Kinetic study on the reaction mechanism of pantothenase: existence of an acyl-enzyme intermediate and role of general acid catalysis.

A kinetic study was performed on the reaction mechanism of pantothenase (EC 3.5.1.22) catalyzed hydrolysis of the pantothenic acid. A nonlinear progress curve is derived if the reaction occurs at low buffer concentrations. The nonlinearity is due to partial reversibility of the reaction; an acylenzyme (pantoyl-enzyme) is formed during the reaction, and beta-alanine, the other end product, is able to react with the acyl-enzyme and return back to pantothenate. The dependence of the beta-alanine return reaction on buffer concentration and on pH suggests a general acid catalysis during the reaction. A reaction mechanism is suggested, in which the -NH3+ form of beta-alanine participates in the return reaction, and the deacylation of the acyl-enzyme is acid catalyzed.     

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.     

Substrate interactions with the alpha-subunit of the Escherichia coli tryptophan synthase. A study of the activity of mutant alpha-subunits.

Extracts of 19 trpA mutant strains of Escherichia coli were examined for their relative activity in the reversible aldolytic reaction catalyzed by the trpA gene product, the α-subunit of tryptophan synthase, in combination with the β-subunit of this enzyme. The specific activities in this reaction, indoleglycerol-P (InGP) ? indole + glyceraldehyde-3-P, were determined for both the forward reaction (InGP to indole) and the reverse reaction (indole to InGP). The majority of the mutant α-subunits had <10% of the wild-type activity in the forward reaction, as expected since these mutant strains were selected for defects in this reaction. In contrast, the majority of these mutant enzymes had >50% of the wild-type activity in the reverse reaction. Several had 5 to 15% of wild-type specific activity in the forward reaction but 60 to 100% of wild-type specific activity in the reverse reaction. Spontaneous revertant strains, selected for their increased ability to catalyze the forward reaction effectively, contained α-subunits with the expected higher specific activities in the forward reaction but without parallel changes in the reverse reaction activity.     

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.     

Effects of Cations and Other Medium Components on the Zona-induced Acrosome Reaction of Hamster Spermatozoa

Although the acrosome reaction in lively motile hamster spermatozoa can occur independently of the egg or its investments ("spontaneous" acrosome reaction), it appears to be the egg investments, particularly the zona pellucida, that induces the acrosome reaction in fertilizing spermatozoa of many mammalian species. The latter is referred to as "zona-induced" acrosome reaction. Experiments were conducted to determine if the zona-induced acrosome reaction has different ion requirements from the spontaneous reaction. Like the spontaneous acrosome reaction, the zona-induced acrosome reaction required extracellular Na⁺, K⁺ and Ca²⁺. The absence of Cl⁻ and albumin in the medium inhibited the reaction. The zona-induced acrosome reaction could occur in a HCO₃⁻-free medium, but far less efficiently than in medium containing this ion. Proteinase inhibitors, benzamidine and TLCK, inhibited the zona-induced acrosome reaction. These results suggest that the chemical reactions involved in the spontaneous and zona-induced acrosome reactions are similar although the reaction-triggering mechanism is probably different.     

Sensitivity of the (Na+ + k+)-atpase to state-dependent inhibitors. Effects of digitonin and Triton X-100

Treatment of a purified (NA+ + 5+)-ATPase preparation from dog kidney with digitonin reduced enzymatic activity, with the (Na+ + k+)-atpase reaction inhibited more than the K+-phosphatase reaction that is also catalyzed by this enzyme. Under the usual assay conditions oligomycin inhibits the (Na+ + k+)-atpase reaction but not the K+-phosphatase reaction; however, treatment with digitonin made the K+-phosphatase reaction almost as sensitive to oligomycin as the (Na+ + k+)-atpase reaction. The non-ionic detergents, Triton X-100, Lubrol WX and Tween 20, also conferred sensitivity to oligomycin on the K+-phosphatase reaction (in the absence of oligomycin all these detergents, unlike digitonin, inhibited the K+-phosphatase reaction more than the (Na+ + k+)-atpase reaction). Both digitonin and Triton markedly increased the K0.5 for K+ as activator of the K+-phosphatase reaction, with little effect on the K0.5 for K+ as activator of the (Na+ + k+)-ATpase reaction. In contrast, increasing the K0.5 for K+ in the K+-phosphatase reaction by treatment of the enxyme with acetic anhydride did not confer sensitivity to oligomycin. Both digitonin and Triton also increased the inhibition of the K+-phosphatase reaction by ATP and increased the inhibition by inorganic phosphate and vanadate. These observations are interpreted as digitonin and Triton favoring the E1 conformational state of the enzyme (manifested by sensitivity to oligomycin and a greater affinity for ATP at the low-affinity substrate sites), as opposed to the E2 state (manifested by insensitivity to oligomycin, greater sensitivity to phosphate and vanadate, and a lower K0.5 for K+ in the K+-phosphatase reaction). In addition, digitonin blocked activation of the phosphatase reaction by Na+ plus CTP. This effect is consistent with digitonin dissociating the catalytic subunits of the enzyme, the interaction of which may be essential for activation by Na+ plus nucleotide.     

