Microbial reduction of ethyl acetoacetate to ethyl (R)-3-hydroxybutyrate in an ionic liquid containing system

A hydrophilic ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]BF₄) was successfully employed as co-solvent for asymmetric bioreduction of ethyl acetoacetate (EOB) to ethyl (R)-3-hydroxybutyrate (R-EHB) catalyzed by Pichia membranaefaciens Hansen ZJPH07 cells. The results demonstrated that the addition of [BMIM]BF₄ in reaction system can markedly reduce the substrate inhibition and moderately improve the enantioselectivity compared to that in monophasic aqueous system. Among different alcohols and carbohydrates tried as co-substrate, glucose was a proper electron donor. Although isopropanol gave the best enantioselectivity with the highest yield, S-enantiomer was obtained. To optimize the bioreduction, some reaction parameters for the biosynthesis of R-EHB in this IL-containing system were investigated, such as temperature, buffer pH, shaking speed, substrate concentration, wet cells concentration and reaction time. Under the optimum conditions, best conversion of 77.8% and product enantiomeric excess (e.e.) of 73.0% were obtained. A comparative study was performed either in the presence or in the absence of [BMIM]BF₄, higher reaction yield (77.8% versus 68.5%) and product e.e. (73.0% versus 65.1%) were observed in IL-containing system with 0.55 M of the substrate, but 0.35 M of substrate concentration for the reduction in aqueous system without the addition of [BMIM]BF₄.     

Modeling speciation effects on biodegradation in mixed metal/chelate systems

A new model, CCBATCH, comprehensively couples microbially catalyzed reactions to aqueous geochemistry. The effect of aqueous speciation on biodegradation reactions and the effect of biological reactions on the concentration of chemical species (e.g. H₂CO₃, NH ₄ ⁺ , O₂) are explicitly included in CCBATCH, allowing systematic investigation of kinetically controlled biological reactions. Bulk-phase chemical speciation reactions including acid/base and complexation are modeled as thermodynamically controlled, while biological reactions are modeled as kinetically controlled. A dual-Monod kinetic formulation for biological degradation reactions is coupled with stoichiometry for the degradation reaction to predict the rate of change of all biological and chemical species affected by the biological reactions. The capability of CCBATCH to capture pH and speciation effects on biological reactions is demonstrated by a series of modeling examples for the citrate/Fe(III) system. pH controls the concentration of potentially biologically available forms of citrate. When the percentage of the degradable substrate is low due to complexation or acid/base speciation, degradation rates may be slow despite high concentrations of substrate Complexation reactions that sequester substratein non-degradable forms may prevent degradation or stopdegradation reactions prior to complete substrate utilization. The capability of CCBATCH to couple aqueous speciation changes to biodegradation reaction kinetics and stoichiometry allows prediction of these key behaviors in mixed metal/chelate systems.     

Description of the ratios between metabolite concentrations in a polyenzyme system

It was demonstrated that the relations between substrate and product concentrations for a reaction catalyzed by michaelian enzyme incorporated in a multienzyme system can be graphically represented by a diverging set of straight lines intersecting in one point, the flux velocity being treated as a parameter. A competitive inhibitor shifts the intersection point along the line of equilibrium state. The relations between the concentrations of more than two reagents are represented by a set of equivelocity surfaces. The relations between substrate and product concentrations for a kinetically cooperative reaction conforming to the graphical representation by the second--order curves were analyzed. The stability criterion was obtained for a multienzyme system with the first enzyme allosterically regulated by products of subsequent reactions.     

