植物体系中甲酯酶的底物专一性的理论研究（英文）

酶对天然底物的高度专一性是酶的特点之一.然而关于酶是如何对底物具有高度专一性以及识别能力,我们的理解仍然缺乏.本文以植物体系中发现的一组甲酯酶(MESs)对一些底物[包括水杨酸甲酯(Me SA),茉莉酮酸甲酯(Me JA)和吲哚-3-乙酸甲酯(Me IAA)]的催化反应为例,报道了同源建模和理论计算对茉莉酮酸甲酯酶(At MES10)和水杨酸结合蛋白2(SABP2)的研究结果.基于简单的锁-钥匙理论(底物与酶结合时不发生基团的碰撞或严重排斥),以底物对接到酶的活性部位(即底物中—COO的一部分占据可被催化丝氨酸亲核进攻的位置)为原则,可以在空间上为酶对底物的专一性提供解释.模拟结果表明,SABP2可对Me SA有高活性,对Me JA和Me IAA有低或无活性;At MES10可对Me JA有高活性,而对Me SA和Me IAA有低或无活性,这与实验结果相一致.因此,相关酶的结构预测与计算机模拟对了解酶的底物专一性具有重要的意义.     

茉莉酮酸甲酯类似物的新方法

茉莉酮酸甲酯是茉莉花的主香成份。本文报道了另一类茉莉酮酸甲酯的类似物2-烃基-3-氧-环戊基-乙酸甲酯, 2-亚苄基-3-氧-环戊基-乙酸甲酯, 和2-(1-羟基-戊基)-3-氧-环戊基-乙酸甲酯, 及其合成的新方法。     

简法合成二氢茉莉酮酸甲酯和二氢新茉莉酮酸甲酯

以环戊二烯为原料,先合成了环戊-2-烯酮(1),(1)经过Michael加成反应得到3-酮-环戊基乙酸甲酯(4)。再经过Aldol缩合反应和催化氢化,得到二氢茉莉酮酸甲酯和二氢新茉莉酮酸甲酯。     

二氢茉莉酮酸甲酯的简便合成方法

本文报道二氢茉莉酮酸甲酯的简便合成方法。先由丁二酸和庚酰氯反应得到2-戊基-1,3-环戊二酮(1),再用甲醇醚化1,可得到2-戊基-3-甲氧基-环戊-2-烯酮(2)。2与丙二酸二甲酯反应生成(2-戊基-3-酮-1-环戊烯-)基乙酸甲酮(3)。最后,催化氢化3,便可得到二氢茉莉酮酸甲酯(4)。     

羊肝源穿山龙薯蓣皂苷-α-L-鼠李糖苷酶的分离及其动力学特性

对羊肝中含有的水解穿山龙薯蓣皂苷鼠李糖糖基的穿山龙薯蓣皂苷-α-L-鼠李糖苷酶进行了分离、纯化, 并对其动力学特性进行了研究. 结果表明, 粗酶液经DEAE-Cellulose离子交换层析柱纯化后, 其比活提高了19.9倍. 在pH＝6.8、反应温度为42 ℃、反应时间为8 h和底物浓度为23 mmol/L的条件下, 该酶达到其最高活力. 在10—200 mmol/L范围内, Fe3+和Cu2+对酶活力有明显的抑制作用, Mg2+和Zn2+对酶活力有微弱的激活作用, 而Ca2+对酶有较强的激活作用. 采用SDS-PAGE方法测得酶蛋白分子量为71000. 选择穿山龙薯蓣皂苷、人参皂苷Re和芦丁为酶反应底物, 进行酶的底物专一性研究发现, 穿山龙薯蓣皂苷-α-L-鼠李糖苷酶对其底物具有高度专一性.     

