Oxidation-reduction reactions of hemoglobin A, hemoglobin M Iwate, and hemoglobin M Hyde Park

The kinetics and equilibrium of the redox reactions of hemoglobin A, hemoglobin M Iwate, and hemoglobin M Hyde Park using the iron (II) and iron (III) complexes of trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetate (CDTA4-) as the reducing and oxidizing agents have been studied. With respect to the equilibrium it was found that hemoglobin M Iwate (where the beta chains were reduced) was more readily reduced than hemoglobin M Hyde Park (where the alpha chains are reduced). This difference was shown to be a result of a difference in the rate constant for reduction but not oxidation. The observed rate contants for the reduction of all three hemoglobins were shown to decrease with increasing pH. This was attributed to a decrease in the [T]/[R] ratio. The observed rate contants for the oxidation reaction were shown to increase with increasing pH. Accompanying this increase was a change in the kinetic profile for hemoglobin A from pseudo first order to one in which the rate increased as the extent of reaction increased. Inositol hexaphosphate had no effect on the rate of oxidation of deoxyhemoglobin A. This was a result of binding of FeCDTA2- or HCDTA3- to the protein. However, in the presence of inositol hexaphosphate, the reduction of methemoglobin A exhibited biphasic kinetics. This result was interpreted in terms of the production of a small amount of a conformation which was more readily reduced.     

Liquid-metering device for continuous culture

A device is described for aseptically metering liquids at rates as low as 10 ml./hr. The metering rate is constant, but can be readily changed. The device delivers a measured increment of liquid every 10 sec. The volume added is controlled by electrical contants in an electrolyte tube. The medium does not enter this tube.     

A simulation model of sulfur transformations in forested Spodosols

Transformations of organic and inorganic S in two forested Spodosols from the Hubbard Brook Experimental Forest, New Hampshire and the Huntington Forest in the Adirondack Mts. of New York were investigated using laboratory³⁵SO₄ ^2- incorporation experiments. Sulfur transformations were modeled as a set of three reversible, first-order reactions in which soluble SO ₄ ^2- is converted to adsorbed SO ₄ ^2- , ester sulfate and carbon-bonded S. Reaction rate contants for³⁵SO ₄ ^2- adsorption/desorption and immobilization reactions involving ester sulfate and carbon-bonded S were determined using a fifth order Runge-Kutta-Fehlberg integration routine combined with least squares fitting. Model simulations were able to account for over 93% of the variation in the distribution of³⁵S in S fractions. A hypothetical application of immobilization rate constants to field situations at the Hubbard Brook Experimental Forest suggests that large quantities of S cycle through organic forms in Northern Hardwood Forest Ecosystems.     

Competitive and uncompetitive effects of 2,4-dinitrophenol on ATPase activities of rabbit skeletal actomyosin and myosin.

A kinetic study of the ATPase reactions catalyzed by myosin and actomyosin was carried out by varying the concentrations of ATP and 2,4-dinitrophenol (DNP). Mg-ATPase of myosin in the initial burst and that of actomyosin were both inhibited competitively by DNP. The dissociation contants for the DNP-myosin interaction (Ki) were estimated to be very similar, that is, 4.2 mM in the initial burst of ATP splitting, and 3.3 mM for the actomyosin ATPase. It is therefore suggested that DNP acts at the same site when it inhibits the burst splitting of ATP and the actomyosin ATPase. In contrast, Mg,-Ca-, and EDTA-ATPase activities of myosin in the steady state were all affected uncompetitively by DNP. Moreover, the Ki value for Mg-ATPase of myosin in the steady state was found to be 31 mM, which is much higher than those mentioned above for the initial burst and actomyosin ATPase. It is therefore suggested that the site at which DNP acts to inhibit the burst splitting of ATP is different from the site at which DNP acts to affect Mg-, Ca-, and EDTA-ATPases in the steady state.     

A pulse-radiolysis study of the manganese-containing superoxide dismutase from Bacillus stearothermophilus.