Rapid and specific assay of collagen glucosyltransferase with a Sepharose-bound substrate

A simple and specific assay has been developed for collagen glucosyltransferase in which a solid-phase substrate, consisting of a mixture of Type II collagen peptides linked to CNBr-activated Sepharose 4B, is used. Following incubation with enzyme, the substrate is simply washed, and its radioactivity is determined. The specificity of the procedure has been validated by the isolation of radiolabeled Glc-Gal-Hyl from the reaction products after incubation with a crude enzyme preparation from embryonic chick cartilage. Under the conditions described, product formation was linear for 6 h and was proportional to the concentration of enzyme protein up to 180 μg/ml. The K_m was 33 μm for UDP-glucose and 48 μm for the gel-bound collagen substrate, expressed as Gal-Hyl. The V_max for the Sepharose-bound substrate was 30% of the value observed for the identical substrate in soluble form, suggesting that the solid matrix exerted some sterical hindrance on the bound substrate.     

Sugar transport into protoplasts isolated from developing soybean cotyledons : I. Protoplast isolation and general characteristics of sugar transport

A procedure is described to isolated functional protoplasts from developing soybean (Glycine max L. Merr. cv Wye) cotyledons. Studies of sucrose and hexose uptake into these protoplasts show that the plasmalemma of cotyledons during the stage of rapid seed growth contains a sucrose-specific carrier which is energetically and kinetically distinct from the system(s) involved in hexose transport. For example, sucrose, but not hexose uptake: (a) is inhibited by alkaline pH and the nonpermeant SH modifier, p-chloromercuribenzene sulfonic acid; (b) is stimulated by fusicoccin; (c) shows both a saturable and a linear component of uptake in response to substrate concentration; and (d) displays a sharp temperature response (high Q₁₀ value and high activation energies).     

Steady-state kinetics of immobilized enzymes at very low substrate concentrations studied using the asarcoplasmic reticulum (Ca2+ + Mg2+)-ATPase

A method for determining initial velocities of enzymatic reactions at very low substrate concentrations is presented. It is based on teh continuous perfusiion of substrate-containing media through the enzyme, previously deposited as a thin layer on a solid support. An analytical rationalization of the dependence of the enzymatic activity upon the substrate supply and the flow rate was developed (substrate supply (μmol/min) = flow rate (ml/min) × inflowing substrate concentration (μmol/ml). This paper shows that a straight line should be expected from a double-reciprocal plot of the velocity of the enzymatic reaction and flow rate. The reciprocal of the ordinate at the origin is the strict initial velocity for a given, constant, and very low substrate concentration, since substrate consumption and product accumulation tend to zero. Results obtained with two different sarcoplasmic reticulum (Ca²⁺ + Mg²⁺)-ATPase preparations agree with the theoretical predictions. The method enabled the use of ATP concentrations in the range of 10^?8 M: it required neither an ATP-regerating system nor the dilution of the enzyme protein, and it presented no limitations for the reaction time. Both ATPase preparations showed two apparent K_m values for the substrate in the submicromolar and micromolar ranges: 0.25–12.0 μM for the purified ATPase, and 0.17–1.65 μM for the microsomal ATPase.     

Primary enzyme quantitation using substrates labeled with a second indicator enzyme. I. Elastase determination using peroxidase-labeled elastin

Quantitation of proteolytic enzyme concentration can be accomplished by measuring the release, due to primary enzyme catalysis, of a second enzyme bound to a particulate substrate. As the primary enzyme acts on the substrate, release of the indicator enzyme into the surrounding medium occurs, which in turn can be quantitated colorimetrically, and under suitable reaction conditions the amount of indicator enzyme released is directly proportional to the amount of primary enzyme present. A specific example of such an assay is that for elastolytic activity using powdered elastin labeled with horseradish peroxidase. The detection sensitivity of the system described is 1 ng/ml of pancreatic elastase, and the dynamic range of the assay is 2 orders of magnitude. The reaction time for optimal elastase detection sensitivity is 3 h. For the assay, horseradish peroxidase is coupled to insoluble elastin. Labeled elastin is incubated with varying amounts of pancreatic elastase. The elastase in the test sample solubilizes the elastin and the horseradish peroxidase bound to it. The amount of peroxidase released is then quantified using the colorimetic reaction produced by catalysis of 2,2′-azino-di-(3-ethyl-benzthiazoline-6-sulfonate)-H₂O₂. For a fixed, nonsaturating concentration of elastase, the amount of peroxidase released is proportional to the elastase concentration.     

