Steady-state kinetic studies of the negative co-operativity and flip-flop mechanism for Escherichia coli alkaline phosphatase.

1. A study of variations in experimental error of velocity measurement with substrate concentration for alkaline phosphatase reveals that the standard error is not constant or strictly proportional to velocity, but obeys a more complex dependence. 2. By using an approach based on error estimates at each individual substrate concentration, we show that the double-reciprocal plots in general are curved, necessitating a high-degree rate equation. The curves are analysed according to a recent classification of possible curve shapes for the 3:3 function, which is shown to be the lowest-degree rate equation satisfying the experimental data. 4. Other workers have supposed the enzyme to follow Michaelis-Menten kinetics, and it is shown that this assumption is approximately true at low temperatures in the absence of phosphate. 5. A study of the effects of phosphate concentration, pH and temperature on the kinetics shows that there is a gradual alteration in curve shape with these experimental variables, resulting in an apparent reduction in degree under certain special conditions, and particularly at low temperature. 6. It is shown that the steady-state kinetics do not require a flip-flop or half-of-sites reactivity mechanism as claimed, and a mechanism is proposed, a rate equation calculated and an analysis attempted. 7. An analysis of the product-inhibition effects for a linked two-sited Uni Bi enzyme is given. Alterations of asymptotic double-reciprocal slopes and limiting (1/nu) intercepts with products is discussed, and it is shown how the theory of product inhibition can be extended to complex kinetic situations to extract information as to molecular mechanism. 8. Deviations from Michaelis-Menten kinetics are expressed in terms of the magnitude of the appropriate Sylvester resultants.     

Kinetic studies of enzymatic hydrolysis of insoluble cellulose: analysis of the initial rates

A study was conducted on the kinetics of enzymatic hydrolysis of pure insoluble cellulose using unpurified culture filtrate Trichoderma reesei, with the emphasis on the initial reaction period. The initial hydrolysis rate and extent of enzyme (soluble protein)adsorption, either apparent or initial, were evaluated under various experimental conditions. It has been found that the various mass-transfer steps do not control the overall hydrolysis rate and that the hydrolysis rate is mainly controlled by the surface reaction step promoted by the adsorbed enzyme. It has also been found that the initial hydrolysis rate strongly depends on the initial extent of soluble protein adsorption and the effectiveness of the adsorbed soluble protein to promote the hydrolysis. The initial extent of soluble protein adsorption, in turn, is related to the initial cellulose concentration, enzyme concentration, and specific surface area of cellulose, whereas the effectiveness of the initially adsorbed soluble protein to promote the derived to interrelate these parameters without resorting to the Michaelis-Menten kinetics. The present result appear to imply that the role of enzyme-substrate complex formation should not be ignored in deriving a mechanistic kinetic model for enzymatic hydrolysis of cellulose.     

Basis for the anomalous effect of competitive inhibitors on the kinetics of hydrolysis of short-chain phosphatidylcholines by phospholipase A2.

The effect of four specific competitive inhibitors on the kinetics of hydrolysis of short-chain diacyl-sn-glycero-3-phosphocholines below their critical micelle concentrations was examined. The kinetics of hydrolysis of short-chain substrates dispersed as solitary monomers were generally consistent with the classical Michaelis-Menten formalism; i.e., hydrolysis began without any latency period, the steady-state rate was observed at higher substrate concentrations, the steady-state initial rate showed a linear dependence on the enzyme concentration, and the hyperbolic dependence of the initial rate on the substrate concentration could be described in terms of KM and Vmax parameters. The competitive nature of the inhibitors used in this study has been established by a variety of techniques, and the equilibrium dissociation constants for the inhibitors bound to the enzyme were measured by the protection method [Jain et al. (1991) Biochemistry 30, 7306-7317]. The kinetics of hydrolysis in the presence of competitive inhibitors could be described by a single dissociation constant. However, the value of the dissociation constant obtained under the kinetic conditions was comparable to that obtained by the protection method for the inhibitor-enzyme complex bound to a neutral diluent, rather than to the value of the dissociation constant obtained with solitary monomeric inhibitors and the enzyme in the aqueous phase. Spectroscopic methods showed that the effectively lower dissociation constant of an inhibitor bound to PLA2 at the interface is due to the stabilization of the enzyme-inhibitor complex by interaction with other amphiphiles present in the reaction mixture.(ABSTRACT TRUNCATED AT 250 WORDS)     

