Modification of Cyclodextrins for Use as Artificial Enzymes

The magical powers of enzymes have been attributed to their ability to bind specific substrates and catalyze reactions of the bound substrate. Artificial enzymes synthetically mimic the binding and the catalytic site to produce molecules that are not only smaller in size but also potentially have similar activity to the real enzymes. The main objective of our research is to create artificial redox enzymes by using cyclodextrins as binding sites and attaching flavin derivatives as the catalytic site. We have developed a strategy to attach a catalytic site to cyclodextrin exclusively at the 2-, 3- or the 6-position. The evaluation of the artificial enzyme in which flavin is attached to the 2-position gives a 647-fold acceleration factor. Although this is modest compared to those of real enzymes (which can have acceleration factors of a trillion), the artificial enzymes allow us to understand the elements that contribute to the incredible catalytic power of enzymes.     

纳米通道内酶组装及其催化反应研究进展

研究酶的组装和催化反应不仅有利于探索生命活动的本质,同时对开发酶在工业合成、分析检测、疾病治疗等领域的实际应用价值具有重要的指导意义. 研究发现,酶的有效固定和有序组装是保持酶活性、酶促反应的稳定性和对酶催化过程进行控制的重要途径,而在纳米通道内进行单酶或多酶的有序组装,利用纳米通道的限域效应可有效保持酶的构型进而提高酶催化反应的选择性和催化效率,增强酶级联反应的动力学进程. 本文概述了近年来基于纳米通道的酶反应器在生物传感领域的研究进展,着重描述纳米通道限域空腔内酶的组装方法、酶催化反应及其动力学机制,并展望了基于纳米通道的酶反应器的应用前景.     

Bioelectrochemical application of some PQQ-dependent enzymes.

This paper focuses on the use of PQQ-dependent enzymes (PQQ enzymes) in amperometrical biosensors and gives emphasis on their innovative designs and applications. The study covers some aspects in the evolution of biosensors based on PQQ enzymes. Main attention is focused on the electrochemical properties of PQQ enzymes as very promising materials for the formation of electrochemical biosensors. Immobilization approaches and redox mediators recently used in PQQ enzymes based biosensors are reviewed. The acceptance of polypyrrole as a very promising immobilization matrix for some PQQ enzymes is discussed.     

基于液相色谱-质谱联用的肝微粒体中药物代谢酶定量方法研究进展

肝微粒体中的药物代谢酶是参与药物代谢的主要酶类,不管是合成药物,还是组成复杂的中药,主要经过肝脏中药物代谢酶的代谢转化成易于排泄的化合物。由于药物代谢酶的表达水平具有较大的个体差异性,因此,药物代谢酶的准确定量对药物的药理、药物相互作用和临床应用具有重要意义。本文综述了近十年来药物代谢酶定量方法的研究进展。     

Recycle of the cellulase— enzyme complex after hydrolysis of steam-exploded wood

Cellulases can be recovered in high yields by contacting fresh substrate with hydrolysis filtrate and by extraction of spent hydrolysis residue with pH 7 buffer. Recycled enzymes give hydrolysis rates about equal to those with fresh enzymes. Steam-exploded wood (SEW) is washed with water to remove sugars and byproducts from breakdown of hemicellulose, and recycle of enzymes proceeds better if lignin is also removed prior to hydrolysis. Oven drying of SEW interferes with recycle, and the recovery of enzymes is only one-half of that with SEW that is kept moist. Effectiveness of enzyme recovery depends on the completeness of hydrolysis, as determined by contact time and enzyme concentration. For cost-effective operation, enzyme should not be recovered until appreciable filter paper activity and carboxylmethylcellulase activity appear in the hydrolysate.     

Evolutionary relationship and application of a superfamily of cyclic amidohydrolase enzymes

Cyclic amidohydrolases belong to a superfamily of enzymes that catalyze the hydrolysis of cyclic C-N bonds. They are commonly found in nucleotide metabolism of purine and pyrimidine. These enzymes share similar catalytic mechanisms and show considerable structural homologies, suggesting that they might have evolved from a common ancestral protein. Homology searches based on common mechanistic properties and three-dimensional protein structures provide clues to the evolutionary relationships of these enzymes. Among the superfamily of enzymes, hydantoinase has been highlighted by its potential for biotechnological applications in the production of unnatural amino acids. The enzymatic process for the production of optically pure amino acids consists of three enzyme steps: hydantoin racemase, hydantoinase, and N-carbamoylase. For efficient industrial application, some critical catalytic properties such as thermostability, catalytic activity, enantioselectivity, and substrate specificity require further improvement. To this end, isolation of new enzymes with desirable properties from natural sources and the optimization of enzymatic processes were attempted. A combination of directed evolution techniques and rational design approaches has made brilliant progress in the redesign of industrially important catalytic enzymes; this approach is likely to be widely applied to the creation of designer enzymes with desirable catalytic properties.     