In the preceding paper the mechanism of catalysis of the manganese-containing superoxide dismutase from Bacillus stearothermophilus was shown to involve a 'fast cycle' and a 'slow cycle' [McAdam, Fox, Lavelle & Fielden, 1977 (Biochem. J. 165, 71-79)]. Further properties of the enzyme was considered in the present paper. Pulse-radiolysis studies, under conditions of low substrate concentration to (i.e. when the fast cycle predominates), showed that enzyme activity decreases as pH increases (6.5-10.2). Activity was unaffected by the addition of H2O2 or NaN3 but slightly decreased by KCN. Both H2O2 and the reducing radical anion CO2-- caused a decrease in A480 of the native enzyme. The rate of the fast catalytic cycle was independent of temperature (5-55 degrees C), and as temperature increases the slow cycle becomes relatively more important. Arrhenius parameters of the rate contants were estimated. The possible identity of the various forms of the enzyme is considered.     

Isobaric titration of readine monolayers: kinetics of hydrolysis of glycerides by pancreatic lipase B.

The rate of lipolytic enzyme-catalyzed reactions yielding water-soluble products can be measured by isobaric titration. The method is based upon the measurement of the amount of substrate that must be added to a monalayer to maintain constant surface pressure during the course of the enzymatic reaction. The rate constants determined for the hydrolysis of trioctanion and 1,2-diotanoin by pancreatic lipase were identical with those determined by the variable surface pressure method and by a radioactive substrate technique. This direct titrimetric method has a wider dynamic range and more versatility for following surface reactions that previously described systems.     

Prediction of Rate‐Limiting Reactions for Growth‐Associated Production Using a Constraint‐Based Approach

Identification of a rate‐limiting step in pathways is a key challenge in metabolic engineering. Although the prediction of rate‐limiting steps using a kinetic model is a powerful approach, there are several technical hurdles for developing a kinetic model. In this study, an in silico screening algorithm of key enzyme for metabolic engineering is developed to identify the possible rate‐limiting reactions for the growth‐coupled target production using a stoichiometric model without any experimental data and kinetic parameters. In this method, for each reaction, an upper‐bound flux constraint is imposed and the target production is predicted by linear programming. When the constraint decreases the target production at the optimal growth state, the reaction is thought to be a possible rate‐limiting step. For validation, this method is applied to the production of succinate or 1,4‐butanediol (1,4‐BDO) in Escherichia coli, in which the experimental engineering for eliminating rate‐limiting steps has been previously reported. In succinate production from glycerol, nine reactions including phosphoenolpyruvate carboxylase are predicted as the rate‐limiting steps. In 1,4‐BDO production from glucose, eight reactions including pyruvate dehydrogenase are predicted as the rate‐limiting steps. These predictions include experimentally identified rate‐limiting steps, which would contribute to metabolic engineering as a practical tool for screening candidates of rate‐limiting reactions.     

Optimization of Protease-Catalyzed Acyl Transfer Reactions. Determination of the Partition Constant Characterizing Nucleophile Efficiency

The partitioning of the acyl-enzyme between aminolysis by an added nucleophile and hydrolysis plays a key-role in protease-catalyzed acyl transfer reactions. It can be characterized by the partition constant, which is equal to the nucleophile concentration for which aminolysis and hydrolysis proceed at the same velocity. We describe a method for calculation of the partition constant from the product ratio which is based on the integrated rate equation. Therefore, it can be applied to reactions performed under synthesis-like conditions, i.e. a high degree of nucleophile consumption during the reaction. In principle, the dependence of the partition constant on nucleophile concentration can be determined from a single reaction. V8-protease-catalyzed acyl transfer reactions using Z-Glu-OMe as acyl donor and amino acid amides as nucleophiles were investigated as an application of the method. The central role of the partition constant in optimization of preparative protease-catalyzed acyl transfer reactions is discussed.     