Critical analysis of the use of the acrolein-Schiff method as a possible DNA reaction

Summary Histophotometric examination was carried out on nuclei of lymphocytes in human peripheral blood, which were subjected to various tests in order to assess the acrolein-Schiff method as a possible DNA specific reaction, in comparison with the traditional Feulgen reaction. Special attention was paid to the degree of difference between responses attributable to a direct Schiff reaction obtained in the fraction of nuclear proteins after treatment with acrolein. From the results obtained it appears that an acrolein-Schiff reaction, following extraction of proteins, may be considered a qualitative reaction for DNA. Our findings also show that there is no relationship between the degree of response to the acrolein-Schiff reaction and that to the Feulgen reaction, which is to be expected in view of the different mechanisms of the two reactions.     

Alterations of RNase H sensitivity of the 3'' splice site region during the in vitro splicing reaction.

We have developed a splicing assay system with an immobilized pre-mRNA to study the mechanism of the splicing reaction after spliceosome assembly. Using this system, we have found that the second step of the splicing reaction could be dissected into two stages. After the 5' splice site reaction, at least two factors interact with the pre-formed spliceosome containing intermediate molecules in an ATP-independent manner to convert the spliceosome into a form competent for the 3' splice site reaction. Then, the 3' splice site reaction occurs on this spliceosome, if ATP is supplied to the reaction mixture. We have also investigated the dynamic state of the 3' splice site region in the spliceosomes during the splicing reaction by probing with RNase H sensitivity. Prior to the 5' splice site reaction, the 3' splice site region was protected from RNase H attack. The region became sensitive immediately after the 5' splice site reaction, and subsequently became resistant again as the spliceosome competent for the 3' splice site reaction was formed. These results suggest that the interaction of the 3' splice site region with some spliceosome components changes significantly during the splicing reaction.     

A kinetic model of the cleavage of permutational variants of the antigenomic HDV-ribozyme

The kinetic characteristics have been studied for noncircularly permuted variants of the human hepatitis delta virus (HDV) antigenomic ribozyme to find out the cause of the two-phase kinetics of the self-cleavage reaction. Different ways of reaction initiation, suboptimal conditions, and jumpwise changes of reaction conditions have been used, and the temperature dependences have been studied. A correlation has been shown between the apparent kinetic constant of the first reaction phase and the portion of the ribozyme molecules that self-cleaved during the first phase. Partial restoration of the initial reaction characteristics has been shown by the reinitiation of reaction being stopped after completing the first phase. On the basis of all the data obtained, a scheme of the self-cleavage reaction has been proposed including: (i) activation of the ribozyme with energy of 40-50 kcal/mol and a characteristic time of several deciminutes under optimal reaction conditions; (ii) fast and reversible reaction of the phosphodiester bond cleavage; (iii) reaction leading to isomerization of the 3',5'-phosphodiester bond to the 2',5' bond in the self-cleavage site with a characteristic activation time of tens of minutes; and (iv) practically irreversible conformational change leading to fixation of the cleavage by immobilization of the 5'-terminal nucleotide of the product in the center of the formed structure and displacement of the 3'-terminal nucleotide to the periphery. The latter process has a characteristic time of tens of minutes and a low activation energy.     

Kinetics of ATP-stimulated nuclease activity of the Escherichia coli RecBCD enzyme

The RecBCD enzyme is an ATP-dependent nuclease on both single-stranded and double-stranded DNA substrates. We have investigated the kinetics of the RecBCD-catalyzed reaction with small, single-stranded oligodeoxyribonucleotide substrates under single-turnover conditions using rapid-quench flow techniques. RecBCD-DNA complexes were allowed to form in pre-incubation mixtures. The nuclease reactions were initiated by mixing with ATP. The reaction time-courses were fit to several possible reaction mechanisms and quantitative estimates were obtained for rate constants for individual reaction steps. The relative rates of forward reaction versus dissociation from the DNA, and the fact that inclusion of excess non-radiolabeled single-stranded DNA to trap free RecBCD has no effect on the nuclease reaction, indicates that the reaction is processive. The reaction products show that the reaction begins near the 3'-end of the [5'-32P]DNA substrates and the major cleavage sites are two to four phosphodiester bonds apart. The product distribution is unchanged as the ATP concentration varies from 10 microM to 100 microM ATP, while the overall reaction rate varies by about tenfold. These observations suggest that DNA cleavage is tightly coordinated with movement of the enzyme along the DNA. The reaction time-courses at low concentrations of ATP (10 microM and 25 microM) have a significant lag before cleavage products appear. We propose that the lag represents ATP-dependent movement of the DNA from an initial binding site in the helicase domain of the RecB subunit to the nuclease active site in a separate domain of RecB. The extent of reaction of the substrate is limited (approximately 50%) under all conditions. This may indicate the formation of a non-productive RecBCD-DNA complex that does not dissociate in the 1-2 s time-scale of our experiments.     