Facilitated diffusion with consecutive reaction: optimal carrier affinity

The interplay between facilitated diffusion of a substrate through a membrane and a consecutive enzymic reaction, both of which follow Michaelis-Menten kinetics, has been theoretically investigated and the effect of the kinetic and transport parameters on the rate of substrate uptake is graphically illustrated. At steady state two characteristic features of the system have been identified. First, the substrate concentration at the internal enzymic side of the membrane cannot exceed a given value even at much higher external substrate concentrations. Second, the uptake rate is maximum at a given value of K_T, the kinetic parameter of the transport system that expresses the reciprocal carrier affinity of the substrate. The optimum value of K_T is approximately equal to the external substrate concentration. This particular dependence of the uptake rate on the carrier affinity is expected to play an important role in hormonal regulation.     

Mass transfer induced interchange of the kinetic and thermodynamic control of enzymic peptide synthesis in biphasic water-organic systems

The α-chymotrypsin catalysed kinetically controlled peptide synthesis in water and in biphasic water-methyl iso-butyl ketone system was compared. Due to the substrate and product partitioning in the biphasic system an interchange of the reaction control was observed at high enzyme concentration. Under these conditions, the rate of mass transfer between the phases was the rate limiting step and the hydrolysis product concentration was found to have a transient maximum ≫ equilibrium value. In this case, most of the peptide was sythetized in a thermodynamically controlled process. In an aqueous one phase system, the peptide synthesis was kinetically controlled.     

The autocatalytic step is an integral part of the hydrogenase cycle

We earlier proved the involvement of an autocatalytic step in the oxidation of H₂ by HynSL hydrogenase from Thiocapsa roseopersicina, and demonstrated that two enzyme forms interact in this step. Using a modified thin-layer reaction chamber which permits quantitative analysis of the concentration of the reaction product (reduced benzyl viologen) in the reaction volume during the oxidation of H₂, we now show that the steady-state concentration of the product displays a strong enzyme concentration dependence. This experimental fact can be explained only if the previously detected autocatalytic step occurs inside the catalytic enzyme-cycle and not in the enzyme activation process. Consequently, both interacting enzyme forms should participate in the catalytic cycle of the enzyme. As far as we are aware, this is the first experimental observation of such a phenomenon resulting in an apparent inhibition of the enzyme. It is additionally concluded that the interaction of the two enzyme forms should result in a conformational change in the enzyme–substrate form. This scheme is very similar to that of prion reactions. Since merely a few molecules are involved at some point of the reaction, this process is entirely stochastic in nature. We have therefore developed a stochastic calculation method, calculations with which lent support to the conclusion drawn from the experiment.     

Estimation of kinetic parameters for substrate and inhibitor in a reaction with an enzyme sample containing different types of inhibitor

The method of kinetic analysis is developed to obtain the maximum velocity (V_m), the Michaelis constant (K_m) and the parameters characterizing the inhibitors in an impure enzyme reaction, contaminated with one of four types of inhibitor (competitive, noncompetitive, uncompetitive and mixed-type). Although the reaction rate decreases with the increasing concentration of the enzyme sample containing an inhibitor, the double-reciprocal plot of the rate against the sample concentration becomes linear. The slopes of these linear plots at several different concentrations of substrate provide K_m and the specific enzyme activity, which is proportional to V_m, in the sample. These linear straight lines intersect in a point, of which the coordinates give the unique parameters for the inhibitor. To prove the validity of this kinetic method, the model experiments were carried out with acetylcholinesterase and its inhibitors, phenyltrimethylammonium and trimethylammonium. The present method was applied to the measurement of the specific activity of galactosylceramide galactosidase in the mouse cerebral homogenate. In addition, a kinetic method is indicated for the inhibition of an enzymatic reaction by a contaminant which binds the substrate to reduce the fraction available to the enzyme.     

