酶反应速率方程的普适形式

酶反应速率方程的普适形式是应用于相互关联的大规模代谢途径动力学建模的重要方法.把酶反应速率方程写成Michaelis-Menten-King-Altman方程形式可以使得动力学参数(或函数)容易与数据库中的实验数据相接轨,并可以处理任意数量的底物和产物,有利于大规模的计算.普适形式可以同时描述正、负反应方向,并能精确地用于准稳态条件.展示了在三类生物体系中广泛存在的酶反应机制中普适方程的严格推导过程,并讨论了普适方程的特点,针对不可逆反应酶反应产生的产物抑制效应可以自然消除,总结了在普适速率方程中体现调节剂的作用和协同作用.     

包埋法制备珠型固定化细胞

随着固定化酶技术的进步,固定化细胞技术随之发展起来。第一代固定化细胞大部分是催化比较简单的酶反应,如水解酶、异构酶等。第二代固定化细胞主要是利用细胞内复杂的酶体系或整个代谢过程生产某     

酶促水解大豆分离蛋白动力学模型的研究

本文对AS1.398中性蛋白酶在pH6.9和温度49℃条件下水解大豆分离蛋白的动力学机制进行了研究．结果表明：酶水解速率随水解反呈指数递减．为了解释实验结果,我们提出了如下假设：对底物而言水解反应终为零级反应,水解过程中由于游离酶攻击酶-底物中间络合物而造成的不可逆酶变性是一个二级动力学过程．在此基础上,由实验数据推导得到了描述AS1.398中性蛋白酶催化水解大豆分离蛋白的动力学方程,该方程可用于指导和优化酶解反应实验．     

反胶束中单宁酶催化没食子酸烷基酯的生物合成

为了研究单宁酶在有机相中的催化性能,建立了AOT/异辛烷／水反胶束单宁酶催化没食子酸与脂肪醇酯合成反应体系。结果显示：反胶束单宁酶催化体系可成功催化合成C3-C5脂肪醇与没食子酸的酯合成反应。不同反应体系中由于不同脂肪醇的存在,单宁酶的动力学参数和紫外光谱存在差别。结果表明单宁酶对脂肪醇的专一性不强,根据Vmax/Km比值,丁醇与异丁醇是其最适底物,单宁酶催化没食子酸烷基酯合成的动力学符合米氏方程。反应体系中不同的脂肪醇导致了单宁酶构象的差别。     

中华绒螯蟹（Eriocheir sinensis）N-乙酰-β-D-氨基葡萄糖苷酶的分离纯化及性质的初步研究

本研究以中华绒螯蟹内脏为材料,经过硫酸铵沉淀分级分离、两次DEAE-32离子交换柱层析和Sephadex G-100分子筛柱层析纯化,获得比活力为4490.79U/mg、纯化倍数为28.07倍的聚丙烯酰胺凝胶电泳纯的N-乙酰-β-D-氨基葡萄糖苷酶制剂。酶分子中各亚基的分子量分别为121.219、8.63和73.48 kD,等电点为4.5。以对-硝基苯-N-乙酰-β-D-氨基葡萄糖为底物,进行酶催化底物水解的反应动力学研究,结果表明：酶催化底物反应的最适pH为5.5,最适温度为45℃。该酶在pH4.9—9.3区域或40℃以下处理30min,酶活力保持稳定。酶促反应动力学符合米氏双曲线方程,测得米氏常数Km为0.357 mmol/L,最大反应速度Vm为10.41μmol/L.min。酶催化pNP-β-D-GlcNAc反应的活化能为76.50kJ/mol。金属离子对酶的效应试验表明：Mg^2＋、Ca^2＋和Ba^2＋对酶活力没有影响。Na＋对酶有激活作用,Li^＋、K^＋、Zn^2＋、Hg^2＋、Pb^2＋、Cu^2＋和Al3＋对酶活力表现出不同程度的抑制作用。     