Simultaneous immobilization of glucose oxidase and peroxidase to urea derivative of regenerated acetylcellulose granules

A method for simultaneous covalent immobilization of glucose oxidase and peroxidase with previously oxidized carbohydrate residues to urea derivative of regenerated acetylcellulose granules is described. The effect of immobilization on the catalytic properties of the separately immobilized enzymes are studied. The immobilized enzymes manifested no change in their pH and temperature optima and slight increase ofK _m x compared to data for the soluble enzymes. A column packed with simultaneously immobilized enzymes is used for manual glucose determination in blood sera. The results are in high correlation with those obtained by the Beckman Glucose Analyzer method (r = 0.976). The method is economic (the enzyme-carrier conjugate may be used more than 300 times), easy to perform, and less time consuming than the manual methods utilizing soluble enzymes. The established manual method can be proposed for emergency clinical analysis and smaller clinical laboratories.     

溶胶-凝胶固定化多酶催化二氧化碳转化为甲醇反应初探

 为了探索温室气体CO2的固定和利用的新途径，以正硅酸乙酯为\r\n前驱体，用改进的溶胶－凝胶法对甲酸脱氢酶、甲醛脱氢酶和乙醇脱氢\r\n酶进行了包埋共固定化，并以包埋的三种酶为催化剂，以还原型烟酰胺\r\n腺嘌呤二核苷酸（NADH）为电子供体，在低温低压下将CO2转化为甲醇\r\n．初步研究了反应温度、pH值、酶含量及NADH用量对甲醇收率的影响．\r\n实验结果表明，在37℃和pH7．0的条件下，甲醇的收率可达92．4％．\r\n由于酶空间构型的微小变化和空间位阻效应的存在，与液相酶反应结果\r\n相比，包埋后的酶活性略有降低．     

Broad-spectrum peptide inhibitors of aminoglycoside antibiotic resistance enzymes

The action of aminoglycoside antibiotics is inhibited by chemical modification catalyzed by aminoglycoside inactivating enzymes, which bind these cationic saccharides with active site pockets that contain a preponderance of negatively charged residues. In this study, it was observed that several cationic antimicrobial peptides, representing different structural classes, could serve as inhibitors of such aminoglycoside resistance enzymes. The bovine antimicrobial peptide indolicidin and synthetic analogs appeared to be especially effective against a range of resistance enzymes, inhibiting enzymes belonging to both aminoglycoside phosphotransferase and aminoglycoside acetyltransferase classes, where the mode of action was dependent on the class of antibiotic resistance enzyme. These peptides represent the first example of broad-spectrum inhibitors of aminoglycoside resistance enzymes.     

人工模拟酶的研究与应用进展

人工模拟酶具有性质稳定、易于制备、环境耐受性强等优点,在某种程度上解决了天然酶易失活、难制备的缺点。本文按照人工模拟酶的分类,综述对比了传统模拟酶与纳米材料模拟酶的研究现状,对人工模拟酶优缺点进行总结分析,并对其应用前景进行了展望。     

Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes

The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular interaction networks. Interestingly, the current data suggest that a family-centered point of view is necessary in the comparative analyses of cold- and warm-adapted enzymes. In fact, enzymes belonging to the same family or superfamily, thus sharing at least the three-dimensional fold and common features of the functional sites, have evolved similar structural and dynamic patterns to overcome the detrimental effects of low temperatures.     

Stereochemistry of reactions of the inhibitor/substrates L- and D-beta-chloroalanine with beta-mercaptoethanol catalysed by L-aspartate aminotransferase and D-amino acid aminotransferase respectively

Two members of the alpha-family of PLP-dependent enzymes, L-aspartate aminotransferase and D-amino acid aminotransferase, have been shown to catalyse beta-substitution of L- and D-beta-chloroalanine respectively with beta-mercaptoethanol, reactions typical of the beta-family of PLP-dependent enzymes. The reaction catalysed by L-aspartate aminotransferase has been shown to occur with retention of stereochemistry, a typical outcome for reactions catalysed by beta-family enzymes. There are also indications that the reaction catalysed by D-amino acid aminotransferase may involve retention of stereochemistry. Both enzymes have been shown to catalyse exchange at C-3 when the appropriate enantiomer of beta-chloroalanine is the substrate.     

