubbe. Evidence for the direct transfer of thecarboxylate of N 5-carboxyaminoimidazole ribonucleotide (N 5-CAIR) to generate4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutase [J]. Biochemistry, 1999, 38(10):3012-3018.
[5] Ivanovics G., E. Marjai, A. Dobozy. The growth of purine mutants of Bacillus anthracisin the body of the mouse [J]. Journal of general microbiology, 1968, 53(2):147-162.
[6] Samant S., H. Lee, M. Ghassemi, J. Chen, J.L. Cook, A.S. Mankin, A.A. Neyfakh.Nucleotide biosynthesis is critical for growth of bacteria in human blood [J]. PLoSpathogens, 2008, 4(2):e37.
[7] Donovan M., J.J. Schumuke, W.A. Fonzi, S.L. Bonar, K. Gheesling-Mullis, G.S. Jacob,V.J. Davisson, S.B. Dotson. Virulence of a PhosphoribosylaminoimidazoleCarboxylase-DeficientCandida albicans Strain in an Immunosuppressed Murine Modelof Systemic Candidiasis [J]. Infection and immunity, 2001, 69(4):2542-2548.
[8] Thoden J.B., H.M. Holden, S.M. Firestine. Structural Analysis of the Active SiteGeometry of N 5-Carboxyaminoimidazole Ribonucleotide Synthetase fromEscherichia coli , [J]. Biochemistry, 2008, 47(50):13346-13353.
[9] Hoskins A.A., M. Morar, T.J. Kappock, I.I. Mathews, J.B. Zaugg, T.E. Barder, P. Peng,A. Okamoto, S.E. Ealick, J.A. Stubbe. N 5-CAIR Mutase: Role of a CO2 Binding Siteand Substrate Movement in Catalysis [J]. Biochemistry, 2007, 46(10):2842-2855.
[10] Becke A.D. Density‐functional thermochemistry. IV. A new dynamical correlationfunctional and implications for exact‐exchange mixing [J]. The Journal of chemicalphysics, 1996, 104:1040.
[11] Foresman Jb, A. Frisch, Exploring Chemistry with Electronic Structure Methods, ;Gaussian: Pittsburgh, PA, 1996, Chapter.
[12] Miehlich B., A. Savin, H. Stoll, H. Preuss. Chem Phys Lett 157: 200; c) Lee C [J].Yang W, Parr G (1988) Phys Rev B, 1989, 37:785.
[13] Trucks Gw, Hb Schlegel, Ge Scuseria, Ma Robb, Jr Cheeseman, Ja Montgomery Jr, T.Vreven, Kn Kudin, Jc Burant, Jm Millam. Gaussian 03, revision C. 02; Gaussian [J].Inc.: Wallingford, CT, 2004.
[14] Cammi R., B. Mennucci, J. Tomasi. Second-order M ller-Plesset analyticalderivatives for the polarizable continuum model using the relaxed density approach [J].The Journal of Physical Chemistry A, 1999, 103(45):9100-9108.
[15] Cammi R., B. Mennucci, J. Tomasi. An attempt to bridge the gap betweencomputation and experiment for nonlinear optical properties: macroscopicsusceptibilities in solution [J]. The Journal of Physical Chemistry A, 2000,104(20):4690-4698.
[16] Cossi M., V. Barone. Time-dependent density functional theory for molecules in liquidsolutions [J]. The Journal of chemical physics, 2001, 115:4708.
[17] Cossi M., G. Scalmani, N. Rega, V. Barone. New developments in the polarizablecontinuum model for quantum mechanical and classical calculations on molecules insolution [J]. The Journal of chemical physics, 2002, 117:43.
[18] Estroff L.A., A.D. Hamilton. Water gelation by small organic molecules [J].ChemInform, 2004, 35(20):no-no.
[19] Barreto P., H. Kim, B. Lynn, M. Scott. Efficient algorithms for pairing-basedcryptosystems [J]. Advances in Cryptology—CRYPTO 2002, 2002:354-369.
