Kinetic modeling of omega-transamination for enzymatic kinetic resolution of alpha-methylbenzylamine

A kinetic model for omega-transaminase from Bacillus thuringiensis JS64 was developed by using the King-Altman method to simulate the kinetic resolution of alpha-methylbenzylamine (alpha-MBA). Starting from a ping-pong bi-bi mechanism, a complete kinetic model including substrate inhibition only in the reverse reaction (i.e., transamination between acetophenone and L-alanine) was developed. The asymmetric synthesis of (S)-alpha-MBA proved to be difficult due to a much lower maximum reverse reaction rate than the maximum forward reaction rate, thermodynamically exergonic forward reaction (i.e., transamination between (S)-alpha-MBA and pyruvate), and the severe product and substrate inhibition of the reverse reaction. Experimental values for kinetic parameters show that the product inhibition constant of (S)-alpha-MBA is the most important parameter on determining the resolution reaction rate, suggesting that the resolution reaction rate will be very low unless (S)-alpha-MBA strongly inhibits the reverse reaction. Using the kinetic model, the kinetic resolution of alpha-MBA in aqueous buffer was simulated, and the simulation results showed a high degree of consistency with experimental data over a range of reaction conditions. Various simulation results suggest that the crucial bottleneck in the kinetic resolution of alpha-MBA lies mainly in the accumulation of acetophenone in reaction media as the reaction proceeds, whereas L-alanine exerts a little inhibitory effect on the reaction. The model predicts that removing acetophenone produced during the reaction can enhance the reaction rate dramatically. Indeed, the biphasic reaction system is capable of extracting acetophenone from the aqueous phase, showing a much higher reaction rate compared to a monophasic reaction system. The kinetic model was also useful in predicting the properties of other, better enzymes as well as the optimal concentrations of amino acceptor and enzyme in the resolution reaction.     

Stochastic simulation of chemical reactions with spatial resolution and single molecule detail

Methods are presented for simulating chemical reaction networks with a spatial resolution that is accurate to nearly the size scale of individual molecules. Using an intuitive picture of chemical reaction systems, each molecule is treated as a point-like particle that diffuses freely in three-dimensional space. When a pair of reactive molecules collide, such as an enzyme and its substrate, a reaction occurs and the simulated reactants are replaced by products. Achieving accurate bimolecular reaction kinetics is surprisingly difficult, requiring a careful consideration of reaction processes that are often overlooked. This includes whether the rate of a reaction is at steady-state and the probability that multiple reaction products collide with each other to yield a back reaction. Inputs to the simulation are experimental reaction rates, diffusion coefficients and the simulation time step. From these are calculated the simulation parameters, including the 'binding radius' and the 'unbinding radius', where the former defines the separation for a molecular collision and the latter is the initial separation between a pair of reaction products. Analytic solutions are presented for some simulation parameters while others are calculated using look-up tables. Capabilities of these methods are demonstrated with simulations of a simple bimolecular reaction and the Lotka-Volterra system.     

Reaction rate calculations for cosubstrates diffusing into catalyst layer from opposite sides

The effects of diffusion on a reaction taking place in a permeable catalyst are examined theoretically for the case where the reaction has two substrates supplied from opposite sides of a catalytic slab. The solutions of the reaction-diffusion equation for combinations of zeroth-and first-order kinetics are given in terms of an effectiveness factor and a parameter describing the position in the layer where the reaction occurs. In these terms, the results vary only weakly with reaction order. The use of the exact solutions for a reaction that is zeroth order in both sub strates is proposed as a general rule for estimating the reaction rate and the reaction position.     