The origin of kinetic cooperativity in prehiotic catalysts

A polyallylamine carrying long hydrophobic dodecyl groups and adenine residues as side chains (PALAD C₁₂) may be able to catalyze the hydrolysis ofN-carbobenzoxy-l-alaninep-nitrophenyl ester (N-Cbz-Ala) as well asp-nitrophenyl acetate (pNPA). The progress curve of hydrolysis of the former displays a long lag and apparently no steady state. After this transient the rate falls off due to the accumulation of the products. Conversely, the hydrolysis ofp-nitrophenyl acetate displays classical burst kinetics followed by a slow decline of the reaction rate. Theoretical considerations show that a steady state may be expected to occur only if the concentration of the free catalyst is very small during the reaction. This condition is sufficient to allow the rate of disappearance of the substrate to be equal to the rate of appearance of the products, which is precisely a condition for the existence of a steady state. If the catalyst is poorly active and has a loose affinity for its substrate and product, the measurement of a significant reaction rate will require a much larger concentration of the catalyst. Therefore, under these conditions, one cannot expect a steady state to occur. The mathematical expression of the error made in the steady-state assumption has been derived. This error increases with the catalyst concentration and decreases if the affinity of the substrate for the catalyst is high. Therefore the lack of steady state is associated with the affinity (or the dissociation) of the substrate and the product for the catalyst. When this affinity is low, the free concentration of the catalyst during the reaction is high and one cannot expect a steady state to occur. This is precisely what takes place with N-Cbz-Ala. A mathematical expression of the rate of hydrolysis of N-Cbz-Ala and of any reactant that displays this type of kinetics may be derived at the end of the transient when the rate is close to its maximum value. Under these conditions the rate cannot follow classical Michaelis-Menten kinetics and displays positive cooperativity. It may therefore be speculated that primordial template-like catalysts that were displaying a poor affinity for their substrates and products were already exhibiting apparent positive cooperativity in the kinetic reactions they were able to catalyze. Correspondence to: J. Ricard     

Reaction of oxygen with the respiratory chain in cells and tissues

This paper considers the way in which the oxygen reaction described by Dr. Nicholls and the ADP control reactions described by Dr. Racker could cooperate to establish a purposeful metabolic control phenomenon in vivo. This has required an examination of the kinetic properties of the respiratory chain with particular reference to methods for determinations of oxygen affinity (K_m). The constant parameter for tissue respiration is k ₁, the velocity constant for the reaction of oxygen with cytochrome oxidase. Not only is this quantity a constant for a particular tissue or mitochondria; it appears to vary little over a wide range of biological material, and for practical purposes a value of 5 x 10⁷ at 25° close to our original value (20) is found to apply with adequate accuracy for calculation of K_m for mammalia. The quantity which will depend upon the tissue and its metabolic state is the value of K_m itself, and K_m may be as large as 0.5 µM and may fall to 0.05 µM or less in resting, controlled, or inhibited states. The control characteristic for ADP may depend upon the electron flux due to the cytochrome chain (40); less ADP is required to activate the slower electron transport at lower temperatures than at higher temperatures. The affinity constants for ADP control appear to be less dependent upon substrate supplied to the system. The balance of ADP and oxygen control in vivo is amply demonstrated experimentally and is dependent on the oxygen concentration as follows. In the presence of excess oxygen, control may be due to the ADP or phosphate (or substrate), and the kinetics of oxygen utilization will be independent of the oxygen concentration. As the oxygen concentration is diminished, hemoglobin becomes disoxygenated, deep gradients of oxygen concentration develop in the tissue, and eventually cytochrome oxidase becomes partially and then completely reduced. DPN at this point will become reduced and the electron flow diminished. The rate of ATP production falls and energy conservation previously under the control of the ADP concentration will now be controlled by the diffusion of oxygen to the respiratory enzymes in the mitochondria. Under these conditions the rate of reaction of cytochrome oxidase with oxygen and the reaction of cytochromes with one another become of key importance. The rise of ADP and the depletion of energy reserves evoke glycolytic activity, and failure of biological function may result.     