The Application of Ultrasound in the Enzymatic Hydrolysis of Switchgrass

In a series of experiments, untreated and ammonium hydroxide pretreated Klenow lowland variety switchgrasses are converted to reducing sugars using low-frequency (20 kHz) ultrasound and commercially available cellulase enzyme. Results from experiments using untreated and pretreated switchgrasses with and without ultrasound are presented and discussed. In untreated switchgrass experiments, the combination of ultrasound and enzymes resulted in an increase of 7.5% in reducing sugars compared to experiments using just enzymes. In experiments using ammonium hydroxide pretreated switchgrass, the combination of ultrasound and enzymes resulted in an increase of 9.3% in reducing sugars compared to experiments using just enzymes. Experimental evidence indicates that there is a synergistic effect from the combination of ultrasound and enzymes which lowers the diffusion-limiting barrier to enzyme/substrate binding and results in an increase in reaction rate. Scanning electron microscopic images provide evidence that ultrasound-induced pitting increases substrate surface area and affects reaction rate and yield.     

保留型与反转型β-木糖苷酶活性位点的分子动力学模拟

木聚糖是潜在的重要可再生能源, 如何提高其降解效率已成为近年来的研究热点. β-木糖苷酶是木聚糖降解过程中的关键酶之一, 按其水解机制可分为保留型与反转型酶. 目前虽然对于这两种催化机制的研究不断深入, 但很少有工作从溶液环境的角度出发探究它们的差异. 本文采用分子动力学模拟方法, 对4 个典型的β-木糖苷酶进行了显式溶剂模拟研究, 详细分析了酶的催化氨基酸间的距离和质子供体氨基酸pK_a值的动态变化. 结果显示, 反转型酶催化氨基酸间的距离约为0.8-1.0 nm, 大于保留型的0.5-0.6 nm, 与先前对糖苷酶晶体结构的统计分析结果一致. 令人意外的是, 保留型酶的质子供体通过与其附近组氨酸的相互作用, 其pK_a在两个不同的高、低值之间交替变换, 使保留型酶的双取代反应得以发生; 而反转型酶的质子供体则由附近的天冬氨酸调节, 其pK_a稳定在某个较高值, 这可能有利于其在反应pH值下获得水溶液中的氢离子, 进行反转型酶特有的单取代反应. 因此, 本工作加深了人们对β-木糖苷酶保留型与反转型水解机制的认识, 并为后续酶的理性改造与高效利用提供具有指导价值的结构与机理信息.     

Understanding enzyme catalysis by means of supramolecular artificial enzymes

Enzymes are biomacromolecules responsible for the abundant chemical biotransformations that sustain life. Recently, biochemists have discovered that multiple conformations and numerous parallel paths are involved during the processes catalyzed by enzymes. It is plausible that the entire macromolecular scaffold is involved in catalysis via cooperative motions that result in incredible catalytic efficiency. Moreover, some enzymes can very strongly bind the transition state with an association constant of up to 1024 M-1, suggesting that covalent bond formation is a possible process during the conversion of the transition state in enzyme catalysis, in addition to the concatenation of noncovalent interactions. Supramolecular chemistry provides fundamental knowledge about the relationships between the dynamic structures and functions of organized molecules. By tak-ing advantage of supramolecular concepts, numerous supramolecular enzyme mimics with complex and hierarchical structures have been designed and investigated. Through the study of supramolecular enzyme models, a great deal of information to aid our understanding of the mechanism of catalysis by natural enzymes has been acquired. With the development of supramolec-ular artificial enzymes, it is possible to replicate the features of natural enzymes with regards to their constitutional complexity and cooperative motions, and eventually decipher the conformation-based catalytic mystery of natural enzymes.     

Enzyme active sites: bioinformatics,architecture, and mechanisms of action

A comparative analysis of the amino acid sequences of some enzymes which comprise superfamilies of enzymes belonging to different classes was carried out. Based on the amino acid sequence alignment for enzymes belonging to different classes with the use of the information entropy as a criterion, the amino acid residues involved in the catalytic portion of the active site are demonstrated to be most conservative. The rating scale for conservativeness of amino acids in enzymes is created. Glycine and aspartic acid are the most commonly occurring conservative amino acids essential for the catalysis. The role of aspartic acid and histidine in the mechanism of molecule activation in the catalytic site is considered using hydrolases as examples. The role of glycine, proline, and cysteine in the structural organization of the active sites is discussed.     