A Kinetic Analysis of Coupled (or Auxiliary) Enzyme Reactions

As a case study, we consider a coupled (or auxiliary) enzyme assay of two reactions obeying the Michaelis–Menten mechanism. The coupled reaction consists of a single-substrate, single-enzyme non-observable reaction followed by another single-substrate, single-enzyme observable reaction (indicator reaction). In this assay, the product of the non-observable reaction is the substrate of the indicator reaction. A mathematical analysis of the reaction kinetics is performed, and it is found that after an initial fast transient, the coupled reaction is described by a pair of interacting Michaelis–Menten equations. Moreover, we show that when the indicator reaction is fast, the quasi-steady-state dynamics are governed by three fast variables and one slow variable. Timescales that approximate the respective lengths of the indicator and non-observable reactions, as well as conditions for the validity of the Michaelis–Menten equations, are derived. The theory can be extended to deal with more complex sequences of enzyme-catalyzed reactions.     

An autocatalytic step in the reaction cycle of hydrogenase from Thiocapsa roseopersicina can explain the special characteristics of the enzyme reaction

A moving front has been observed as a special pattern during the hydrogenase-catalyzed reaction of hydrogen uptake with benzyl viologen as electron acceptor in a thin-layer reaction chamber. Such fronts start spontaneously and at random times at different points of the reaction chamber; blue spheres are seen expanding at constant speed and amplitude. The number of observable starting points depends on the hydrogenase concentration. Fronts can be initiated by injecting either a small amount of completed reaction mixture or activated hydrogenase, but not by injecting a low concentration of reduced benzyl viologen. These characteristics are consistent with an autocatalytic reaction step in the enzyme reaction. The special characteristics of the hydrogen-uptake reaction in the bulk reaction (a long lag phase, and the enzyme concentration dependence of the lag phase) support the autocatalytic nature. We conclude that there is at least one autocatalytic reaction step in the hydrogenase-catalyzed reaction. The two possible autocatalytic schemes for hydrogenase are prion-type autocatalysis, in which two enzyme forms interact, and product-activation autocatalysis, where a reduced electron acceptor and an inactive enzyme form interact. The experimental results strongly support the occurrence of prion-type autocatalysis.     

Extra-weak chemiluminescence of drugs. XII. Effect of the molar ratio of amino acid to sugar on extra-weak chemiluminescence in the Maillard reaction

The extra-weak chemiluminescence in the Maillard reaction caused by the reaction between L -lysine and D -arabinose was measured, and a linear relationship was found between the chemiluminescence and the amount of L -lysine added. After a 1-hour reaction equimolar amounts of D -arabinose and L -lysine were consumed regardless of the initial concentration of D -arabinose. The chemiluminescence of the Maillard reaction originates from Maillard reaction products formed by the equimolar reaction between sugar and amino acid and depends on the concentration of amino acid.     

Theoretical calculations on hydrogenase kinetics: explanation of the lag phase and the enzyme concentration dependence of the activity of hydrogenase uptake

Two models of the hydrogenase reaction cycle were investigated by means of theoretical calculations and model simulations. The first model is the widely accepted triangular hydrogenase reaction cycle with minor modifications; the second is a modified triangular model, where we have introduced an autocatalytic step into the reaction cycle. Both models include a one-step activation reaction. The theoretical calculations and model simulations corroborate the assumed autocatalytic reaction step concluded from the experimental characteristics of the hydrogenase reaction.     

Enzymatic hydrolysis of hydrophobic triolein by lipase in a mono-phase reaction system containing cyclodextrin; Reaction characteristics

A hydrophobic substrate triolein was hydrolyzed by lipase in a mono-phase reaction system containing cyclodextrin(CD) as emulsifier. The triolein was transformed to an emulsion-like state in the CD containing reaction system in contrast to the oil-droplet like state without CD due to the formation of an inclusion complex between the lipids and CDs. The hydrolysis reaction increased substantially in the CD containing reaction system, and the optimum reaction conditions including the amount of lipase, β-CD concentration, and mixing ratio of triolein and β-CD, were determined. The performance of the enzyme reaction in a mono-phase reaction system was compared with that of a two-phase reaction system which used water immiscible hexane as the organic solvent. The role of a CD in the mono-phase reaction system was elucidated by comparing the degree of the inclusion complex formation with triolein and oleic acid, K_m and V_max values, and product inhibition by oleic acid in aqueous and CD containing reaction systems. The resulting enhanced reaction seems to be caused by two phenomena; the increased accessibility of lipase to triolein and reduced product inhibition by oleic acid through the formation of an inclusion complex.     

