Genome-length copies of poliovirion RNA are synthesized in vitro by the poliovirus RNA-dependent RNA polymerase

A soluble RNA-dependent RNA polymerase was purified from the cytoplasm of poliovirus-infected HeLa cells. A single virus-specific protein designated as p63 (or NCVP4) copurified with this activity. The purified polymerase was free of ribonuclease activity and was shown to copy poliovirion RNA when oligo(U) was added to the in vitro reaction mixture. Characterization of the product RNA by electrophoresis in methylmercury (II) hydroxide-agarose gels showed that genome-sized copies of poliovirion RNA were synthesized in vitro by the purified polymerase. The product RNA was shown to be heteropolymeric, complementary to virion RNA, and covalently linked to oligo(U). The product RNA contained the expected distribution of UMP and GMP containing dinucleotide pairs which included a very low frequency of CpG pairs. The amount, size distribution, and rate of synthesis of product RNA was very dependent on the in vitro reaction conditions. Full sized product RNA was synthesized in about 6 min when reaction conditions were used that yielded maximum elongation rates (pH 8.0, 7 mM Mg2+, 37 degrees C). Under these conditions, most of the product RNA recovered from a 1-h reaction was full sized. Thus, the polymerase was found to specifically initiate synthesis at the 3'-end of the template using an oligo(U) primer and to carry out an elongation reaction at about 1250 nucleotides/min that resulted in the synthesis of full sized product RNA.     

General theory of determining intraparticle active immobilized enzyme distribution and rate parameters

A general theory is presented in this article for determining the intrinsic rate constants for the main reaction and deactivation reaction, the effective diffusivity of the substrate, and the active enzyme distribution within porous solid supports from deactivation study of a continuous stirred-basket reactor (CSBR). For the parallel deactivation five reaction kinetics are considered: (a) Michaelis-Menten, (b) substrate inhibition, (c) product inhibition (competitive), (d) product inhibition (anticompetitive), and (e) zero-order kinetics. The experimental results of the system of hydrogen-peroxide-immobilized catalase on controlled-pore glass particles are analyzed to demonstrate the application of the theory developed for parallel deactivation of active immobilized enzyme (IME). For series deactivation only first-order kinetics is treated, and a numerical procedure is proposed to deter mine the rate parameters and the internal active enzyme distribution. The experimental data of the system of glucose-immobilized glucose oxidase on silica-alumina and controlled-pore glass particles are used to verify the theory.     

Molecular weight distribution of polymeric DNA-products, formed upon the action of matrix enzymes

Models of processive and distributive DNA synthesis and degradation catalysed by matrix enzymes were investigated. Distribution of polymer products dependent on the reaction model chosen, on the type of the matrix and on the enzyme-matrix initial concentration ratio were determined by methods of numerical modeling. Conditions were found where the scattering of the reaction polymer products was minimal. The homopolymer matrix choice of experimental condition may generate a distribution of product that obeys the Poisson distribution. Numerical investigations of polymerization (hydrolysis) processes showed that for a number of heteropolymer matrixes a distribution may exist with scattering much less than that for homopolymer matrixes. Conditions are found when processive and distributive models give different distributions of the reaction product.     

Immobilized enzymes: Electrokinetic effects on reaction rates under external diffusion

The rates of reactions catalyzed by enzymes immobilized on a nonporous solid surface have been computed employing a Nernst film model. The Nernst-Planck equations for the transport of the charged substrate and product species in the film and the Poisson equation for the distribution of electrical potential are solved numerically with the appropriate boundary conditions. The electrical charge at the surface is assumed to arise from the dissociation equilibria of the acidic and basic surface groups of the enzyme. The pH at the surface affects both the surface charge as well as the intrinsic kinetics of the enzyme-catalyzed reaction. Factors which determine the pH at the surface include the pH in the bulk solution and the release of H(+) ions in the enzyme-catalyzed reaction. The latter causes a lowering of pH at the surface, causing the reaction rate to differ from that computed assuming an equilibrium distribution of electrical potential. Another kind of nonequilibrium contribution is caused by unequal charges or diffusivities of the substrate and products, which results in a diffusion potential being set up. Two moduli are introduced to evaluate the significance of the reaction-generated lowering of pH and the diffusion potential effect. The effect of changing various parameters, e.g., reaction rate constant, substrate concentration, enzyme concentration, pH, etc., on the overall reaction rate are studied.     