The deactivation of Photosystem II in Chlorella as a second-order process

The kinetics of deactivation of the S₃ state in Chlorella have been observed under a variety of conditions. The S₃ state appears to decline in a dark period coming after a sequence of 30 saturating flashes in a second-order reaction, the rate constant of which is 0.132/[S*₃] s⁻¹ and which involves an electron donor, D₁, of concentration 1.25[S*₃] where [S*₃] is the concentration of the S₃ state when the oxygen yield of the light flashes is constant. If a 1 min period of 650 nm illumination is employed after the sequence of flashes, the subsequent S₃ state deactivation kinetics are more complex. There is an initial phase of S₃ state deactivation, accounting for about 35% of the original S₃ state, which is complete in less than 100 ms. The remaining 65% of the S₃ state appears to deactivate in a second-order reaction, the rate constant of which is 1.36/[S*₃] s⁻¹ and which involves an electron donor of initial concentration 0.58[S*₃]. If a 1 min period of 710 nm illumination comes after the 30 flashes, at least 98% of the S₃ state deactivates according to first-order kinetics. It is shown that this can be explained using a second-order model if there is an electron donor present of which the concentration is large compared with [S*₃]. However, S₃ state deactivation observed after 5 min of dark and two saturating flashes can be described neither by a first-order model nor a second-order model. Deactivation of the S₂ state after a 5 min dark period and one saturating flash follows second-order kinetics with a rate constant of 0.2/[S*₃] s⁻¹ and appears to involve an electron donor of initial concentration 1.3[S*₃]. Arguments are presented which tend to rule out the primary electron acceptor to Photosystem II as being any of the electron donors but it appears quite possible that the large plastoquinone pool is involved.     

Conformational isomerization of lactate dehydrogenase complexes formed by pyruvate and coenzyme analogs]

The kinetics of LDH-catalyzed reduction of pyruvate involving APADH were studied. It was shown that under conditions of a single turnover reaction the first order rate constant is equal to 37+/-4 sec-1. The reaction rate (vo) did not change when a deutero-coenzyme was used. The relationship between vo and pyruvate concentration is hyperbolic. It is concluded that isomerization of the ternary LDH-APADH-pyruvate complex limits the reaction rate. The spectral properties and the kinetics of formation and dissociation of abortive LDH complexes with pyruvate and NAD analogs (APAD and PAAD) were studied. The participation of the carboxamide group of NAD in conformational isomerization of the LDH-NADH-pyruvate and LDH-NAD-pyruvate complexes was studied.     

A differential effect of 3-(3′4′ dichlorophenyl)-1,1 dimethyl urea and atrazine on fluorescence kinetics in chloroplasts

It was found that DCMU had a differential effect at two concentration ranges on variable fluorescence kinetics in isolated chloroplasts. The increase in fluorescence rate at low concentrations of DCMU was abolished by preincubation of chloroplasts with ferricyanide or formate, treatments which were shown to convert Fe in the PS II reaction center (i.e., the FeQ_A complex) into a non-oxidizable form, but it was not affected by Tris treatment. Increase in fluorescence kinetics (at the initial linear rate) at high concentrations of DCMU was found to be abolished by Tris treatment but it was only marginally affected by ferricyanide or formate treatments. The effect of Tris could be abolished by addition of hydroquinone-ascorbate, which restored electron flow to the pool of secondary acceptors.Contrary to the effect of DCMU, no such differential concentration dependence of the variable fluorescence kinetics was found for atrazine.The increase in fluorescence kinetics (at the initial linear rate) at a low concentration rate of DCMU is presumably restricted to units which contain an oxidizable Fe in the FeQ_A complex. Increase in fluorescence kinetics (at the initial linear rate) at high DCMU concentration is probably related to the effect of DCMU at the Q_B site.Abbreviations DCMU 3-(34 dichlorophenyl)-1,1 dimethyl urea - PS II Photosystem II - Tris tris (hydroxymethyl) aminomethane     

Experimental determination of water equilibration rates in the hanging drop method of protein crystallization