植物甜菜碱合成酶的分子生物学和基因工程

甜菜碱是一种非毒性的渗透调节剂,多种高等植物在盐碱或缺水的环境下在细胞中积累甜菜碱,以维持细胞的正常膨压,甜菜碱的积累使得许多代谢中的重要酶类在渗透胁迫下能保持活性,在植物中甜菜碱由胆碱经两步氧化得到,催化第一步反应的酶是胆碱单加氧酶（CMO）,催化第二步反应的酶是甜菜碱醛脱氢酶（BADH）。本文综述了这两种酶的分子生物学及基因工程研究的最新进展,讨论了基因工程研究的意义。     

植物甜菜碱合成酶的分子生物学和基因工程

甜菜碱是一种非毒性的渗透调节剂。多种高等植物在盐碱或缺水的环境下在细胞中积累甜菜碱 ,以维持细胞的正常膨压。甜菜碱的积累使得许多代谢中的重要酶类在渗透胁迫下能保持活性。在植物中甜菜碱由胆碱经两步氧化得到 ,催化第一步反应的酶是胆碱单加氧酶 (CMO) ,催化第二步反应的酶是甜菜碱醛脱氢酶 (BADH)。本文综述了这两种酶的分子生物学及基因工程研究的最新进展 ,讨论了其基因工程研究的意义。     

槲皮素的热降解机理及其分解动力学研究

利用TG-DTG技术测得槲皮素在氮气气氛中不同升温速率β下的热分解曲线,协同使用Achar法、Coats-Redfern法、Kissinger法和Ozawa法等4种方法同时进行动力学处理,根据热分解的表观活化能Eα和指前因子A计算推断槲皮素的贮存期.随着升温速率的提高,槲皮素的热分解温度逐渐升高;槲皮素热二步分解的机理依次是随机成核与随后生长控制和化学反应控制,对应的函数名称是Avrami-Erofeev方程和反应级数方程;经Gaussian模拟和热重数据结合分析,槲皮素在第一步分解时,失去两个O原子;第二步分解时失去一个苯环;根据第一步热分解的表观活化能Eα和指前因子A推断,在室温25℃下,槲皮素的贮存期为1.5 ～2年.     

刺芹侧耳栽培料及菌体中漆酶介体分子的挖掘

虽然真菌能够分泌漆酶从木质素中获取碳源,然而纯化后真菌漆酶降解木质素的能力却极低。本文利用萃取方法提取刺芹侧耳栽培料及菌体中可溶性化合物,通过快速漆酶介体体系（LMS）动力学实验确定其对漆酶催化氧化反应的促进或抑制能力,进一步利用HPLC-MS和代谢组学差异分析的方法从最高活性萃取液的柱层析组分中挖掘潜在的活性成分。研究结果表明栽培料中可能含有活性介体成分,生物信息学XCMS代谢产物组分析揭示了CTE05分离组分中富含的木质素代谢产物,涉及到软木脂单体合成、香豆素合成、丁香油酚或异丁香油酚合成、质体醌醇合成、由苯丙氨酸合成硫代葡萄糖苷和安息香酸合成等代谢途径。最后讨论了其中11种潜在的天然介体分子物理化学性质,其中4种为已有文献报道的天然介体小分子。本研究暗示木质素降解与合成代谢在分子机制上存在有某种联系,相关的代谢产物可能参与了真菌降解木质素的代谢过程。     

简单节杆菌转化氢化可的松的△-脱氢反应动力学I．简单节杆菌BY-2-13自由细胞转化氢化可的松的△-脱氢反应动力学

本文研究了简单节杆菌(Arthrobacter simplex) By-2-13转化氢化可的松为氢化泼尼松韵△一脱氢反应动力学。其中包括溶解底物的底物浓度对反应速度的影响,反应初速度与底物浓度的关系;固体悬浮液中底物总浓度对反应速度的影响,反应初速度与底物浓度的关系;酶量对反应的影响以及产物的抑制作用等。溶解底物和固体悬浮液底物的反应初速度与底物浓度的关系都符合简单米氏方程,米氏常数Km分别为0．33mg／mJ和29．41n,g／ml,而两者的反应过程曲线均与简单米氏方程不符。无论在较低或较高浓度的固体悬浮液底物转化过程中,产物对A’。脱氢反应都呈现抑制作用。由此建立了该反应的反应动力学模型及相应的动力学方程,井经线性化后回归得出反应的动力学参数。当反应时间小于‘(达到约85％的转化率所需要的时间)时,用此动力学方程拟合所得的数据与实验测定值相符。     