[20] Swaminathan S., N. Khanna. Dengue: recent advances in biology and current status oftranslational research [J]. Current molecular medicine, 2009, 9(2):152-173.
[21] Himo F. Quantum chemical modeling of enzyme active sites and reaction mechanisms[J]. Theoretical Chemistry Accounts: Theory, Computation, and Modeling (TheoreticaChimica Acta), 2006, 116(1):232-240.
[22] Georgieva P., F. Himo. Density functional theory study of the reaction mechanism ofthe DNA repairing enzyme alkylguanine alkyltransferase [J]. Chemical Physics Letters,2008, 463(1-3):214-218.
[23] Hopmann K.H., F. Himo. Theoretical study of the full reaction mechanism of humansoluble epoxide hydrolase [J]. Chemistry-A European Journal, 2006,12(26):6898-6909.
[24] Georgieva P., F. Himo. Quantum chemical modeling of enzymatic reactions: The caseof histone lysine methyltransferase [J]. Journal of computational chemistry, 2010,31(8):1707-1714.
[25] Velichkova P., F. Himo. Methyl transfer in glycine N-methyltransferase. A theoreticalstudy [J]. The Journal of Physical Chemistry B, 2005, 109(16):8216-8219.
[26] Lundberg M., P.E.M. Siegbahn, K. Morokuma. The mechanism for isopenicillin Nsynthase from density-functional modeling highlights the similarities with otherenzymes in the 2-his-1-carboxylate family [J]. Biochemistry, 2008, 47(3):1031-1042.
[27] Lucas A., J.L. Valverde, P. Sánchez, F. Dorado, M.J. Ramos. Hydroisomerization of n-octane over platinum catalysts with or without binder [J]. Applied Catalysis A:General, 2005, 282(1):15-24.
[28] Velichkova P., F. Himo. Theoretical study of the methyl transfer in guanidinoacetatemethyltransferase [J]. The Journal of Physical Chemistry B, 2006, 110(1):16-19.
[29] Sousa S.F., E.S. Carvalho, D.M. Ferreira, I.S. Tavares, P.A. Fernandes, M.J. Ramos,J. .A.N.F. Gomes. Comparative analysis of the performance of commonly availabledensity functionals in the determination of geometrical parameters for zinc complexes[J]. Journal of computational chemistry, 2009, 30(16):2752-2763.
[30] Dourado D.F.A.R., P.A. Fernandes, B. Mannervik, M.J. Ramos. Glutathionetransferase A1-1: catalytic importance of arginine 15 [J]. The Journal of PhysicalChemistry B, 2010, 114(4):1690-1697.
[31] Francois J.A., C.M. Starks, S. Sivanuntakorn, H. Jiang, A.E. Ransome, J.W. Nam, C.Z.Constantine, T.J. Kappock. Structure of a NADH-insensitive hexameric citratesynthase that resists acid inactivation [J]. Biochemistry, 2006, 45(45):13487-13499.
[32] Acevedo O., W.L. Jorgensen. Medium effects on the decarboxylation of a biotinmodel in pure and mixed solvents from QM/MM simulations [J]. The Journal oforganic chemistry, 2006, 71(13):4896-4902.
[33] Yu J., J. Wang, W. Lin, S. Li, H. Li, J. Zhou, P. Ni, W. Dong, S. Hu, C. Zeng. Thegenomes of Oryza sativa: a history of duplications [J]. PLoS biology, 2005, 3(2):e38.
[34] Mauser H., W.A. King, J.E. Gready, T.J. Andrews. CO2 fixation by RuBisCO:Computational dissection of the key steps of carboxylation, hydration, and CC bondcleavage [J]. Journal of the American Chemical Society, 2001, 123(44):10821-10829.
[35] Tranchimand S., C.M. Starks, I.I. Mathews, S.C. Hockings, T.J. Kappock. Treponemadenticola PurE Is a Bacterial AIR Carboxylase [J]. Biochemistry, 2011.
[1] Savolainen K., P. Bhaumik, W. Schmitz, T.J. Kotti, E. Conzelmann, R.K. Wierenga, J.K.Hiltunen.α-Methylacyl-CoA Racemase from Mycobacterium tuberculosis [J]. Journalof Biological Chemistry, 2005, 280(13):12611-12620.