A kinetic study of lipase-catalyzed reversible kinetic resolution involving verification at miniplant-scale

Lipase-catalyzed kinetic resolution of racemates is a popular method for synthesis of chiral synthons. Most of these resolutions are reversible equilibrium limited reactions. For the first time, an extensive kinetic model is proposed for kinetic resolution reactions, which takes into account the full reversibility of the reaction, substrate inhibition by an acyl donor and an acyl acceptor as well as alternative substrate inhibition by each enantiomer. For this purpose, the reversible enantioselective transesterification of (R/S)-1-methoxy-2-propanol with ethyl acetate catalyzed by Candida antarctica lipase B (CAL-B) is investigated. The detailed model presented here is valid for a wide range of substrate and product concentrations. Following model discrimination and the application of Haldane equations to reduce the degree of freedom in parameter estimation, the 11 free parameters are successfully identified. All parameters are fitted to the complete data set simultaneously. Six types of independent initial rate studies provide a solid data basis for the model. The effect of changes in substrate and product concentration on reaction kinetics is discussed. The developed model is used for simulations to study the behavior of reaction kinetics in a fixed bed reactor. The typical plot of enantiomeric excess versus conversion of substrate and product is evaluated at various initial substrate mixtures. The model is validated by comparison with experimental results obtained with a fixed bed reactor, which is part of a fully automated state-of-the-art miniplant.     

Kinetic manifestations of allosteric interactions in models of regulatory enzymes with "indirect" co-operativity

The shape of the plots of initial reaction rate (ν) versus initial substrate concentration ([S]₀) and versus initial concentration of allosteric effector ([F]₀) for the model of allosteric enzyme of Monod, Wyman &; Changeux (1965) and for the model of dissociating regulatory enzyme has been analysed by means of the inconstant exponent (q) for substrate or effector concentration, respectively. It has been shown that allosteric interactions in above-mentioned models with “indirect” co-operativity may be manifested not only by the sigmoidal shape of the plot of ν versus [S]₀ or ν versus [F]₀ (with one point of inflexion) but also by the increase in the magnitude of exponent q in progress of saturation process of the enzyme by the substrate or by the effector in the absence of the sigmoidal shape of these plots. It has been shown also that the plot of ν versus [S]₀ has two inflexion points when the parameters have certain definite values. One of these inflexion points (or even both at definite values of the parameters) is hardly discernible. At certain definite values of the parameters two inflexion points may be kinetically manifested by such phenomenon as “negative” co-operativity (q < 1). This is possible if one of the interconvertable enzyme forms exceeds another not only in the affinity to the substrate but also in the value of the rate constant for catalytic breakdown of the enzyme-substrate complex.     

Studies of enzyme reactions in open systems

An experimental arrangement is described which allows studies of the temporal performance of enzyme reactions (also reactions of complexes of enzyme chains) under conditions of open systems. The various steady-state properties of such open systems can be recognized by measuring their input and output [1,2]. The various levels of flowing equilibria are perturbed by applying molecular modulators to the system, and the data obtained are compared to those found in closed systems. In order to prove the accuracy of the experimental configuration, the determination of K_m in a one-substrate reaction is carried out in the open system, using only one concentration of substrate at various flow rates.     

Accurate determination of the oxidative phosphorylation affinity for ADP in isolated mitochondria

Background

Mitochondrial dysfunctions appear strongly implicated in a wide range of pathologies. Therefore, there is a growing need in the determination of the normal and pathological integrated response of oxidative phosphorylation to cellular ATP demand. The present study intends to address this issue by providing a method to investigate mitochondrial oxidative phosphorylation affinity for ADP in isolated mitochondria.