Interfacial versus homogeneous enzymatic cleavage of mandelonitrile by hydroxynitrile lyase in a biphasic system

The question of an interfacial versus a homogeneous reaction is carefully addressed for the enzymatic biphasic cleavage of mandelonitrile to benzaldehyde by Prunus amygdalus hydroxynitrile lyase (pa-Hnl) (Hickel et al. [1999] Biotechnol Bioeng 36:425-436). Experimental evidence, including 1) the reaction ceases when the interface is populated by previously adsorbed denatured pa-Hnl, 2) the reaction continues even after washout of the bulk enzyme from the aqueous phase, 3) highly nonpolar organic solvents initially promote fast reaction kinetics that relatively quickly decay to zero product production, and 4) the reaction rate is nonlinear in the bulk enzyme concentration, provide robust grounds for an interfacial reaction. We also model enzymatic mandelonitrile cleavage assuming a homogeneous aqueous-phase reaction. The homogeneous reaction scheme does not simultaneously account for the experimental observations of a linear dependence of the reaction rate on organic/water interfacial area, no dependence on the aqueous-phase volume, and a nonlinear dependence on pa-Hnl aqueous concentration. Further, simple calculations demonstrate that the homogeneous reaction rate is at least three orders of magnitude slower than those observed by Hickel et al. (1999). We again conclude that enzyme adsorbed at the organic solvent/water interface primarily catalyzes the biphasic mandelonitrile cleavage reaction.     

alpha-Chymotrypsin in plastein synthesis: influence of substrate concentration on enzyme activity.

The role of alpha-chymotrypsin in the plastein reaction was studied using a peptic hydrolysate of albumin as substrate. Study of this reaction simultaneously by different methods showed that the plastein reaction is enzyme catalyzed and is highly dependent on environmental conditions. A gel permeation chromatography study of the plastein reaction showed simultaneous increases in the high- and low-molecular-weight oligopeptide fractions; a transpeptidation mechanism may be involved in the reaction. A study of the effect of substrate concentration on the plastein reaction catalyzed by alpha-chymotrypsin showed a profile with both hydrolytic and synthetic activities. This effect was also observed when the reaction course was followed by quantification of the free amino groups at different substrate concentrations, showing that a condensation mechanism is responsible for the synthetic activity when the substrate concentration is very high. These results have led us to conclude that the plastein reaction involves a transpeptidation and/or condensation mechanism, which is a function of the substrate concentration.     

Modular decomposition of metabolic systems via null-space analysis

We describe a method by which the reactions in a metabolic system may be grouped hierarchically into sets of modules to form a metabolic reaction tree. In contrast to previous approaches, the method described here takes into account the fact that, in a viable network, reactions must be capable of sustaining a steady-state flux. In order to achieve this decomposition we introduce a new concept--the reaction correlation coefficient, phi, and show that this is a logical extension of the concept of enzyme (or reaction) subsets. In addition to their application to modular decomposition, reaction correlation coefficients have a number of other interesting properties, including a convenient means for identifying disconnected subnetworks in a system and potential applications to metabolic engineering. The method computes reaction correlation coefficients from an orthonormal basis of the null-space of the stoichiometry matrix. We show that reaction correlation coefficients are uniquely defined, even though the basis of the null-space is not. Once a complete set of reaction correlation coefficients is calculated, a metabolic reaction tree can be determined through the application of standard programming techniques. Computation of the reaction correlation coefficients, and the subsequent construction of the metabolic reaction tree is readily achievable for genome-scale models using a commodity desk-top PC.     