Biosynthesis of Chlorophyll of Photosystem II Reaction Centers in Plant Leaves in Early Stages of Etiolation

Spectral methods were used to study the sequences of chlorophyll biosynthesis reactions in etiolated pea, bean, and maize plants in early stages (3-4 days) of growth. For these juvenile plants, along with the reaction chain known for mature (7-9 day-old) plants, a new reaction chain was found which started with phototransformation of the long-wavelength form PChld 686/676 into PChld 653/648. (PChld 653/648 differs from the main known precursor form PChld 655/650). The subsequent photoreduction of PChld 653/648 leads to the formation of Chld 684/676, which is transformed into Chl 688/680 in the course of a dark reaction. After completion of this reaction, fast (20-30 sec) quenching of the fluorescence of the reaction product is observed with the formation of non-fluorescent Chl 680. The reaction accompanied by pigment fluorescence quenching is absent in pea mutants with depressed function of Photosystem II reaction centers. This suggests that the newly found reaction chain leads to the formation of chlorophyll of the Photosystem II reaction center.     

Effect of food reductones on the generation of the pyrazine cation radical and on the formation of the mutagens in the reaction of glucose, glycine and creatinine

One of the possible pathways of the formation of mutagens in heated foods is through the pyrazine cation radical generated in the early stage of the Maillard reaction. The aim of the present study was to elucidate how food reductones contribute to the pyrazine cation radical generation in the reaction of glucose (Glc) and glycine (Gly), and to the formation of the mutagens in the reaction of Glc, Gly and creatinine. Electron spin resonance (ESR) studies showed that fragrant reductones, 2,5-dimethyl-4-hydroxy-3(2H)-furanone (DMHF) and 4-hydroxy-2(or 5)-ethyl-5(or 2)-methyl-3(2H)-furanone (HEMF), generated in the Maillard reactions, enhanced the generation of the pyrazine cation radical in the reaction of Glc and Gly, and the reaction of DMHF or HEMF with Gly generated a larger amount of the pyrazine cation radical than the reaction of Glc and Gly, indicating that the furanones were intermediates of the pyrazine cation radical. By contrast, food antioxidants, ascorbic acid and erythorbic acid, effectively scavenged the pyrazine cation radical generated in the reaction of Glc and Gly. DMHF and HEMF were not effective to modulate the mutagen formation in the reaction of Glc, Gly and creatinine, and the mutagenicity produced in the reaction of DMHF or HEMF, Gly and creatinine was lower than that produced in the reaction of Glc, Gly and creatinine. On the other hand, ascorbic acid and erythorbic acid were effective to decrease the mutagen formation in the reaction of Glc, Gly and creatinine.     

Estimation of the contribution of the bioluminescent reaction rate and quantum yield to the enhancement of firefly bioluminescence in the presence of cationic liposomes.

Cationic liposomes containing phosphatidylcholine, cholesterol and distearyldimethylammonium chloride (DSDAC) enhanced maximum light emission (BL intensity) and total light emission from the firefly bioluminescence (BL) reaction. The increase in BL intensity was interpreted on the basis of the increase in both BL reaction rate and BL quantum yield (PhiBL) of the BL reaction. The increase in BL reaction rate was due to the increase in the localized concentration of BL reactants on the surface of cationic liposomes by electrostatic interaction. On the other hand, the increase in PhiBL was due to the change of light-emitting species in the presence of cationic liposomes. Each contribution of BL reaction rate and PhiBL to the enhancement of the BL intensity was estimated by measuring the BL reaction rate and PhiBL in the presence of cationic liposomes containing various amounts of DSDAC. The contribution of the BL reaction rate to the increase in the BL intensity was found to be two-fold greater than that of PhiBL.     