Methodology/Principal Findings

The proposed method is based on the simultaneous monitoring of substrate oxidation (determined polarographically) and phosphorylation (determined using the glucose - hexokinase - glucose-6-phosphate dehydrogenase - NADP⁺ enzymatic system) rates, coupled to the determination of actual ADP and ATP concentrations by bioluminescent assay. This enzymatic system allows the study of oxidative phosphorylation during true steady states in a wide range of ADP concentrations. We demonstrate how the application of this method allows an accurate determination of mitochondrial affinity for ADP from both oxidation (K_mVox) and phosphorylation (K_mVp) rates. We also demonstrate that determination of K_mVox leads to an important overestimation of the mitochondrial affinity for ADP, indicating that mitochondrial affinity for ADP should be determined using phosphorylation rate. Finally, we show how this method allows the direct and precise determination of the mitochondrial coupling efficiency. Data obtained from rat skeletal muscle and liver mitochondria illustrate the discriminating capabilities of this method.

Conclusions/Significance

Because the proposed method allows the accurate determination of mitochondrial oxidative phosphorylation affinity for ADP in isolated mitochondria, it also opens the route to a better understanding of functional consequences of mitochondrial adaptations/dysfunctions arising in various physiological/pathophysiological conditions.     

A miniaturized assay for measuring small molecule phosphorylation in the presence of complex matrices

We describe here a simple, miniaturized radiation-based phosphorylation assay that can be used to monitor phosphorylation of a diverse range of small molecule substrates in the presence of purified and crude enzyme preparations. Ba(OH)₂ and ZnSO₄ are used to terminate phosphoryl transfer and to precipitate selectively the phosphorylated reaction product in a single step; non-phosphorylated substrate is removed by filtration prior to quantification. The key advantages over alternative radiation-based assays are that: (i) high-energy/short-lived radioactive emitters are not required; (ii) high-quality data can be obtained without the need for high radioactivity concentrations; and (iii) the assay is compatible with high-throughput applications.     

NMR for direct determination of Km and Vmax of enzyme reactions based on the Lambert W function-analysis of progress curves

¹H NMR spectroscopy was used to follow the cleavage of sucrose by invertase. The parameters of the enzyme's kinetics, K_m and V_max, were directly determined from progress curves at only one concentration of the substrate. For comparison with the classical Michaelis-Menten analysis, the reaction progress was also monitored at various initial concentrations of 3.5 to 41.8 mM. Using the Lambert W function the parameters K_m and V_max were fitted to obtain the experimental progress curve and resulted in K_m = 28 mM and V_max = 13 μM/s. The result is almost identical to an initial rate analysis that, however, costs much more time and experimental effort. The effect of product inhibition was also investigated. Furthermore, we analyzed a much more complex reaction, the conversion of farnesyl diphosphate into (+)-germacrene D by the enzyme germacrene D synthase, yielding K_m = 379 μM and k_cat = 0.04 s^− 1. The reaction involves an amphiphilic substrate forming micelles and a water insoluble product; using proper controls, the conversion can well be analyzed by the progress curve approach using the Lambert W function.     

A completely automated system for on-line monitoring of the production of a growth factor secreted during fermentation of Escherichia coli

The production of IGF-1 (insulin-like growth factor 1), expressed in Escherichia coli as a secreted fusion protein with affinity for the Fc region of IgG, was monitored automatically during fermentations. A sampling device was used to automatically inject filtered culture medium from the fermentor onto a small affinity column (IgG Sepharose(R) Fast Flow) connected to a chromatographic system. The area of the eluted peak was proportional to the concentration of the fusion protein. The relationship was linear over the range 25-630 mug/mL with relative standard deviation of around 1% at the higher concentrations. Samples could be monitored automatically every half hour during fermentation (48 h). The method of analysis is nondestructive, allowing further analysis of product quality. A complete evaluation of the monitoring system is described. With this system, fermentations based on the described expression system can be optimized on the basis of product concentration; this will lead to more effective fermentations and higher product yields. It should also be possible to monitor other secreted products with this system by using other affinity gels.