[2] Schmitz W., R. Fingerhut, E. Conzelmann. Purification and properties of anα‐methylacyl‐CoA racemase from rat liver [J]. European Journal of Biochemistry,1994, 222(2):313-323.
[3] Russell D.W. The enzymes, regulation, and genetics of bile acid synthesis [J]. Annualreview of biochemistry, 2003, 72(1):137-174.
[4] Hiltunen J.K., Y.M. Qin. [beta]-Oxidation-strategies for the metabolism of a widevariety of acyl-CoA esters [J]. Biochimica et Biophysica Acta (BBA)-Molecular andCell Biology of Lipids, 2000, 1484(2-3):117-128.
[5] Wierzbicki A.S., M.D. Lloyd, C.J. Schofield, M.D. Feher, F.B. Gibberd. Refsum'sdisease: a peroxisomal disorder affecting phytanic acidα‐o xidation [J]. Journal ofneurochemistry, 2002, 80(5):727-735.
[6] Mukherji M., C.J. Schofield, A.S. Wierzbicki, G.A. Jansen, R.J.A. Wanders, M.D.Lloyd. The chemical biology of branched-chain lipid metabolism [J]. Progress in lipidresearch, 2003, 42(5):359-376.
[7] Lloyd M.D., D.J. Darley, A.S. Wierzbicki, M.D. Threadgill.α‐Methylacyl‐CoAracemase–an‘obscure’metabolic enzyme takes centre stage [J]. FEBS Journal, 2008,275(6):1089-1102.
[8] Qin Y.M., M.H. Poutanen, H.M. Helander, A.P. Kvist, K.M. Siivari, W. Schmitz, E.Conzelmann, U. Hellman, J.K. Hiltunen. Peroxisomal multifunctional enzyme ofbeta-oxidation metabolizing D-3-hydroxyacyl-CoA esters in rat liver: molecularcloning, expression and characterization [J]. Biochemical Journal, 1997, 321(Pt 1):21.
[9] Ferdinandusse S., H. Rusch, Aem Van Lint, G. Dacremont, Rja Wanders, P. Vreken.Stereochemistry of the peroxisomal branched-chain fatty acidα-andβ-oxidationsystems in patients suffering from different peroxisomal disorders [J]. Journal of lipidresearch, 2002, 43(3):438-444.
[10] Ogino S., T. Kawasaki, G.J. Kirkner, M. Loda, C.S. Fuchs. CpG island methylatorphenotype-low (CIMP-low) in colorectal cancer: possible associations with male sexand KRAS mutations [J]. The Journal of molecular diagnostics: JMD, 2006, 8(5):582.
[11] Lakis S., T. Papamitsou, C. Panagiotopoulou, R. Kotakidou, V. Kotoula. AMACR isassociated with advanced pathologic risk factors in sporadic colorectal adenomas [J].World journal of gastroenterology: WJG, 2010, 16(20):2476.
[12] Daugherty S.E., Y.Y. Shugart, E.A. Platz, M.D. Fallin, W.B. Isaacs, R.M. Pfeiffer, R.Welch, W.Y. Huang, D. Reding, R.B. Hayes. Polymorphic variants inα‐m ethylacyl‐CoA racemase and prostate cancer [J]. The Prostate, 2007,67(14):1487-1497.
[13] Bhaumik P., P. Kursula, V. Ratas, E. Conzelmann, J.K. Hiltunen, W. Schmitz, R.K.Wierenga. Crystallization and preliminary X-ray diffraction studies ofan-methylacyl-CoA racemase from Mycobacterium tuberculosis [J]. ActaCrystallographica Section D: Biological Crystallography, 2003, 59(2):353-355.
[14] Darley D.J., D.S. Butler, S.J. Prideaux, T.W. Thornton, A.D. Wilson, T.J. Woodman,M.D. Threadgill, M.D. Lloyd. Synthesis and use of isotope-labelled substrates for amechanistic study on humanα-methylacyl-CoA racemase 1A (AMACR; P504S) [J].Org. Biomol. Chem., 2009, 7(3):543-552.