Phosphoenolpyruvate-dependent flavinylation of 6-hydroxy-D-nicotine oxidase

The reaction leading to the flavinylation of apo-6-hydroxy-D-nicotine oxidase was investigated in cell-free extracts of Eschericia coli carrying the 6-hydroxy-D-nicotine oxidase (6-HDNO) gene on the expression plasmid pDB222. It was demonstrated that the reaction required phosphoenolpyruvate (P-pyruvate) in addition to FAD. When [32P]P-pyruvate or [14C]P-pyruvate were used in the reaction with apo-6-HDNO, no phosphorylated or pyruvylated apo-protein could be detected, however. In order to drive the reaction to completion, FAD and P-pyruvate had to be present simultaneously in the reaction mixture. When apo-6-HDNO, highly purified by affinity chromatography, was used in the reaction with P-pyruvate and FAD, no additional protein fraction was required. A possible reaction scheme for the formation of holoenzyme from 6-HDNO is discussed.     

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.     

The effect of agitation intensity on alkali-catalyzed methanolysis of sunflower oil

The sunflower oil methanolysis was studied in a stirred reactor at different agitation speeds. The measurements of drop size, drop size distribution and the conversion degree demonstrate the effects of the agitation speed in both non-reaction (methanol/sunflower oil) and reaction (methanol/KOH/sunflower oil) systems. Drop size distributions were found to become narrower and shift to smaller sizes with increasing agitation speed as well as with the progress of the methanolysis reaction at a constant agitation speed. During the methanolysis reaction, the Sauter-mean drop diameter stays constant in the initial slow reaction region, rapidly decreases during the fast reaction period and finally reaches the equilibrium level. Due to the fact that the interfacial area increases, one can conclude that the rate of reaction occurring at the interface will also be enhanced progressively. The "autocatalytic" behavior of the methanolysis reaction is explained by this "self-enhancement" of the interfacial area, due to intensive drop breakage process.     

Kinetics of the reaction of nitroblue tetrazolium reduction by human blood neutrophils

Kinetics of Nitro blue tetrazolium (NBT) reduction to diformasan by neutrophils was investigated using 27 samples of human blood. Analysis of alteration in the share of activated neutrophils (ANP) and activated neutrophil index (ANI) was done in relation to the reaction time. The former reaction is an irreversible reaction of zero (pseudozero) order, while the latter is an irreversible reaction of the first (pseudofirst) order. It has been found out that an induced NBT reduction occurs in parallel with a spontaneous reaction, and that neutrophils have essentially different oxidizing power. The kinetic approach enabled us to discover some indices (NBT quantity involved in the reaction, and reaction speed constant of the first order) which in different samples varied within broader limits than ANP or ANI (within the limits of an order), i.e. provided a possibility to make a more delicate analysis of processes in neutrophils.     

Model sclerotization studies. 4. Generation of N-acetylmethionyl catechol adducts during tyrosinase-catalyzed oxidation of catechols in the presence of N-acetylmethionine

Incubation of catechol with mushroom tyrosinase in the presence of N-acetylmethionine resulted in the generation of an adduct. This product was identified to be N-acetylmethionyl catechol, on the basis of spectral characteristics and well-characterized chemical reaction of o-benzoquinone with N-acetylmethionine. Enzyme-catalyzed oxidation of catechol and the subsequent nonenzymatic addition of the resultant quinone to N-acetylmethionine accounted for the observed reaction. That the reaction is not confined to catechol alone, but is of general occurrence, can be demonstrated by the facile generation of similar adducts in incubation mixtures containing N-acetylmethionine, tyrosinase, and different N-acetylmethionines, such as 4-methylcatechol and N-acetyldopamine. Attempts to duplicate the reaction with insect cuticular phenoloxidases were not successful, as the excess N-acetylmethionine used in the reaction inhibited their activity. Nevertheless, occurrence of this nonenzymatic reaction between N-acetylmethionine and mushroom tyrosinase-generated quinones indicates that a similar reaction between enzymatically generated quinones in the cuticle with protein-bound methionine moiety is likely to occur during in vivo quinone tanning as well. Arch. Insect Biochem. Physiol. 38:44–52, 1998. © 1998 Wiley-Liss, Inc.     

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.     

Engineering aspects of immobilized lipases on esterification: A special emphasis of crowding,confinement and diffusion effects

Cross‐linked enzyme crystal (CLEC) and sol‐gel entrapped pseudomonas sp. lipase were investigated for the esterification of lauric acid with ethanol by considering the effects of reaction conditions on reaction rate. The activation energy for the reaction was estimated to be 1097.58 J/mol and 181.75 J/mol for sol‐gel and CLEC entrapped lipase respectively. CLEC lipase exhibited a marginal internal diffusion effect on reaction rate over sol‐gel lipases and found to be interesting. The overall reaction mechanism was found to conform to the Ping Pong Bi Bi mechanism. The higher efficiency of sol‐gel lipases over CLEC lipases in esterification reaction is mainly due to the combined effects of crowding, confinement and diffusional limitations.