Solubilization and characterization of the initial enzymes of the dolichol pathway from yeast

Preparation and purification of substrate amounts of radioactive as well as non-radioactive dolichyl diphosphate N-acetylglucosamine and dolichyl diphosphate chitobiose made it possible to test and characterize tentatively the first three reactions of the dolichol pathway (enzyme I-III). The test conditions are described in detail. All three enzymes were solubilized from yeast membranes with detergents. Enzyme II and III were purified to give a purification factor of 35-fold and 70-fold, respectively. The reactions required divalent metal ions with an optimum concentration of 10 mM Mg2+. Enzyme II was stimulated almost to the same extent also by Ca2+. The Km values for UDP-N-acetylglucosamine for enzyme I and II were 15 and 10 muM, respectively, and for GDP-mannose (enzyme III) 7 muM. The apparent Km values for the lipophilic acceptor was 180 muM for enzyme I (dolichyl phosphate), 40 muM for enzyme II (dolichyl diphosphate N-acetylglucosamine) and 17 muM for enzyme III (dolichyl diphosphate chitobiose). The corresponding V values were approximately 1, 10, and 50 nmol X h-1 X mg protein-1. All reactions were inhibited by nucleoside diphosphates.     

Purification and characterization of two human erythrocyte arylamidases preferentially hydrolysing N-terminal arginine or lysine residues.

Two arylamidases (I and II) were purified from human erythrocytes by a procedure that comprised removal of haemoglobin from disrupted cells with CM-Sephadex D-50, followed by treatment of the haemoglobin-free preparation subsequently with DEAE-cellulose, gel-permeation chromatography on Sephadex G-200, gradient solubilization on Celite, isoelectric focusing in a pH gradient from 4 to 6, gel-permeation chromatography on Sephadex G-100 (superfine), and finally affinity chromatography on Sepharose 4B covalently coupled to L-arginine. In preparative-scale purifications, enzymes I and II were separated at the second gel-permeation chromatography. Enzyme II was obtained as a homogeneous protein, as shown by several criteria. Enzyme I hydrolysed, with decreasing rates, the L-amino acid 2-naphtylamides of lysine, arginine, alanine, methionine, phenylalanine and leucine, and the reactions were slightly inhibited by 0.2 M-NaCl. Enzyme II hydrolysed most rapidly the corresponding derivatives of arginine, leucine, valine, methionine, proline and alanine, in that order, and the hydrolyses were strongly dependent on Cl-. The hydrolysis of these substrates proceeded rapidly at physiological Cl- concentration (0.15 M). The molecular weights (by gel filtration) of enzymes I and II were 85 000 and 52 500 respectively. The pH optimum was approx. 7.2 for both enzymes. The isoelectric point of enzyme II was approx. 4.8. Enzyme I was activated by Co2+, which did not affect enzyme II to any noticeable extent. The kinetics of reactions catalysed by enzyme I were characterized by strong substrate inhibition, but enzyme II was not inhibited by high substrate concentrations. The Cl- activated enzyme II also showed endopeptidase activity in hydrolysing bradykinin.     

The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction.

The structures of enzymes catalyzing the reactions in central metabolic pathways are generally well conserved as are their catalytic mechanisms. The two types of 3-dehydroquinate dehydratase (DHQase) are therefore most unusual since they are unrelated at the sequence level and they utilize completely different mechanisms to catalyze the same overall reaction. The type I enzymes catalyze a cis-dehydration of 3-dehydroquinate via a covalent imine intermediate, while the type II enzymes catalyze a trans-dehydration via an enolate intermediate. Here we report the three-dimensional structures of a representative member of each type of biosynthetic DHQase. Both enzymes function as part of the shikimate pathway, which is essential in microorganisms and plants for the biosynthesis of aromatic compounds including folate, ubiquinone and the aromatic amino acids. An explanation for the presence of two different enzymes catalyzing the same reaction is presented. The absence of the shikimate pathway in animals makes it an attractive target for antimicrobial agents. The availability of these two structures opens the way for the design of highly specific enzyme inhibitors with potential importance as selective therapeutic agents.     