促进非水相酶反应的研究进展

198 6年 klibanov[1] 发现 ,许多酶可以在有机相中进行有效的催化 ,而且有些酶在有机相中的活性和稳定性比在水相中还高 .随后十几年 ,对非水相酶反应的研究取得了突破性的进展 ,而且还实现了一些非水相酶反应在工业生产方面的应用 (如油脂改良等 ) .与水相中的酶反应相比 ,非水相中的酶反应有它独特的优越性 ,尤其是在有机合成方面 .主要表现在 :有利于疏水性物质的反应 ;可改变反应的平衡方向 ;可催化水相中不能进行的反应 ;可以控制底物专一性 ;可提高酶的稳定性 ;便于消除底物和产物的抑制作用 ;酶和产物易于回收 ;可减少微生物的污染 .…     

二氢新茉莉酮酸甲酯和二氢茉莉酮酸甲酯的合成

本文报道了二氢茉莉酮酸甲酯(1)和二氢新茉莉酮酸甲酯(2)的新合成路线.以丙二酸二乙酯为原料,依次与溴代戊烷和烯丙基溴进行烷基化反应,得到α-戊基-α-烯丙基-丙二酸二乙酯(5),5经过水解、脱羧得到γ-烯酸3.酰氯化合物6进行Friedel-Crafts反应得到2-戊基-环戊4-烯-1-酮(7),7通过Michael加成、水解、脱羧和酯化,得到2,总产率为24.4％.7可以异构化为2-戊基-环戊-2-烯-1-酮(9),9用通常的方法合成了1.1和2可以明显地从核磁共振谱、红外光谱和气相色谱识别.     

二氢新茉莉酮酸甲酯和二氢茉莉铜酸甲酯的合成

本文报道了二氢茉莉酮酸甲酯(1)和二氢新茉莉酮酸甲酯(2)的新合成路线,以丙二酸二乙酯为原料,依次与溴代戊烷和烯丙基溴进行烷基化反应,得到α-戊基-α-烯丙基-丙二酸二乙酯(5),5经过水解、脱羧得到γ-烯酸3.酰氯化合物6进行Friendel-Crafts反应得到2-戊基-环戊-4-烯-1-酮(7),7通过Michael加成、水解、脱羧和酯化,得到2,总产率为24.4%.7可以异构化为2-戊基-环戊-2-烯-1-酮(9),9用通常的方法合成了1.1和2可以明显地从核磁共振谱、红外光谱和气相色谱识别。     

基于离子液体共溶剂效应的氯过氧化物酶催化氧化邻苯二胺的研究

通过缓冲液-离子液体混合溶剂中氯过氧化物酶(CPO)催化氧化邻苯二胺(OPD)的产物结构和性能的表征,证实此酶促反应的产物为2,3-二氨基吩嗪(DAP);OPD-H2O2-CPO反应体系有望用于荧光酶联免疫分析;酶动力学分析表明以咪唑类离子液体(ILS)为共溶剂时,CPO对底物的亲和力及对底物识别的专一性都得以改善,从而有效提高了产物收率;酶促反应主要受CPO的稳定性及酶的用量等因素控制.在最佳条件下,产率可达81.16%.     

以透明质酸为骨架的新型谷胱甘肽过氧化物酶(GPX)模拟酶的制备及性质研究

用修饰法合成以透明质酸为骨架的两种新型GPX模拟酶: 硒化透明质酸SeHA及碲化透明质酸TeHA. 用红外光谱和核磁共振波谱对模拟酶的结构进行研究, 证明其修饰位点位于透明质酸的N-乙酰氨基葡萄糖的—CH2OH. 用二硫代双硝基苯甲酸(DTNB)法测定模拟酶的硒含量为1.2%. 通过模拟酶对3种不同底物过氧化氢(H2O2)、过氧化氢正丁烷(t-BuOOH)和过氧化氢异丙苯(CuOOH)的催化活性的研究结果表明CuOOH为该反应的最佳底物. 研究模拟酶催化谷胱甘肽(GSH)还原3种过氧化物的动力学发现, 反应速率与底物浓度的双倒数曲线均为平行的直线, 说明模拟酶反应的动力学机制与天然GPX相同, 为乒乓机制. 用2,4-二叔丁基甲基苯酚(BHT)法证明了该催化反应为非自由基机理, 且模拟酶不易被碘乙酸抑制.     