The hanging drop method for protein crystallization consists of equilibrating a water droplet containing the protein and a precipitant against a reservoir solution at a higher precipitant concentration. The time for water equilibration--which affects the kinetics of crystallization--to reach 90% of completion is shown to vary between about 25 h and more than 25 days, depending on experimental conditions. Experiments were performed with three of the most widely used precipitants (ammonium sulfate, polyethylene glycol, 2-methyl-2,4-pentanediol), combining various parameters expected to affect the rate of water evaporation. The most dramatic effects were obtained when varying temperature and initial drop volume. A simple empirical equation for estimating the kinetics of water equilibration under given crystallization conditions is proposed.     

The heme oxygenase(s)-phytochrome system of Pseudomonas aeruginosa

For many pathogenic bacteria like Pseudomonas aeruginosa heme is an essential source of iron. After uptake, the heme molecule is degraded by heme oxygenases to yield iron, carbon monoxide, and biliverdin. The heme oxygenase PigA is only induced under iron-limiting conditions and produces the unusual biliverdin isomers IXbeta and IXdelta. The gene for a second putative heme oxygenase in P. aeruginosa, bphO, occurs in an operon with the gene bphP encoding a bacterial phytochrome. Here we provide biochemical evidence that bphO encodes for a second heme oxygenase in P. aeruginosa. HPLC, (1)H, and (13)C NMR studies indicate that BphO is a "classic" heme oxygenase in that it produces biliverdin IXalpha. The data also suggest that the overall fold of BphO is likely to be the same as that reported for other alpha-hydroxylating heme oxygenases. Recombinant BphO was shown to prefer ferredoxins or ascorbate as a source of reducing equivalents in vitro and the rate-limiting step for the oxidation of heme to biliverdin is the release of product. In eukaryotes, the release of biliverdin is driven by biliverdin reductase, the subsequent enzyme in heme catabolism. Because P. aeruginosa lacks a biliverdin reductase homologue, data are presented indicating an involvement of the bacterial phytochrome BphP in biliverdin release from BphO and possibly from PigA.     

Reaction of proteinases with alpha 2-macroglobulin: rapid-kinetic evidence for a conformational rearrangement of the initial alpha 2-macroglobulin-trypsin complex.

The kinetics of the reaction of trypsin with alpha 2M were examined under pseudo-first-order conditions with excess inhibitor. Initial studies indicated that the fluorescent dye TNS is a suitable probe for monitoring the reaction over a wide concentration range of reactants. Titration experiments showed that the conformational changes associated with the binding of trypsin to alpha 2M result in an increased affinity of the inhibitor for TNS. Two distinct phases were observed when this dye was used to monitor the progress of the reaction. Approximately half of the fluorescence signal was generated during a rapid phase, with the remainder generated during a second, slower phase. The observed pseudo-first-order rate constant of the first phase varied linearly with the concentration of alpha 2M up to the highest concentration of inhibitor used, whereas the rate constant of the second phase was independent of alpha 2M concentration. The data fit a mechanism in which the association of trypsin with alpha 2M occurs in two consecutive, essentially irreversible steps, both leading to alterations in TNS fluorescence. The initial association occurs with a second-order rate constant of (1.0 +/- 0.1) X 10(7) M-1 s-1 and is followed by a slower, intramolecular conformational rearrangement of the initial complex with a rate constant of 1.4 +/- 0.2 s-1. The data are consistent with a previously proposed model for the reaction of proteinases with alpha 2M [Larsson et al. (1989) Biochemistry 28, 7636-7643].2+ this model, once an initial 1:1 alpha 2M-proteinase     

Production of lactobionic acid and sorbitol from lactose/fructose substrate using GFOR/GL enzymes from Zymomonas mobilis cells: a kinetic study