[15] Bhaumik P., W. Schmitz, A. Hassinen, J.K. Hiltunen, E. Conzelmann, R.K. Wierenga.The catalysis of the 1, 1-proton transfer byα-methyl-acyl-CoA racemase is coupled toa movement of the fatty acyl moiety over a hydrophobic, methionine-rich surface [J].Journal of Molecular Biology, 2007, 367(4):1145-1161.
[16] Frisch Mj, Gw Trucks, Hb Schlegel, Ge Scuseria, Ma Robb, Jr Cheeseman, JaMontgomery Jr, T. Vreven, Kn Kudin, Jc Burant. Gaussian 03, Rev. C. 02. Gaussian[J]. Inc., Wallingford, CT, 2004.
[17] Cammi R., B. Mennucci, J. Tomasi. Second-order M ller-Plesset analyticalderivatives for the polarizable continuum model using the relaxed density approach [J].The Journal of Physical Chemistry A, 1999, 103(45):9100-9108.
[18] Cammi R., B. Mennucci, J. Tomasi. An attempt to bridge the gap betweencomputation and experiment for nonlinear optical properties: macroscopicsusceptibilities in solution [J]. The Journal of Physical Chemistry A, 2000,104(20):4690-4698.
[19] Cossi M., N. Rega, G. Scalmani, V. Barone. Polarizable dielectric model of solvationwith inclusion of charge penetration effects [J]. The Journal of chemical physics, 2001,114:5691.
[20] Cossi M., G. Scalmani, N. Rega, V. Barone. New developments in the polarizablecontinuum model for quantum mechanical and classical calculations on molecules insolution [J]. The Journal of chemical physics, 2002, 117:43.
[21] Chen S.L., W.H. Fang, F. Himo. Theoretical study of the phosphotriesterase reactionmechanism [J]. The Journal of Physical Chemistry B, 2007, 111(6):1253-1255.
[22] Sevastik R., F. Himo. Quantum chemical modeling of enzymatic reactions: The caseof 4-oxalocrotonate tautomerase [J]. Bioorganic chemistry, 2007, 35(6):444-457.
[23] Hopmann K.H., J.D. Guo, F. Himo. Theoretical investigation of the first-shellmechanism of nitrile hydratase [J]. Inorganic chemistry, 2007, 46(12):4850-4856.
[24] Tanner M.E. Understanding nature's strategies for enzyme-catalyzed racemization andepimerization [J]. Accounts of chemical research, 2002, 35(4):237-246.
[25] Benning M.M., H. Shim, F.M. Raushel, H.M. Holden. High resolution X-raystructures of different metal-substituted forms of phosphotriesterase fromPseudomonas diminuta [J]. Biochemistry, 2001, 40(9):2712-2722.
[26] Georgieva P., F. Himo. Density functional theory study of the reaction mechanism ofthe DNA repairing enzyme alkylguanine alkyltransferase [J]. Chemical PhysicsLetters, 2008, 463(1-3):214-218.
[1] Armstrong R.N. Glutathione S-transferases: reaction mechanism, structure, andfunction [J]. Chemical research in toxicology, 1991, 4(2):131-140.
[2] Liu S., P. Zhang, X. Ji, Ww Johnson, Gl Gilliland, Rn Armstrong. Contribution oftyrosine 6 to the catalytic mechanism of isoenzyme 3-3 of glutathione S-transferase[J]. Journal of Biological Chemistry, 1992, 267(7):4296-4299.
[3] Graminski G.F., Y. Kubo, R.N. Armstrong. Spectroscopic and kinetic evidence for thethiolate anion of glutathione at the active site of glutathione S-transferase [J].Biochemistry, 1989, 28(8):3562-3568.
[4] Josephy P.D., B. Mannervik. Molecular toxicology [M]. Oxford University Press, USA.2006.
[5] Josephy Pd, B. Mannervik. Glutathione transferases [J]. Molecular Toxicology,2006:333-364.