使用估计的反应自由能预测组成性和可变剪接位点

基因结构预测中的一个重要步骤是精确地识别剪接位点。基于剪接反应的基本物理原则,最大信息原理被应用到剪接反应的理论分析中,进而导出了反应自由能估计表达式。作为一个简化模型,这个表达式能被用来估计一个5′剪接区或者3′剪接区所参与的剪接反应中的自由能变化。它不但较全面地概括了各个碱基之间的关联,而且还考虑了基因组背景概率的影响。这个反应自由能表达式被用来预测了人类基因中的组成性和可变剪接位点,预测结果是令人满意的,其预测能力比得上当前的一些流行方法。这说明最大信息原理可以作为研究某些核酸-蛋白质相互作用系统（如剪接反应）的理论出发点,导出的反应自由能表达式较好地符合了剪接反应过程。     

The effect of detergents on firefly luciferase reactions

The reaction rate of ATP-limited firefly luciferase-catalysed reactions, is affected by the presence of detergents. Anionic detergents inhibit luciferase activity without causing significant enzyme inactivation during the reaction. Cationic detergents increase reaction rate several-fold with a sharply defined optimum concentration of detergent for the effect. However, cationic detergents inactivate firefly luciferase during the reaction, resulting in a continuously decreasing reaction rate. Under such conditions, peak light intensity must be used as an indication of initial reaction rate. The inactivation rate increases with increasing detergent concentration. Non-ionic and zwitterionic detergents increase reaction rate over a broad range of detergent concentrations. Enzyme stability during the reaction is not affected by non-ionic detergents and only affected by zwitterionic detergents at high detergent concentration. Cyclodextrins, which can increase reaction rates of some chemiluminescent reactions, have little effect on firefly luciferase activity. Assays for ATP using firefly luciferase must be internally standardized by the constant addition technique in which a known amount of ATP is added to the test sample, since external calibration of such assays, by reference to a previously prepared standard curve, can lead to imprecision when detergents are present.     

Kinetics of biomass catalytic pyrolysis

The Coats–Redfern method was used to analyze the kinetic characteristics of biomass catalytic pyrolysis, indicating that it can be described by multi-step reactions, rather than as a simple first-order reaction. Friedman model-free calculations were used to describe the starting reaction types and the corresponding initial kinetic parameters. Finally, nonlinear regression of biomass catalytic pyrolysis showed that the reaction mechanism of the whole process could be kinetically characterized by three successive reactions: a one-dimensional diffusion reaction, followed by an apparent first-order reaction, and then by a two-dimensional diffusion reaction. The kinetic parameters and equations were also calculated.     

Organocatalytic aza-Michael/retro-aza-Michael reaction: pronounced chirality amplification in aza-Michael reaction and racemization via retro-aza-Michael reaction

A detailed experimental investigation of an aza-Michael reaction of aniline and chalcone is presented. A series of Cinchona alkaloid-derived organocatalysts with different functional groups were prepared and used in the aza-Michael and retro-aza-Michael reaction. There was an interesting finding that a complete reversal of stereoselectivity when a benzoyl group was introduced to the cinchonine and cinchonidine. The chirality amplification vs. time proceeds in the quinine-derived organocatalyst containing silicon-based bulky group, QN-TBS, -catalyzed aza-Michael reaction under solvent-free conditions. In addition, we have demonstrated for the first time that racemization was occurred in suitable solvents under mild conditions due to retro-aza-Michael reaction of the Michael adduct of aniline with chalcone. These indicate the equilibrium of retro-aza-Michael reaction and aza-Michael reaction produce the happening of chirality amplification in aza-Michael reaction and racemization via retro-aza-Michael reaction under different conditions, which would be beneficial to the development of novel chiral catalysts for the aza-Michael reactions.     

The kinetics and mechanism of oxidation of reduced spinach ferredoxin by molecular oxygen and its reduced products

Reduced spinach ferredoxin reacts with molecular oxygen in an autocatalytic reaction characterized by a hyperbolic dependence on oxygen concentration. The kinetics of the reaction indicate formation of a reduced ferredoxin-oxygen intermediate complex and production of superoxide anion which may also react with reduced ferredoxin. Hydrogen peroxide, which is formed from superoxide, in turn reoxidizes reduced ferredoxin at a rate nearly 10-times faster than that of the comparable reaction with oxygen. The kinetics of reaction of hydrogen peroxide with reduced ferredoxin are biphasic. The substrate dependence of the first phase of the reaction is consistent with a simple one-step equilibrium reaction. The second phase of the reaction could be eliminated by addition of the radical trapper, sodium formate.     