Enzyme promiscuity: mechanism and applications

Introductory courses in biochemistry teach that enzymes are specific for their substrates and the reactions they catalyze. Enzymes diverging from this statement are sometimes called promiscuous. It has been suggested that relaxed substrate and reaction specificities can have an important role in enzyme evolution; however, enzyme promiscuity also has an applied aspect. Enzyme condition promiscuity has, for a long time, been used to run reactions under conditions of low water activity that favor ester synthesis instead of hydrolysis. Together with enzyme substrate promiscuity, it is exploited in numerous synthetic applications, from the laboratory to industrial scale. Furthermore, enzyme catalytic promiscuity, where enzymes catalyze accidental or induced new reactions, has begun to be recognized as a valuable research and synthesis tool. Exploiting enzyme catalytic promiscuity might lead to improvements in existing catalysts and provide novel synthesis pathways that are currently not available.     

Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure

CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase], a template-independent RNA polymerase, adds the defined 'cytidine-cytidine-adenosine' sequence onto the 3' end of tRNA. The archaeal CCA-adding enzyme (class I) and eubacterial/eukaryotic CCA-adding enzyme (class II) show little amino acid sequence homology, but catalyze the same reaction in a defined fashion. Here, we present the crystal structures of the class I archaeal CCA-adding enzyme from Archaeoglobus fulgidus, and its complexes with CTP and ATP at 2.0, 2.0 and 2.7 A resolutions, respectively. The geometry of the catalytic carboxylates and the relative positions of CTP and ATP to a single catalytic site are well conserved in both classes of CCA-adding enzymes, whereas the overall architectures, except for the catalytic core, of the class I and class II CCA-adding enzymes are fundamentally different. Furthermore, the recognition mechanisms of substrate nucleotides and tRNA molecules are distinct between these two classes, suggesting that the catalytic domains of class I and class II enzymes share a common origin, and distinct substrate recognition domains have been appended to form the two presently divergent classes.     

Crystal structure of 3-carboxy-cis,cis-muconate lactonizing enzyme from Pseudomonas putida, a fumarase class II type cycloisomerase: enzyme evolution in parallel pathways

3-Carboxy-cis,cis-muconate lactonizing enzymes (CMLEs), the key enzymes in the protocatechuate branch of the beta-ketoadipate pathway in microorganisms, catalyze the conversion of 3-carboxy-cis,cis-muconate to muconolactones. We have determined the crystal structure of the prokaryotic Pseudomonas putida CMLE (PpCMLE) at 2.6 A resolution. PpCMLE is a homotetramer and belongs to the fumarase class II superfamily. The active site of PpCMLE is formed largely by three regions, which are moderately conserved in the fumarase class II superfamily, from three respective monomers. It has been proposed that residue His141, which is highly conserved in all fumarase class II enzymes and forms a charge relay with residue Glu275 (both His141 and Glu275 are in adenylosuccinate lyase numbering), acts as the general base in most fumarase class II superfamily members. However, this charge relay pair is broken in PpCMLE. The residues corresponding to His141 and Glu275 are Trp153 and Ala289, respectively, in PpCMLE. The structures of prokaryotic MLEs and that of CMLE from the eukaryotic Neurospora crassa are completely different from that of PpCMLE, indicating MLEs and CMLEs, as well as the prokaryotic and eukaryotic CMLEs, evolved from distinct ancestors, although they catalyze similar reactions. The structural differences may be related to recognition by substrates and to differences in the mechanistic pathways by which these enzymes catalyze their respective reactions.     

DNA polymerases from bakers' yeast.