In this work, we have investigated the kinetics of the biotechnological production of lactobionic acid (LBA) and sorbitol by the catalytic action of glucose-fructose oxidoreductase (GFOR) and glucono-δ-lactonase (GL) enzymes. The cells of bacterium Zymomonas mobilis ATCC 29191 containing this enzymatic complex were submitted to permeabilization and reticulation procedures. The effect of the concentration of substrates on the rate of product formation using a mobilized cell system was investigated. The application of higher fructose concentration seems to not affect the initial rate of formation of the bionic acid. Under conditions of low initial concentration of lactose, the experimental kinetic data of the bi-substrate reaction were modelled by assuming a rate equation of the classical ping-pong mechanism. The found kinetic parameters displayed a low affinity of the GFOR enzyme for both substrates. The enzymatic system did not exhibit normal Michaelis-Menten kinetics in response to a change of concentration of lactose, when fructose was held constant, presenting a sigmoid relationship between initial velocity and substrate concentration. A rate equation based on Hill kinetics was used to describe the kinetic behaviour of this enzyme-substituted reaction at higher lactose concentrations. The results from batch experiments using immobilized cells within Ca-alginate beads revealed that there is no pronounced occurrence of mass transfer limitations on LBA production for beads with 1.2 mm in average diameter. This discussion aids for defining the best operating conditions to maximize the productivity for LBA and sorbitol in this bioconversion and also for reducing the complexity of downstream separation processes.     

Proton decay kinetics for vesicles containing buffers—an analytical solution

The problem of predicting the kinetics of proton efflux and the decay of the internal proton concentration for vesicles containing one or more buffers for which the internal proton concentration is initially higher than that of the surrounding medium is examined. An analytical solution is derived that describes the time course of the proton efflux from vesicles and the decay of the internal proton concentration under conditions of zero transmembrane electric potential. The effect of the internal buffers is to increase the time required for the proton concentration gradient to equilibrate across the membrane. To simplify the analysis we assume that the equilibration of the internal and external proton activity is due primarily to proton diffusion through the membrane, and not to hydroxyl ion flux. For a vesicle containing a single buffer the solution requires six independent physical parameters: the initial internal proton concentration, the external proton concentration, the ratio of the vesicle surface area to the internal volume, the permeability coefficient of the membrane for protons, the total concentration of the internal buffer, and the equilibrium constant for the dissociation of the internal buffer. Determination of these physical values is sufficient to predict the time dependence of the internal proton concentration and of the proton efflux. Over a pH range that is below or near the pK of the internal buffer the solution is complex. However, if the initial pH is one unit or more higher than the pK of the internal buffer the kinetics of the internal proton concentration and proton efflux can be described by a pseudo first order reaction. In this case the apparent rate constant depends linearly on the permeability coefficient and is dominated by the total internal buffer concentration and its pK. For example, increasing the internal buffer concentration inside a vesicle by 10-fold results in an approximately 10-fold increase in the half-time of the proton efflux kinetics. The theoretical analysis is applied to thylakiod vesicles using experimentally determined values for the physical parameters. The predictions of the analysis are compared to experimentally observed kinetics.     

Theoretical investigation of the ring opening process of verdoheme to biliverdin in the presence of dioxygen

The conversion of ferrous verdoheme to ferric biliverdin in the presence of O₂ was investigated using the B3LYP method. Both 6-31G and 6-31G (d) basis sets were employed for geometry optimization calculation as well as energy stabilization estimation. Three possible pathways for the conversion of iron verdoheme to iron biliverdin were considered. In the first route oxygen and reducing electron were employed. In this path formation of ferrous verdoheme-O₂ complex was followed by the addition of one electron to the ferrous-oxycomplex to produce ferric peroxide intermediate. The ferric peroxide intermediate experienced an intramolecular nucleophilic attack to the most positive position at 5-oxo carbons on the ring to form a closed ring biliverdin. Subsequently the ring opening process took place and the iron (III) biliverdin complex was formed. Closed ring iron biliverdin intermediate and open ring iron biliverdin formed as a product of verdoheme cleavage were respectively 13.20 and 32.70 kcal mol⁻¹ more stable than ferric peroxide intermediate. Barrier energy for conversion of ferric peroxide to closed ring Fe (III) biliverdin and from the latter to Fe (III) biliverdin were respectively 8.67 and 3.35 kcal mol⁻¹. In this path spin ground states are doublet except for iron (III) biliverdin in which spin state is quartet. In the second path a ferrous-O₂ complex was formed and, without going to a one electron reduction process, nucleophilic attack of iron superoxide complex took place followed by the formation of iron (III) biliverdin. This path is thermodynamically and kinetically less favorable than the first one. In addition, iron hydro peroxy complex or direct attack of O₂ to macrocycle to form an isoporphyrin type intermediate have shown energy surfaces less favorable than aforementioned routes.     