Chemical dynamic approach to synergetics and instability in biological systems

Based on Haken's theory, self-organization or synergetics is discussed using chemical dynamics to represent an autocatalytic reaction. In a simple case the changes in a self-organizing system are given by a set of two rate equations for a primary and a partial system. When these systems mutually form a feedback loop under the adiabatic condition, the rate equation of self-organization is described by a generalized Gibbs' free energy change delta U (delta x) followed by the reaction. The sign of the parameter k'3 (k0-kex; k0, kex: rate constants with or without an external stimulus) determines the instability of the coupled system in quasi-equilibrium (k'3 approximately greater than 0; k0 greater than kex). When the product exceeds the threshold (k'3 less than 0; k0 less than kex), the system transfers into a new state, or a phase transition appears. Considering the Boltzmann distribution, the transition parameter k'3 is evaluated by an average distribution of the states and the instability is discussed using the reaction velocities vqe and vqe in the quasi-equilibrium state. As an example of this model membrane excitation is discussed briefly.     

Quantitative assessment of Na+,K+-ATPase localization by direct and indirect p-nitrophenyl phosphatase methods

Na+,K+-ATPase histochemistry, using direct (Pb) and indirect (Mg/Sr-Co) p-nitrophenyl phosphatase methods, was assessed by scanning integrative microdensitometry of three classes of tubules in mouse and guinea pig kidneys. The methods yielded similar and appropriate patterns of activity distribution and inhibitor response. The indirect method gave preferable results, in that non-enzymic background was lower and rate of reaction product accumulation was considerably higher.     

Enzymatic peptide synthesis in organic media: a comparative study of water-miscible and water-immiscible solvent systems.

Peptide synthesis was carried out in a variety of organic solvents with low contents of water. The enzyme was deposited on the support material, celite, from an aqueous buffer solution. After evaporation of the water the biocatalyst was suspended in the reaction mixtures. The chymotrypsin-catalyzed reaction between Z-Phe-OMe and Leu-NH2 was used as a model reaction. Under the conditions used ([Z-Phe-OMe]0 less than or equal to 40 mM, [Leu-NH2]0/([Z-Phe-OMe]0 = 1.5) the reaction was first order with respect to Z-Phe-OMe. Tris buffer, pH 7.8, was the best buffer to use in the preparation of the biocatalyst. In water-miscible solvents the reaction rate increased with increasing water content, but the final yield of peptide decreased due to the competing hydrolysis of Z-Phe-OMe. Among the water-miscible solvents, acetonitrile was the most suitable, giving 91% yield with 4% (by vol.) water. In water-immiscible solvents the reaction rate and the product distribution were little affected by water additions in the range between 0% and 2% (vol. %) in excess of water saturation. The reaction rates correlated well with the log P values of the solvent. The highest yield (93%) was obtained in ethyl acetate; in this solvent the reaction was also fast. Under most reaction conditions used the reaction product was stable; secondary hydrolysis of the peptide formed was normally negligible. The method presented is a combination of kinetically controlled peptide synthesis (giving high reaction rates) and thermodynamically controlled peptide synthesis (giving stable reaction products).     

Fine structure distribution of non-specific acid phosphatase in the head region of mouse spermatozoa from various regions of the male reproductive tract.

The fine structure distribution of non-specific acid phosphatase was determined in the head region of mouse spermatozoa from the testes, the caput, corpus and cauda epididymidis and the ductus deferens. Enzymatic localization was achieved by the Gomori technique. The postacrosomal dense lamina, the nuclear side of the inner acrosomal membrane and the space between the plasmalemma and the outer acrosomal membrane showed reaction product in spermatozoa from the testis and caput epididymidis. Spermatozoa from the cauda epididymidis exhibited reaction product only between the plasmalemma and the outer acrosomal membrane. Spermatozoa from the corpus epididymidis and from the ductus deferens showed no reaction product in the head region. The changes observed in the distribution of acid phosphatase in the sperm head during epididymal transport may reflect maturational events.     

Kinetics of the amylase system of Saccharomycopsis fibuliger

The extracellular amylases produced by Saccharomycopsis fibuliger have been studied with the intent of identifying the kinetic mechanism and product distribution, and modelling the production of d-glucose during starch hydrolysis. High performance liquid chromatography was effectively used to separate and quantify the product oligomers released. α-Amylase rapidly hydrolysed the long substrate chains into smaller oligomers which became the substrate for glucoamylase in the production of d-glucose. The formation of a rate limiting substrate occurred late in the reaction. Glucoamylase and α-amylase rates were fitted to Michaelis-Menten models with d-glucose inhibition included.     

Formation of Hydroxyl Radicals on Reaction of Hypochlorous Acid with Ferrocyanide, a Model IRON(II) Complex

Hypochlorous acid reacts with the model iron(II) complex, ferrocyanide (Fe(CN)₆^4-) in aqueous solution with the rate constant 220 ± 15 dm³ mol^-1 s^-1. Free hydroxyl radicals are formed in this reaction in 27% yield as shown by the hydroxylation of benzoate to give a product distribution identical to that of free (radiolytically generated) hydroxyl radicals. This reaction is three orders of magnitude faster than the analogous reaction involving hydrogen peroxide (the Fenton reaction), suggesting that the hypochlorous acid generated by activated neutrophils may be a source of hydroxyl radicals.     