Two DNA polymerases are present in extracts of commercial bakers' yeast and wild type Saccharomyces cerevisiae grown aerobically to late log phase. Yeast DNA polymerase I and yeast DNA polymerase II can be separated by DEAE-cellulose, hydroxylapatite, and denatured DNA-cellulose chromatography from the postmitochondrial supernatants of yeast lysates. The yeast polymerases are both of high molecular weight (greater than 100,000) but are clearly separate species by the lack of immunological cross-reactivity. Analysis of associated enzyme activities and other reaction properties of yeast DNA polymerases provides additional evidence for distinguishing the two species. Enzyme I has no associated nuclease activity but does carry out pyrophosphate exchange and pyrophosphorolysis reactions, and has an associated 3'-exonuclease activity. Enzyme I does not degrade deoxynucleoside triphosphates and cannot utilize a mismatched template. Enzyme II does carry out a template-dependent deoxynucleoside triphosphate degradation reaction and can excise mismatched 3'-nucleotides from suitable template systems. Earlier studies have shown that both Enzyme I and Enzyme II are inhibited by N-ethylmaleimide. The yeast enzymes are not identical to any known eukaryotic or prokaryotic DNA polymerases. In general, Enzyme I appears to be most similar to eukaryotic DNA polymerase alpha and Ezyme II exhibits properties of prokaryotic DNA polymerases II and III.     

Production and characterization of bifunctional enzymes. Substrate channeling in the aspartate pathway

The direct channeling of an intermediate between enzymes that catalyze consecutive reactions in a pathway offers the possibility of an efficient, exclusive, and protected means of metabolite delivery. Aspartokinase-homoserine dehydrogenase I (AK-HDH I) from Escherichia coli is an unusual bifunctional enzyme in that it does not catalyze consecutive reactions. The potential channeling of the intermediate beta-aspartyl phosphate between the aspartokinase of this bifunctional enzyme and aspartate semialdehyde dehydrogenase (ASADH), the enzyme that catalyzes the intervening reaction, has been examined. The introduction of increasing levels of inactivated ASADH has been shown to compete against enzyme-enzyme interactions and direct intermediate channeling, leading to a decrease in the overall reaction flux through these consecutive enzymes. These same results are obtained whether these experiments are conducted with aspartokinase III, a naturally occurring monofunctional isozyme, with an artificially produced monofunctional aspartokinase I, or with a fusion construct of AK I-ASADH. These results provide definitive evidence for the channeling of beta-aspartyl phosphate between aspartokinase and aspartate semialdehyde dehydrogenase in E. coli and suggest that ASADH may provide a bridge to channel the intermediates between the non-consecutive reactions of AK-HDH I.     

Poly(C) synthesis by class I and class II CCA-adding enzymes

The CCA-adding enzymes [ATP(CTP):tRNA nucleotidyl transferases], which catalyze synthesis of the conserved CCA sequence to the tRNA 3' end, are divided into two classes. Recent studies show that the class II Escherichia coli CCA-adding enzyme synthesizes poly(C) when incubated with CTP alone, but switches to synthesize CCA when incubated with both CTP and ATP. Because the poly(C) activity can shed important light on the mechanism of the untemplated synthesis of CCA, it is important to determine if this activity is also present in the class I CCA enzymes, which differ from the class II enzymes by significant sequence divergence. We show here that two members of the class I family, the archaeal Sulfolobus shibatae and Methanococcus jannaschii CCA-adding enzymes, are also capable of poly(C) synthesis. These two class I enzymes catalyze poly(C) synthesis and display a response of kinetic parameters to the presence of ATP similar to that of the class II E. coli enzyme. Thus, despite extensive sequence diversification, members of both classes employ common strategies of nucleotide addition, suggesting conservation of a mechanism in the development of specificity for CCA. For the E. coli enzyme, discrimination of poly(C) from CCA synthesis in the intact tRNA and in the acceptor-TPsiC domain is achieved by the same kinetic strategy, and a mutation that preferentially affects addition of A76 but not poly(C) has been identified. Additionally, we show that enzymes of both classes exhibit a processing activity that removes nucleotides in the 3' to 5' direction to as far as position 74.