Alpha/Beta-hydrolase fold enzymes: structures,functions and mechanisms

The alpha/beta-hydrolase fold family of enzymes is rapidly becoming one of the largest group of structurally related enzymes with diverse catalytic functions. Members in this family include acetylcholinesterase, dienelactone hydrolase, lipase, thioesterase, serine carboxypeptidase, proline iminopeptidase, proline oligopeptidase, haloalkane dehalogenase, haloperoxidase, epoxide hydrolase, hydroxynitrile lyase and others. The enzymes all have a Nucleophile-His-Acid catalytic triad evolved to efficiently operate on substrates with different chemical composition or physicochemical properties and in various biological contexts. For example, acetylcholine esterase catalyzes the cleavage of the neurotransmitter acetylcholine, at a rate close to the limits of diffusion of substrate to the active site of the enzyme. Dienelactone hydrolase uses substrate-assisted catalysis to degrade aromatic compounds. Lipases act adsorbed at the water/lipid interface of their neutral water-insoluble ester substrates. Most lipases have their active site buried under secondary structure elements, a flap, which must change conformation to allow substrate to access the active site. Thioesterases are involved in a multitude of biochemical processes including bioluminiscence, fatty acid- and polyketide biosynthesis and metabolism. Serine carboxypeptidases recognize the negatively charged carboxylate terminus of their peptide substrates. Haloalkane dehalogenase is a detoxifying enzyme that converts halogenated aliphatics to the corresponding alcohols, while haloperoxidase catalyzes the halogenation of organic compounds. Hydroxynitrile lyase cleaves carbon-carbon bonds in cyanohydrins with concomitant hydrogen cyanide formation as a defense mechanism in plants. This paper gives an overview of catalytic activities reported for this family of enzymes by discussing selected examples. The current state of knowledge of the molecular basis for catalysis and substrate specificity is outlined. Relationships between active site anatomy, topology and conformational rearrangements in the protein molecule is discussed in the context of enzyme mechanism of action.     

Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active‐Site Residues

The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active‐site residues that contribute to their substrate specificity. Swapping such active‐site residues between the demethylases leads to partially switched demethylation activities. Combined evidence from X‐ray structures and enzyme kinetics suggests a role of the active‐site residues in substrate recognition. Such a divergent active‐site sequence may aid the design of selective inhibitors that can discriminate these homologue RNA/DNA demethylases.     

Focusing mutations into the P. fluorescens esterase binding site increases enantioselectivity more effectively than distant mutations

Rational design of enzymes with improved properties, such as enantioselectivity, usually focuses mutations within the substrate binding site. On the other hand, directed evolution of enzymes usually targets the entire protein and discovers beneficial mutations far from the substrate binding site. In this paper, we propose an explanation for this discrepancy and show that a combined approach--random mutagenesis within the substrate binding site--is better. To increase the enantioselectivity (E) of a Pseudomonas fluorescens esterase (PFE) toward methyl 3-bromo-2-methylpropionate, we focused mutagenesis into the substrate binding site at Trp28, Val121, Phe198, and Val225. Five of the catalytically active mutants (13%) showed better enantioselectivity than wild-type PFE. The increases in enantioselectivity were higher (up to 5-fold, reaching E = 61) than with mutants identified by random mutagenesis of the entire enzyme.     

Substrate binding in catechol oxidase activity: biomimetic approach

A series of dicopper(II) complexes have been investigated as model systems for the catechol oxidase active site enzyme, regarding the binding of catechol substrate in the first step of the catalytic cycle. The [Cu(2)(L(R))(mu-OH)](ClO(4))(2) and [Cu(2)(L(R))(H(2)O)(2)](ClO(4))(3) complexes are based on the L(R) ligands (2,6-bis[(bis(2-pyridylmethyl)amino)methyl]-4-R-substituted phenol) with -R = -OCH(3), -CH(3), or -F. Binding studies of diphenol substrates were investigated using UV-vis and EPR spectroscopy, electrochemistry, and (19)F NMR (fluorinated derivatives). All the complexes are able to bind two ortho-diphenol substrates (tetrachlorocatechol and 3,5-di-tert-butylcatechol). Two successive fixation steps, respectively fast and slower, were evidenced for the mu-OH complexes (the bis(aqua) complexes are inactive in catalysis) by stopped-flow measurement and (19)F NMR. From the mu-OH species, the 1:1 complex/substrate adduct is the catalytically active form. In relation with the substrate specificity observed in the enzyme, different substrate/inhibitor combinations were also examined. These studies enabled us to propose that ortho-diphenol binds monodentately one copper(II) center with the concomitant cleavage of the OH bridge. This hydroxo ligand appears to be a key factor to achieve the complete deprotonation of the catechol, leading to a bridging catecholate.     

Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach

A combined molecular dynamics simulation and multiple ligand docking approach is applied to study the binding specificity of acetylcholinesterase (AChE) with its natural substrate acetylcholine (ACh), a family of substrate analogues, and choline. Calculated docking energies are well correlated to experimental k(cat)/K(M) values, as well as to experimental binding affinities of a related series of TMTFA inhibitors. The "esteratic" and "anionic" subsites are found to act together to achieve substrate binding specificity. We find that the presence of ACh in the active site of AChE not only stabilizes the setup of the catalytic triad but also tightens both subsites to achieve better binding. The docking energy gained from this induced fit is 0.7 kcal/mol for ACh. For the binding of the substrate tailgroup to the anionic subsite, both the size and the positive charge of the tailgroup are important. The removal of the positive charge leads to a weaker binding of 1 kcal/mol loss in docking energy. Substituting each tail methyl group with hydrogen results in both an incremental loss in docking energy and also a decrease in the percentage of structures docked in the active site correctly set up for catalysis.     

How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations

A distinct protein lysine methyltransferase (PKMT) only transfers a certain number of methyl group(s) to its target lysine residue in spite of the fact that a lysine residue can be either mono-, di-, or tri-methylated. In order to elucidate how such a remarkable product specificity is achieved, we have carried out ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations on two SET-domain PKMTs: SET7/9 and Rubisco large subunit methyltransferase (LSMT). The results indicate that the methylation state specificity is mainly controlled by the methyl-transfer reaction step, and confirm that SET7/9 is a mono-methyltransferase while LSMT has both mono-and di-methylation activities. It is found that the binding of the methylated lysine substrate in the active site of SET7/ 9 opens up the cofactor AdoMet binding channel so that solvent water molecules get access to the active site. This disrupts the catalytic machinery of SET7/9 for the di-methylation reaction, which leads to a higher activation barrier, whereas for the LSMT, its active site is more spacious than that of SET7/9, so that the methylated lysine substrate can be accommodated without interfering with its catalytic power. These detailed insights take account of protein dynamics and are consistent with available experimental results as well as recent theoretical findings regarding the catalytic power of SET7/9.     

Mutations in distant residues moderately increase the enantioselectivity of Pseudomonas fluorescens esterase towards methyl 3bromo-2-methylpropanoate and ethyl 3phenylbutyrate

Directed evolution combined with saturation mutagenesis identified six different point mutations that each moderately increases the enantioselectivity of an esterase from Pseudomonas fluorescens (PFE) towards either of two chiral synthons. Directed evolution identified a Thr230Ile mutation that increased the enantioselectivity from 12 to 19 towards methyl (S)-3-bromo-2-methylpropanoate. Saturation mutagenesis at Thr230 identified another mutant, Thr230Pro, with higher-than-wild-type enantioselectivity (E=17). Previous directed evolution identified mutants Asp158Asn and Leu181Gln that increased the enantioselectivity from 3.5 to 5.8 and 6.6, respectively, towards ethyl (R)-3-phenylbutyrate. In this work, saturation mutagenesis identified other mutations that further increase the enantioselectivity to 12 (Asp158Leu) and 10 (Leu181Ser). A homology model of PFE indicates that all mutations lie outside the active site, 12-14 A from the substrate and suggests how the distant mutations might indirectly change the substrate-binding site. Since proteins contain many more residues far from the active site than close to the active site, random mutagenesis is strongly biased in favor of distant mutations. Directed evolution rarely screens all mutations, so it usually finds the distant mutations because they are more common, but probably not the most effective.     