The kinetic pathway of folding of barnase

To search for folding intermediates, we have examined the folding and unfolding kinetics of wild-type barnase and four representative mutants under a wide range of conditions that span two-state and multi-state kinetics. The choice of mutants and conditions provided in-built controls for artifacts that might distort the interpretation of kinetics, such as the non-linearity of kinetic and equilibrium data with concentration of denaturant. We measured unfolding rate constants over a complete range of denaturant concentration by using by 1H/2H-exchange kinetics under conditions that favour folding, conventional stopped-flow methods at higher denaturant concentrations and continuous flow. Under conditions that favour multi-state kinetics, plots of the rate constants for unfolding against denaturant concentration fitted quantitatively to the equation for three-state kinetics, with a sigmoid component for a change of rate determining step, as did the refolding kinetics. The position of the transition state on the reaction pathway, as measured by solvent exposure (the Tanford beta value) also moved with denaturant concentration, fitting quantitatively to the same equations with a change of rate determining step. The sigmoid behaviour disappeared under conditions that favoured two-state kinetics. Those data combined with direct structural observations and simulation support a minimal reaction pathway for the folding of barnase that involves two detectable folding intermediates. The first intermediate, I(1), is the denatured state under physiological conditions, D(Phys), which has native-like topology, is lower in energy than the random-flight denatured state U and is suggested by molecular dynamics simulation of unfolding to be on-pathway. The second intermediate, I(2), is high energy, and is proven by the change in rate determining step in the unfolding kinetics to be on-pathway. The change in rate determining step in unfolding with structure or environment reflects the change in partitioning of this intermediate to products or starting materials.     

Gamma-glutamyl hydrolase: kinetic characterization of isopeptide hydrolysis using fluorogenic substrates

Gamma-glutamyl hydrolase, a cysteine peptidase, catalyzes the hydrolysis of poly-gamma-glutamate derivatives of folate cofactors and many antifolate drugs. We have used internally quenched fluorogenic derivatives of glutamyl-gamma-glutamate and (4,4-difluoro)glutamyl-gamma-glutamate to examine the effect of fluorine substitution adjacent to the scissile isopeptide bond. Using a newly developed continuous fluorescence assay, the hydrolysis of both substrates could be described by Michaelis-Menten kinetics. Fluorine substitution resulted in a significant decrease in observed rates of hydrolysis under steady-state conditions due primarily to a approximately 15-fold increase in Km. Using stopped-flow techniques, hydrolysis of the non-fluorinated isopeptide was characterized by a burst phase followed by a steady-state rate, indicating that formation of the acyl enzyme is not rate-limiting for hydrolysis of this isopeptide. This conclusion was confirmed by analysis of the progress curves over a wide range of substrate concentration, which demonstrated that the acylation rate (k2) is approximately 10-fold higher than the deacylation rate (k3). The increased value of Km associated with the difluoro derivative limited the ability to obtain comparable pre-steady-state kinetics data at saturating concentration of substrate due to inner filter effects. However, even under nonsaturating conditions, a modest burst was observed for the difluoro derivative. These data indicate that either deacylation or rearrangement of the enzyme-product complex is rate-limiting in this isopeptide hydrolysis reaction.     

Strand breakage in solutions of DNA and ethidium bromide exposed to visible light.

Breaks are introduced into DNA strands when DNA solutions containing ethidium bromide (EB) are exposed to incandescent light. The nicking rate is sensitive to the concentration of EB and the light intensity. At short exposure times, this rate is limited by photon capture and formation of an intermediate capable of nicking DNA and zero-order nicking kinetics are observed. If the EB is pre-irradiated, the nicking rate is limited by DNA concentration and first-order nicking kinetics are observed. The nicking rate is not greatly affected by the presence of a low frequency of ribonucleotides in the duplex structure. The nicking reaction produces neither double-strand breaks nor interstrand crosslinks. The nicks produced cannot be closed by DNA ligase. The fluorescent light intensities under normal laboratory conditions are insufficient to induce significant nicking.     