Catalytic Diversity of GH30 Xylanases

Catalytic properties of GH30 xylanases belonging to subfamilies 7 and 8 were compared on glucuronoxylan, modified glucuronoxylans, arabinoxylan, rhodymenan, and xylotetraose. Most of the tested bacterial GH30-8 enzymes are specific glucuronoxylanases (EC 3.2.1.136) requiring for action the presence of free carboxyl group of MeGlcA side residues. These enzymes were not active on arabinoxylan, rhodymenan and xylotetraose, and conversion of MeGlcA to its methyl ester or its reduction to MeGlc led to a remarkable drop in their specific activity. However, some GH30-8 members are nonspecific xylanases effectively hydrolyzing all tested substrates. In terms of catalytic activities, the GH30-7 subfamily is much more diverse. In addition to specific glucuronoxylanases, the GH30-7 subfamily contains nonspecific endoxylanases and predominantly exo-acting enzymes. The activity of GH30-7 specific glucuronoxylanases also depend on the presence of the MeGlcA carboxyl, but not so strictly as in bacterial enzymes. The modification of the carboxyl group of glucuronoxylan had only weak effect on the action of predominantly exo-acting enzymes, as well as nonspecific xylanases. Rhodymenan and xylotetraose were the best substrates for exo-acting enzymes, while arabinoxylan represented hardly degradable substrate for almost all tested GH30-7 enzymes. The results expand current knowledge on the catalytic properties of this relatively novel group of xylanases.     

Application of centrifugal precipitation chromatography and high-speed counter-current chromatography equipped with a spiral tubing support rotor for the isolation and partial characterization of carotenoid cleavage-like enzymes in Enteromorpha compressa (L.) Nees

Centrifugal precipitation chromatography and a high-speed counter-current chromatography system equipped with a spiral tubing support rotor (spHSCCC) were successfully applied for the identification and isolation of carotenoid cleavage-like enzymes from Enteromorpha compressa (L.) Nees. This is the first study separating active enzymes from a complex natural matrix by spHSCCC. The target enzymes were identified after fractionation of the proteins in an acetone Tris-buffer gradient by centrifugal precipitation chromatography. Also, an aqueous two-phase solvent system consisting of PEG 1000 and mono- and dibasic potassium phosphate was used for the isolation of the enzymes by spHSCCC. The purified fractions contained two proteins of 65 and 72 kDa, respectively. The enzymes could cleave β-carotene and β-apo-8'-carotenal to produce β-ionone.     

Enzyme-based biocatalysis for the treatment of organic pollutants and bioenergy production

Enzyme-based biocatalysis is emerging as an advanced technique to develop green processes that help to maintain the sustainability of the environment. The bioremediation of toxic organic pollutants and waste to bioenergy production using enzymes as biocatalysts is rapidly growing due to its eco-friendly and sustainable nature. Additionally, a range of microbial species that typically grow on organic wastes can be used to produce these enzymes in an efficient manner. This is seen as a potential strategy for the development of cost-effective manufacturing for a number of biotechnological applications. The present study discusses biocatalysis as a promising and sustainable method toward the bioremediation of hazardous organic pollutants as well as for bioenergy production, based on the immense potential of enzymes as biocatalysts. Emphasis has been placed on evaluating the critical elements that can enhance the production of enzymes used as biocatalysts, as well as their functional effectiveness and stability.     

Application of high-performance liquid chromatography to the study of biogenic amine-related enzymes

The application of high-performance liquid chromatography to the study of biogenic amine-related enzymes is reviewed. Biogenic amines include catecholamines (dopamine, norepinephrine and epinephrine), indoleamines (serotonin and melatonin), imidazoleamines (histamine), polyamines (putrescine, spermidine and spermine) and acetylcholine. Three particular aspects are covered. The first aspect is the assay of enzyme activities of biogenic amine-related enzymes, such as tyrosine hydroxylase, tryptophan hydroxylase, aromatic L-amino acid decarboxylase, dopamine beta-hydroxylase and phenylethanolamine N-methyltransferase. The introduction of highly sensitive assays of biogenic amines with electrochemical detection or fluorescence detection have made possible the non-isotopic assay of these activities, replacing the previously used radioisotopic methods. The second aspect is the purification of these enzymes. Since biogenic amine-synthesizing enzymes are generally unstable, rapid and efficient purification of these enzymes is very useful. The third aspect is the assay of biogenic amines (for example, acetylcholine and polyamines) using post-column derivatization with biogenic amine oxidases and electrochemical detection.