Optimization of Protease-Catalyzed Acyl Transfer Reactions. Determination of the Partition Constant Characterizing Nucleophile Efficiency

The partitioning of the acyl-enzyme between aminolysis by an added nucleophile and hydrolysis plays a key-role in protease-catalyzed acyl transfer reactions. It can be characterized by the partition constant, which is equal to the nucleophile concentration for which aminolysis and hydrolysis proceed at the same velocity. We describe a method for calculation of the partition constant from the product ratio which is based on the integrated rate equation. Therefore, it can be applied to reactions performed under synthesis-like conditions, i.e. a high degree of nucleophile consumption during the reaction. In principle, the dependence of the partition constant on nucleophile concentration can be determined from a single reaction. V8-protease-catalyzed acyl transfer reactions using Z-Glu-OMe as acyl donor and amino acid amides as nucleophiles were investigated as an application of the method. The central role of the partition constant in optimization of preparative protease-catalyzed acyl transfer reactions is discussed.     

The rate constants of the reaction of hydroxyl radicals (*OH) with alcohol dehydrogenase and Glyceraldehyde-3-phosphate dehydrogenase

The rate constants of the reactions of alcohol dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase with hydroxyl radicals were determined using the method of steady-state competitive reactions. Ethanol was used as a scavenger of hydroxyl radicals. The rate constants of the reactions of hydroxyl radicals with alcohol dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase were found to be 2.8 x 10(12) dm(3) mol(-1) s(-1), and 1.6 x 10(12) dm(3) mol(-1) s(-1), respectively.     

Experimentation in Lille with the passive hemagglutination test for the detection of Australia antigen. Comparison with other methods]

Among 5347 blood donors sera, the reverse passive hemagglutination test (RPH) enabled to detect 3,55% of HB ag (whereas 2,43% by EID). On the other hand, among 180 patients, the rate of positive reactions was observed to be the same for both techniques, which must be attributed to the presence of higher titer antigens. In the two series all positive reactions found by RPH method were also tested by RIA; this enabled to eliminate a great number (18% and 27%) of false positive reactions, which remain the disadvantage of the method. It must be also noticed that the complement fixation reaction gave the same results as the RIA.     

On true and apparent Michaelis constants in enzymology. III. Is it linear dependence between apparent michaelis constant and limiting rate and is it possible to determine the substrate constant value using this dependence?

The Slater-Bonner method which is used for graphic determination of substrate constant (Ks) by linear dependence of apparent Michaelis constant (Km(app)) on the limiting rate (V(app)) of enzyme-catalysed reactions with activator participation has been critically analysed. It has been shown that although it is possible to record the mechanisms of such reactions as a scheme similar to Michaelis-Menten model which allow to find correlation Km(app) and V(app) as equation Km(app) = Ks + V(app)/k1[E]0 ([E]0 is a total enzyme concentration, k1 is a rate constant of enzyme-substrate complex formation from free enzyme and substrate) in order to calculate Ks and individual rate constants (k1, k(-1)), but this approach for investigation of all reactions with activator participation ought not to be used. The above equation is not obeyed in general, it may be true for some mechanisms only or under certain ratios of kinetic parameters of enzyme-catalysed reactions.     

The water-sweet aftertaste of neohesperidin dihydrochalcone and thaumatin as a method for determining their sweet persistence

The water–sweet aftertaste produced in humans in responseto tasting intensive sweeteners such as neohesperidin dihydrochalconeand thaumatin was studied. This water–sweet aftertasteincreased with sweetener concentration and diminished with time.The decay in the sweet intensity–time relationships fitteda negative exponential function in a pattern similar to thatwhich occurs when other methods for determining persistenceare employed. Persistence time contants (T) were dependent uponthe maximal perceived sweet intensity (Ip-max) observed at theinitial time of tasting. The use of this procedure is proposedfor determining persistence of intensive sweeteners under circumstanceswhere controlled pH and temperature are desired.     

Identification of flux control in metabolic networks using non-equilibrium thermodynamics

A method is presented to identify flux controlling reactions in metabolic networks using experimentally determined flux distributions. The method is based on the application of Ziegler's principle for the maximization of entropy production. According to this principle a metabolic network tends to maximize the entropy production rate while satisfying mass balances and maximal rate constraints. Experimental flux data corresponding to four different metabolic states of Saccharomyces cerevisiae were used to identify the corresponding flux controlling reactions. The bottleneck nature of several of the identified reactions was confirmed by earlier studies on over-expression of the identified target genes. The method also explains the failure of all the previous trials of increasing the glycolysis rate by direct over-expression of several glycolytic enzymes. These findings point to a wider use of the method for identification of novel targets for metabolic engineering of microorganisms used for sustainable production of fuels and chemicals.     