Development of two inbred strains of rats and characteristics of their skin reactions.

Two inbred strains of rat (Donryu and Sprague-Dawley strains) were developed. The skin reactions of these strains immunized with M. tuberculosis, hen egg albumin (OVA) or hen egg lysozyme and challenged with the purified protein derivative (PPD) or each antigen were even and uniform. The Donryu strain showed a typical Arthus reaction with petechiae and edema and a negligible delayed skin reaction, whereas the Sprague-Dawley strain showed a poor Arthus reaction and a typical delayed skin reaction with central necrosis and induration. The Arthus reaction or delayed skin reaction could be passively transferred to recipient rats of each strain by immune sera or sensitized peritoneal exudate cells (PEC), respectively.     

Wax ester synthesis by lipase-catalyzed esterification with fungal cells immobilized on cellulose biomass support particles

Esterification reactions between long-chain alcohol and oleic acid were performed for producing wax esters. The reaction can be catalyzed efficiently by cell-bound lipase of Rhizopus niveous fungal cells immobilized within cellulose biomass support particles. Carrying out the reaction in a solvent-free system is feasible by adding a molecular sieve for dehydration purposes. To optimize the yield, addition of a molecular sieve should be performed gradually during the whole course starting from the beginning of the reaction. The influence of reaction conditions such as temperature and substrate concentrations on reaction rates and yields were investigated; however, this reaction system is under the influence of both internal and external mass transfer resistance. Conducting the reaction in an organic solvent system with hexane or heptane as the solvent can eliminate diffusional effects. Reaction kinetics were subjected to detailed study in this system. The kinetics of the reaction can be represented satisfactorily by a Ping-Pong Bi Bi mechanism with deadend inhibition by alcohol.     

Serologic diagnosis of syphilis; the use of Treponema pallidum immobilization and immune adherence tests

TPI tests were carried out on 4,060 sera. Among 3,934 patients with reactive STS and no history of syphilis, 2,148 or 54.6 per cent had negative reaction to TPI tests, 1,695 or 43.1 per cent had positive reaction and 91 or 2.3 per cent had doubtful reaction. Two hundred and ninety-two or 73.0 per cent of 400 pregnant women with reaction to STS in the absence of a history of syphilis showed negative results by TPI test, 103 or 25.8 per cent had positive results and five or 1.2 per cent had doubtful reaction.Ninety-five or 75.4 per cent of 126 patients with a history of treated syphilis had positive reaction to TPI tests, 20 or 20.2 per cent had negative reaction and nine or 9.1 per cent had doubtful reaction.TPI and TPIA tests were done on 143 sera carefully selected for the study. Among 102 sera subjected to the TPI test, 46 or 100 per cent of these positive were also positive by TPIA tests, while 52 or 94.5 per cent of 55 TPI-negative sera were also nonreactive by TPIA test. One serum gave doubtful TPI test reaction and positive TPIA test reaction.     

Free radicals in the flavin reduction reaction. Interaction of reduced nicotinamide adenine dinucleotide with flavin in solution]

The study of the flavin mononucleotide (FMN)-reduced nicotinamide adeninedinucleotide (NADH) reaction was carried out both under aerobic and anaerobic conditions, using spectrophotometric and titrimetric methods. The consumption of NADH was shown to exceed two times the consumption of FMN in the anaerobic reaction and the rate constant in the aerobic reaction was found to be about 4 times of that of the anaerobic reaction. Moreover, the replacement of anaerobic conditions by aerobic ones at pH 5.0 resulted in a considerable increase of proton consumption rate in the reaction course. The data obtained are contradictory to the generally accepted hypothesis of hydrid-ion transfer in the reaction of NADH oxidation. It was assumed that this reaction proceeded through a homolytic pathway.