[6] Mcilwain Cc, Dm Townsend, Kd Tew. Glutathione S-transferase polymorphisms:cancer incidence and therapy [J]. Oncogene, 2006, 25(11):1639-1648.
[7] Moyer A.M., O.E. Salavaggione, S.J. Hebbring, I. Moon, M.A.T. Hildebrandt, B.W.Eckloff, D.J. Schaid, E.D. Wieben, R.M. Weinshilboum. Glutathione S-transferase T1and M1: gene sequence variation and functional genomics [J]. Clinical CancerResearch, 2007, 13(23):7207-7216.
[8] Dourado D.F.A.R., P.A. Fernandes, M.J. Ramos. Mammalian cytosolic glutathionetransferases [J]. Current Protein and Peptide Science, 2008, 9(4):325-337.
[9] Dourado D.F.A.R., P.A. Fernandes, M.J. Ramos. Glutathione transferase A1-1: catalyticrole of water [J]. Theoretical Chemistry Accounts: Theory, Computation, andModeling (Theoretica Chimica Acta), 2009, 124(1):71-83.
[10] Habig W.H., M.J. Pabst, W.B. Jakoby. Glutathione S-transferases the first enzymaticstep in mercapturic acid formation [J]. Journal of Biological Chemistry, 1974,249(22):7130-7139.
[11] Armstrong R.N. Structure, catalytic mechanism, and evolution of the glutathionetransferases [J]. Chemical research in toxicology, 1997, 10(1):2-18.
[12] Sheehan D., G. Meade, V.M. Foley, C.A. Dowd. Structure, function and evolution ofglutathione transferases: implications for classification of non-mammalian membersof an ancient enzyme superfamily [J]. Biochemical Journal, 2001, 360(Pt 1):1.
[13] Di Ilio C., A. Aceto, R. Piccolomini, N. Allocati, A. Faraone, L. Cellini, G. Ravagnan,G. Federici. Purification and characterization of three forms of glutathione transferasefrom Proteus mirabilis [J]. Biochemical Journal, 1988, 255(3):971.
[14] Allocati N., L. Federici, M. Masulli, C. Di Ilio. Glutathione transferases in bacteria [J].FEBS Journal, 2009, 276(1):58-75.
[15] Dirr H., P. Reinemer, R. Huber. X‐ray crystal structures of cytosolic glutathioneS‐transferases [J]. European Journal of Biochemistry, 1994, 220(3):645-661.
[16] Ma X.X., Y.L. Jiang, Y.X. He, R. Bao, Y. Chen, C.Z. Zhou. Structures of yeastglutathione-S-transferase Gtt2 reveal a new catalytic type of GST family [J]. EMBOreports, 2009, 10(12):1320-1326.
[17] Adang Ae, J. Brussee, A. Van Der Gen, Gj Mulder. The glutathione-binding site inglutathione S-transferases. Investigation of the cysteinyl, glycyl and gamma-glutamyldomains [J]. Biochemical Journal, 1990, 269(1):47.
[18] Gustafsson A., P.L. Pettersson, L. Grehn, P. Jemth, B. Mannervik. Role of theglutamylα-carboxylate of the substrate glutathione in the catalytic mechanism ofhuman glutathione transferase A1-1 [J]. Biochemistry, 2001, 40(51):15835-15845.
[19] Caccuri A.M., M.L. Bello, M. Nuccetelli, M. Nicotra, P. Rossi, G. Antonini, G.Federici, G. Ricci. Proton release upon glutathione binding to glutathione transferaseP1-1: kinetic analysis of a multistep glutathione binding process [J]. Biochemistry,1998, 37(9):3028-3034.
[20] Párraga A., I. García-Sáez, S.B. Walsh, T.J. Mantle, M. Coll. The three-dimensionalstructure of a class-Pi glutathione S-transferase complexed with glutathione: theactive-site hydration provides insights into the reaction mechanism [J]. BiochemicalJournal, 1998, 333(Pt 3):811.