A new detector for fully automatic peptide synthesis

A new method of monitoring the rate of reactions in solid-phase peptide synthesis is described. A conductivity detector in the reaction cell (patent applied for) enables the deprotection, washing and subsequent coupling stages to be examined in detail. The half-lives of the reactions can be calculated and hence the optimum reaction times can be predicted. Difficult sequences are sensed and appropriate action taken completely automatically.     

A simple conductimetric method as an alternative to the colorimetric p-nitrobenzylpyridine test for the measurement of the reactivity of potentially mutagenic alkylating compounds

A simple method for the measurement of the kinetics of reaction of potentially mutagenic alkyl halides with amines, based on the direct conductimetric monitoring of the quaternary ammonium salt produced in these reactions, is proposed and applied to the alkylation of p-nitrobenzylpyridine (NBP) and triethylamine (TEA) in different solvents. With respect to the classical colorimetric NBP-test, this method has the advantage that the rates can be measured continuously over the entire course of the reactions and the kinetic order and constants can be easily obtained. It is also shown that the previously proposed, NBP modified test', using simultaneously NBP and TEA, gives actually the sum of the rate constants for the reactions of the alkylating reagent with the two amines.     

Application of mobilities in electromagnetic fields to the determination of kinetic parameters

Changes in electrophoretic and/or electromagnetophoretic mobilities during the course of biochemical reactions are related to first order rate constants of those reactions. By linearization of the mobility/reaction-coordinate relations, a method for the determination of rate constants is suggested, an assessment being made of some likely advantages and limitations of this approach to kinetic problems.     

Determination of relative rate constants for in vitro RNA processing reactions by internal competition

Studies of RNA recognition and catalysis typically involve measurement of rate constants for reactions of individual RNA sequence variants by fitting changes in substrate or product concentration to exponential or linear functions. A complementary approach is determination of relative rate constants by internal competition, which involves quantifying the time-dependent changes in substrate or product ratios in reactions containing multiple substrates. Here, we review approaches for determining relative rate constants by analysis of both substrate and product ratios and illustrate their application using the in vitro processing of precursor transfer RNA (tRNA) by ribonuclease P as a model system. The presence of inactive substrate populations is a common complicating factor in analysis of reactions involving RNA substrates, and approaches for quantitative correction of observed rate constants for these effects are illustrated. These results, together with recent applications in the literature, indicate that internal competition offers an alternate method for analyzing RNA processing kinetics using standard molecular biology methods that directly quantifies substrate specificity and may be extended to a range of applications.     

Weighted-ensemble Brownian dynamics simulations for protein association reactions.

A new method, weighted-ensemble Brownian dynamics, is proposed for the simulation of protein-association reactions and other events whose frequencies of outcomes are constricted by free energy barriers. The method features a weighted ensemble of trajectories in configuration space with energy levels dictating the proper correspondence between "particles" and probability. Instead of waiting a very long time for an unlikely event to occur, the probability packets are split, and small packets of probability are allowed to diffuse almost immediately into regions of configuration space that are less likely to be sampled. The method has been applied to the Northrup and Erickson (1992) model of docking-type diffusion-limited reactions and yields reaction rate constants in agreement with those obtained by direct Brownian simulation, but at a fraction of the CPU time (10(-4) to 10(-3), depending on the model). Because the method is essentially a variant of standard Brownian dynamics algorithms, it is anticipated that weighted-ensemble Brownian dynamics, in conjunction with biophysical force models, can be applied to a large class of association reactions of interest to the biophysics community.     

A new detector for fully automatic peptide synthesis

A new method of monitoring the rate of reactions in solid phase peptide synthesis is described. A conductivity detector in the reaction cell enables the deprotection, washing, and subsequent coupling stages to be examined in detail. The half lives of the reactions can be calculated and hence the optimum reaction times predicted. The aggregation of peptide chains and subsequent collapse of the resin is observed. Difficult sequences are sensed and appropriate action taken completely automatically.