Resolution of chiral phosphate, phosphonate, and phosphinate esters by an enantioselective enzyme library

An array of 16 enantiomeric pairs of chiral phosphate, phosphonate, and phosphinate esters was used to establish the breadth of the stereoselective discrimination inherent within the bacterial phosphotriesterase and 15 mutant enzymes. For each substrate, the leaving group was 4-hydroxyacetophenone while the other two groups attached to the phosphorus core consisted of an asymmetric mixture of methyl, methoxy, ethyl, ethoxy, isopropoxy, phenyl, phenoxy, cyclohexyl, and cyclohexoxy substituents. For the wild-type enzyme, the relative rates of hydrolysis for the two enantiomers ranged from 3 to 5.4 x 10(5). Various combinations of site-specific mutations within the active site were used to create modified enzymes with alterations in their enantioselective properties. For the single-site mutant enzyme, G60A, the stereoselectivity is enhanced relative to that of the wild-type enzyme by 1-3 orders of magnitude. Additional mutants were obtained where the stereoselectivity is inverted relative to the wild-type enzyme for 13 of the 16 pairs of enantiomers tested for this investigation. The most dramatic example was obtained for the hydrolysis of 4-acetylphenyl methyl phenyl phosphate. The G60A mutant preferentially hydrolyzes the SP-enantiomer by a factor of 3.7 x 10(5). The I106G/F132G/H257Y mutant preferentially hydrolyzes the RP-enantiomer by a factor of 9.7 x 10(2). This represents an enantioselective discrimination of 3.6 x 10(8) between these two mutants, with a total of only four amino acid changes. The rate differential between the two enantiomers for any given mutant enzyme is postulated to be governed by the degree of nonproductive binding within the enzyme active site and stabilization of the transition state. This hypothesis is supported by computational docking of the high-energy, pentavalent form of the substrates to modeled structures of the mutant enzyme; the energies of the docked transition-state analogues qualitatively capture the enantiomeric preferences of the various mutants for the different substrates. These results demonstrate that the catalytic properties of the wild-type phosphotriesterase can be exploited for the kinetic resolution of a wide range of phosphate, phosphonate, and phosphinate esters and that the active site of this enzyme is remarkably amenable to structural perturbations via amino acid substitution.     

The reaction mechanism of xanthine oxidase: evidence for two-electron chemistry rather than sequential one-electron steps

Current research on xanthine oxidase has favored a mechanism involving base-catalyzed proton abstraction from a Mo-OH group, allowing nucleophilic attack on the substrate and hydride transfer from the substrate to Mo=S group in the active site. During the course of this reaction mechanism, the molybdenum redox cycles from MoVI to MoIV, with reoxidation of the MoIV speices to form the EPR active MoV intermediate. However, it has also been suggested that the reaction occurs in two subsequent one-electron steps. We have determined kinetic parameters kred and kred/Kd for a variety of plausible substrates as well as the one-electron reduction potentials for these substrates. Our data indicate no correlation between these kinetic parameters and their one-electron reduction potentials, as would be expected if the enzyme were using two subsequent one-electron reduction steps. Our results provide additional support to current evidence for the favored two-electron reduction mechanism.     

A modular assembly strategy for improving the substrate specificity of small catalytic peptides

In contrast to large proteins, small peptide catalysts typically display limited specificity for small molecule substrates. This is presumably a result of the limited opportunities small peptides have to fold in a manner that provides for the formation of an isolated reaction vessel that effectively binds and sequesters substrates from bulk solvent while at the same time catalyzing their transformation. For the preparation of small peptide catalysts that possess improved substrate specificity, we have developed a modular assembly strategy that involves appending phage display-derived substrate binding-domain modules to catalytically active peptide domains. We demonstrate the potential of this strategy with the construction of a small 35-amino acid residue aldolase peptide with improved substrate specificity. The advantages of this approach are that it reduces the demand on the functionalization of the catalytic site and it is modular, therefore making its adaptation to a variety of specificities rapid. The modular assembly strategy studied here may present advantages over exhaustive searches of large random-sequence peptide libraries for peptides with singular function.