The oxidation of D-glucose and D-fructose with oxygen in aqueous,alkaline solutions : Part II. The overall kinetics

Based on a previously reported, integral reaction-scheme, a very simple, kinetic model for the homogeneous oxidation of D-glucose and D-fructose in aqueous, alkaline solutions has been developed. It involves the influence of the type and concentration of the hexose, the hydroxyl-ion concentration, the oxygen concentration in the liquid phase, and the temperature on the rate of formation of the acidic reaction products. No attention is paid to the product distribution.     

Histochemical localization of acetylcholinesterase in the cerebral ganglia of Fasciola hepatica, a parasitic flatworm

Acetylcholinesterase activity was found in the cell bodies and extracellularly in the neuropile of the cerebral ganglia of the adult trematode parasite, Fasciola hepatica. Within neuronal cell bodies of the cerebral ganglion, acetylcholinesterase reaction product was found in the endoplasmic reticulum, in the cisternae of the Golgi apparatus, and in secretory vesicles near the inner (releasing face) cisternae. Acetylcholinesterase reaction product was not seen intracellularly within any nerve processes. The reaction product was found around the somatic cell membranes and in the extracellular space between closely apposed nerve processes in the neuropile. Acetylcholinesterase reaction product was associated with synaptic endings that contained clear spheroidal synaptic vesicles, and the reaction product was localized at the site of synaptic contact between the zone of apposition of the pre- and postsynaptic terminals. This intracellular and extracellular distribution of the enzyme is consistent with its function as the degrading enzyme in cholinergic transmission.     

Effect of Macromolecular Crowding on Reaction Rates: A Computational and Theoretical Study

The effect of macromolecular crowding on the rates of association reactions are investigated using theory and computer simulations. Reactants and crowding agents are both hard spheres, and when two reactants collide they form product with a reaction probability, p_rxn. A value of p_rxn < 1 crudely mimics the fact that proteins must be oriented properly for an association reaction to occur. The simulations show that the dependence of the reaction rate on the volume fraction of crowding agents varies with the reaction probability. For reaction probabilities close to unity where most of encounters between reactants lead to a reaction, the reaction rate always decreases as the volume fraction of crowding agents is increased due to the reduced diffusion coefficient of reactants. On the other hand, for very small reaction probabilities where, in most of encounters, the reaction does not occur, the reaction rate increases with the volume fraction of crowding agents—in this case, due to the increase probability of a recollision. The Smoluchowski theory refined with the radiation boundary condition and the radial distribution function at contact is in quantitative agreement with simulations for the reaction rate constant and allows the quantitative analysis of both effects separately.     

Vectorial product concentration obtained with a permeable immobilized enzyme membrane. A new approach to the analysis of biological transport systems.

The theoretical analysis of the distribution on both sides of a flat porous membrane of the product generated by an enzyme covalently bound only on to one side of the membrane separating two compartments of widely different volumes is presented. Contrary to what occurs with heterogeneous symmetric systems, the diffusional limitations at the enzyme level play a prominent role, not only on the apparent enzyme activity, but also on product flux-splitting. The mathematical model developed shows that it is possible to concentrate the reaction product in the compartment opposite to that where the reaction occurs. The influence of the parameters and of the physical characteristics of an asymmetrical system on product distribution is analysed. This theoretical analysis is in excellent agreement with experimental data obtained with glucose oxidase immobilized on a porous collagen membrane.     

Reaction mechanism of non-allosteric phosphofructokinase.

The reaction mechanism of the non-allosteric phosphofructokinase from Lactobacillus plantarum was investigated by initial-rate bisubstrate kinetics and product inhibition kinetics adn by the measurement of equilibrium isotope exchange in the presence of various substrate and product concentrations. The reaction mechanism is clearly sequential. The product inhibition and equilibrium isotope-exchange patterns are consistent with an ordered bi-bi reaction sequence with fructose 6-phosphate as the leading substrate and ADP as the first product released from the enzyme.     

Differential alterations in the distribution of three phosphatase enzymes during the plasma membrane transformation of uterine epithelial cells in the rat.

Ultrastructural and light microscopic cytochemical methods were used to study the distribution and changes in distribution of three phosphatase enzymes: 5'-nucleotidase (5N); thiamine pyrophosphatase (TPP); and adenosine triphosphatase (ATP) in the rat endometrium during early pregnancy up to the time of blastocyst attachment. The authors were particularly interested in changes in the apical plasma membrane and reaction product for all three enzymes was clearly localized along this membrane especially on day 1 of pregnancy. However, the three enzymes showed markedly different patterns of organization of reaction product at later times during early pregnancy. 5N, while showing a continuous lining along the microvilli on day 1 was virtually undetectable by day 6. TPP was also strongly present apically on day 1, but reaction product was not always found as a continuous lining. Again, by day 6, there was no presence of this enzyme along the apical surface. ATP differed from the other two in that it produced a strong, and relatively unchanged reaction product along the apical plasma membrane from day 1 through to day 6 of pregnancy. The changes in distribution of these enzymes was particularly obvious at the electron microscopic level and we consider their contribution to the process of 'plasma membrane transformation' of early pregnancy.     