[21] Dourado D.F.A.R., P.A. Fernandes, B. Mannervik, M.J. Ramos. Glutathionetransferase: new model for glutathione activation [J]. Chemistry-A European Journal,2008, 14(31):9591-9598.
[22] Dourado D.F.A.R., P.A. Fernandes, B. Mannervik, M.J. Ramos. Glutathionetransferase A1-1: catalytic importance of arginine 15 [J]. The Journal of PhysicalChemistry B, 2010, 114(4):1690-1697.
[23] Dourado D.F.A.R., P.A. Fernandes, M.J. Ramos. Glutathione Transferase ClassesAlpha, Pi, and Mu: GSH Activation Mechanism [J]. The Journal of PhysicalChemistry B, 2010.
[24] Frisch M.J., Gw Trucks, Hb Schlegel, Ge Scuseria, Ma Robb, Jr Cheeseman, JaMontgomery Jr, T. Vreven, Kn Kudin, Jc Burant. Gaussian 03, revision B. 04 [J].Gaussian: Pittsburgh, PA, 2003.
[25] Li L., X. Lin, Z. Li. Hydroxylation Reaction Mechanism for Nitrosodimethylamine byOxygen Atom [J].
[26] Liu Y., H. Dong, H. Zhang, G. Wang, Z. Li, H. Chen. Prediction of RNA SecondaryStructure Based on Particle Swarm Optimization [J]. Chem. Res. Chinese Universities,2011, 27(1):108-112.
[27] Cammi R., B. Mennucci, J. Tomasi. Second-order M ller-Plesset analyticalderivatives for the polarizable continuum model using the relaxed density approach [J].The Journal of Physical Chemistry A, 1999, 103(45):9100-9108.
[28] Cossi M., V. Barone. Time-dependent density functional theory for molecules in liquidsolutions [J]. The Journal of chemical physics, 2001, 115:4708.
[29] Gonzalez C., H.B. Schlegel. An improved algorithm for reaction path following [J].The Journal of chemical physics, 1989, 90:2154.
[30] Gonzalez C., H.B. Schlegel. Reaction path following in mass-weighted internalcoordinates [J]. Journal of Physical Chemistry, 1990, 94(14):5523-5527.
[31] Chen S.L., W.H. Fang, F. Himo. Theoretical study of the phosphotriesterase reactionmechanism [J]. The Journal of Physical Chemistry B, 2007, 111(6):1253-1255.
[32] Sevastik R., F. Himo. Quantum chemical modeling of enzymatic reactions: The caseof 4-oxalocrotonate tautomerase [J]. Bioorganic chemistry, 2007, 35(6):444-457.
[33] Zhao Y., R. Hou, H. Zhang, Q. Zheng, C. Sun. Insight into Reaction Mechanism ofSirtuins via Molecular Simulation and Density Functional Theory Study [J].高等学校化学研究:英文版, 2010(005):833-837.
[34] Georgieva P., F. Himo. Density functional theory study of the reaction mechanism ofthe DNA repairing enzyme alkylguanine alkyltransferase [J]. Chemical PhysicsLetters, 2008, 463(1-3):214-218.
[35] Hopmann K.H., F. Himo. Theoretical study of the full reaction mechanism of humansoluble epoxide hydrolase [J]. Chemistry-A European Journal, 2006,12(26):6898-6909.
[36] Hu C.H., T. Brinck, K. Hult. Ab initio and density functional theory studies of thecatalytic mechanism for ester hydrolysis in serine hydrolases [J]. International journalof quantum chemistry, 1998, 69(1):89-103.
[37] Yao Y., Z. Li. Inhibition Mechanism of Cholinesterases by Carbamate: A TheoreticalStudy [J]. Chemical Research in Chinese Universities, 2008, 24(6):778-781.
[38] Bowman A.L., L. Ridder, I.M.C.M. Rietjens, J. Vervoort, A.J. Mulholland. Moleculardeterminants of xenobiotic metabolism: QM/MM simulation of the conversion of1-chloro-2, 4-dinitrobenzene catalyzed by M1-1 glutathione S-transferase [J].Biochemistry, 2007, 46(21):6353-6363.