Photo-cross-linking of guanine nucleotides to the nucleotide binding site of elongation factor G

Elongation factor G (EF-G) is rapidly inactivated when irradiated at 253.7 nm. The inactivation follows first-order single-hit kinetics with a quantum efficiency of 3.15 × 10^?5 μmol/μE. Inclusion of either GTP or GDP in the irradiation mixture does not alter the kinetics of inactivation, but does result in the covalent attachment of nucleotide to between 10 and 20% of the EF-G. This relatively low percentage of cross-linking is due to the rapid rate of photoinactivation as compared to the slower rate of covalent attachment. If EF-G is reacted before irradiation with N-ethylmaleimide, a modification known to block the nucleotide binding site [Rohrbach and Bodley (1976) J. Biol. Chem.251, 930], essentially no nucleotide can be photo-cross-linked to EF-G. Treatment of the photo-cross-linked GTP-EF-G with Raney nickel led to the liberation of the nucleotide moiety, indicating that the photo-cross-link to EF-G occurred through a sulfur atom. Although the formation of the EF-G nucleotide complex has been shown to be an obligatory first step in the formation of the EF-G nucleotide ribosome complex [Rohrbach and Bodley (1976) Biochemistry15, 4565], the covalent EF-G-nucleotide adduct cannot form a ternary complex with the ribosome. The presence of both nucleotide and ribosomes during irradiation drastically alters the kinetics of inactivation. The inactivation under these conditions follows multiple-hit kinetics with an initial period during which no EF-G activity is lost. Following this lag period, EF-G is inactivated at the same rate at which ribosomes lose their ability to bind EF-G. No nucleotide is cross-linked to EF-G or the ribosome under these conditions.     

Conformation inversion of bilirubin formed by reduction of the biliverdin-human serum albumin complex: evidence from circular dichroism.

As shown by circular dichroism spectroscopy, biliverdin preferentially adopts an M-helicity conformation on human serum albumin in aqueous buffer, pH 7.5, whereas biliverdin exhibits only a weak preference for the P-helicity conformation on bovine serum albumin at the same pH. Upon rapid reduction of the complexes with sodium borohydride, P-helicity bilirubin-IX alpha is obtained on the human albumin complex, and M-helicity bilirubin-IX alpha is obtained on the bovine serum albumin complex. Thus, biliverdin in effect undergoes an inversion of chirality upon reduction. Since the reduction did not afford a rubin with the same helicity as that of the verdin, the observations point to a hitherto undetected conformational mobility of albumin-bound bilirubin.     

Thiamine phosphates and regulation of the pyruvate dehydrogenase complex activity in rat liver mitochondria

The possibility of thiamine phosphates to participate in the regulation of pyruvate dehydrogenase complex activity on the level of isolated mitochondria is studied. It is shown that an increase in the thiamine diphosphate concentration in incubation medium produces no significant changes in the pyruvate dehydrogenase activity of mitochondria. The pyruvate dehydrogenase activity decreases when mitochondria are incubated with thiamine triphosphate or ATP under different conditions. Thiamine triphosphate is not able to replace ATP in kinase reaction of the isolated complex, but it inhibits reactivation of the complex with exogenase phosphatase; under the same conditions thiamine diphosphate activates phosphatase. Analysis of these data leads to conclusion that under native conditions an increase of the intramitochondrial thiamine triphosphate concentration can produce a drop in the pyruvate dehydrogenase complex activity by inhibition of the phosphatase reaction.     

Surfactant-induced unfolding of cellulase: kinetic studies

Surfactant-induced unfolding is a significant degradation pathway for detergent enzymes. This study examines the kinetics of surfactant-induced unfolding for endoglucanase III, a detergent cellulase, under conditions of varying pH, temperature, ionic strength, surfactant type, and surfactant concentration. Interactions between protein and surfactant monomer are shown to play a key role in determining the kinetics of the unfolding process. We demonstrate that the unfolding rate can be slowed by (1) modifying protein charge and/or pH conditions to create electrostatic repulsion of ionic surfactants and (2) reducing the amount of monomeric ionic surfactant available for interaction with the enzyme (i.e., by lowering the critical micelle concentration). Additionally, our results illustrate that there is a poor correlation between thermodynamic stability in buffer (DeltaG(unfolding)) and resistance to surfactant-induced unfolding.