The localization of thiamine pyrophosphatase activity in Meckel's cartilage cells during endochondral ossification

The cytochemical distribution of thiamine pyrophosphatase (TPPase) activity in Meckel's cartilage cells of the mouse embryo has been studied during the endochondral ossification. All the cartilage cells contain reaction product within the Golgi apparatus. In immature chondrocytes, at the reserve cell zone, TPPase activity is restricted to several inner cisternae of independent Golgi apparatus. In mature cells at the proliferative cell zone, several Golgi complexes form a Golgi network connecting with each other by the TPPase positive tubular stalks. Golgi cisternae, condensing vacuoles and vesicles also contain reaction product. In the hypertrophic chondrocytes located in the calcifying zone, their disorganized Golgi apparatus still retain reaction product. Some chondrocytes, even those located within calcified or opened lacunae, exhibit intact structures and normal cytochemical enzyme distribution. These data indicate the possibility that some chondrocytes may survive and contribute the formation of mandible.     

A quantitative cytochemical assay for osteoclast acid phosphatase activity in foetal rat calvaria

Summary Acid phosphatase activity is prominent in osteoclasts (bone resorbing cells) and has been implicated in the process of bone resorption, although its precise role is not understood. To study the distribution and activity of this enzyme, a quantitative cytochemical method has been developed using undecalcified fresh frozen sections of foetal rat calvariae. Sections were allowed to react with 3mm naphthol ASBI phosphate at pH 5.0, and the reaction was stopped by rinsing in ice-cold tap water containing 50mm sodium fluoride. The reaction product was post-coupled to Fast Garnet at 4°C. The absorbance of areas of reaction product in the cytoplasm was measured using scanning and integrating microdensitometry. The initial velocity rate was maintained for up to 2 min at pH 5.0 with a substrate concentration of 3mm and a section thickness of 5 µm. Under these conditions reaction product was localized to osteoclasts and the surface of bone matrix beneath these cells. Activities in osteoblasts and chondrocytes were negligible. Osteoclastic acid phosphatase was almost totally inhibited by 10mm fluoride and reduced by 70% by 100mm tartrate.     

The localization of thiamine pyrophosphatase activity in Meckel's cartilage cells during endochondral ossification

Summary The cytochemical distribution of thiamine pyrophosphatase (TPPase) activity in Meckel's cartilage cells of the mouse embryo has been studied during the endochondral ossification. All the cartilage cells contain reaction product within the Golgi apparatus. In immature chondrocytes, at the reserve cell zone, TPPase activity is restricted to several inner cisternae of independent Golgi apparatus. In mature cells at the proliferative cell zone, several Golgi complexes form a Golgi network connecting with each other by the TPPase positive tubular stalks. Golgi cisternae, condensing vacuoles and vesicles also contain reaction product. In the hypertrophic chondrocytes located in the calcifying zone, their disorganized Golgi apparatus still retain reaction product. Some chondrocytes, even those located within calcified or opened lacunae, exhibit intact structures and normal cytochemical enzyme distribution. These data indicate the possibility that some chondrocytes may survive and contribute the formation of mandible.     

The determination of enzyme-substrate dissociation rates by dynamic isotope exchange enhancement experiments

A new method for the determination of dissociation rates of enzyme-substrate complexes has been developed. The rate of exchange of a labeled product back into the substrate is measured during catalysis of the forward reaction when the forward reaction is kept far from equilibrium by the enzymatic removal of the nonexchanging product. The ratio of the exchange rate and the net rate for product formation is then determined at various concentrations of the exchanging product. A plot of this ratio is a diagnostic indication of the kinetic mechanism and the relative rates of product dissociation from the binary and ternary enzyme complexes. This technique has been applied to the reaction catalyzed by bovine liver argininosuccinate lyase. The ratio for the rate of exchange of fumarate into argininosuccinate and the net rate for product formation was found to increase with the concentration of fumarate but to reach a limit of 3.3. The ratio of rates was half-maximal at 36 mM fumarate. The data have been interpreted to indicate the argininosuccinate lyase has a random kinetic mechanism. The calculated lower limit for the rate of release of arginine from the enzyme-fumarate-arginine complex is 0.35 times as fast as the Vmax in the reverse direction. The rate of release of arginine from the enzyme-arginine binary complex is 210 times faster than Vmax in the reverse direction.