scholarly journals Kinetic studies of the polygalacturonase enzyme from Colletotrichum lindemuthianum

1992 ◽  
Vol 285 (2) ◽  
pp. 551-556 ◽  
Author(s):  
G Waksman ◽  
G Turner ◽  
A R Walmsley
Keyword(s):  
Steady State ◽  
Fluorescence Intensity ◽  
Kinetic Studies ◽  
Kinetic Mechanism ◽  
Colletotrichum Lindemuthianum ◽  
Protein Fluorescence ◽  
Substrate Complex ◽  
Single Turnover ◽  
Enzyme Substrate ◽  
Rapid Quench

The intrinsic protein fluorescence of the polygalacturonase from Colletotrichium lindemuthianum was exploited in stopped-flow experiments aimed at elucidating the kinetic mechanism for this enzyme. Binding of the polymeric substrate polygalacturonic acid (PGA) essentially produced a triphasic fluorescence profile. There was an initial rapid quench in fluorescence, consistent with the rapid formation of the enzyme-substrate complex, with an equilibrium constant of about 8 x 10(-4)% (w/v) PGA (about 0.27 microM). There then followed a near-constant fluorescence phase, attributable to turnover of the enzyme-substrate complex as a steady-state intermediate. As the concentration of the steady-state intermediate became depleted, towards the end of the reaction, there was a partial return of the fluorescence intensity. This phase is attributed to a final, single turnover of the enzyme at the end of the reaction. The fluorescence intensity does not return to its original level due to product remaining bound at the end of the reaction.

scholarly journals Single-turnover and steady-state kinetics of hydrolysis of cephalosporins by β-lactamase I from Bacillus cereus

1985 ◽  
Vol 231 (1) ◽  
pp. 83-88 ◽  
Author(s):  
R Bicknell ◽  
S G Waley
Keyword(s):  
Steady State ◽  
Bacillus Cereus ◽  
Substrate Complex ◽  
Single Turnover ◽  
Rate Determining Step ◽  
Enzyme Substrate ◽  
Steady State Kinetics ◽  
Lactam Ring ◽  
Kinetics Of ◽  
Hydrolysis Of

The kinetics of the hydrolysis of two cephalosporins by β-lactamase I from Bacillus cereus 569/H/9 has been studied by single-turnover and steady-state methods. Single-turnover kinetics could be measured over the time scale of minutes when cephalosporin C was the substrate. The other substrate, 7-(2′,4′-dinitrophenylamino)deacetoxycephalosporanic acid, was hydrolysed even more slowly, and has potential for use in crystallographic studies of β-lactamases. Comparison of single-turnover and steady-state kinetics showed that, for both substrates, opening the β-lactam ring (i.e. acylation of the enzyme) was the rate-determining step. Thus the non-covalent enzyme-substrate complex is expected to be the intermediate observed crystallographically.

scholarly journals Kinetic Mechanism of Human dUTPase, an Essential Nucleotide Pyrophosphatase Enzyme

2007 ◽  
Vol 282 (46) ◽  
pp. 33572-33582 ◽  
Author(s):  
Judit Tóth ◽  
Balázs Varga ◽  
Mihály Kovács ◽  
András Málnási-Csizmadia ◽  
Beáta G. Vértessy
Keyword(s):  
Steady State ◽  
Active Site ◽  
Reaction Pathway ◽  
Three Dimensional ◽  
Kinetic Mechanism ◽  
Dimensional Structure ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Novel Target ◽  
Rate Limiting

Human dUTPase is essential in controlling relative cellular levels of dTTP/dUTP, both of which can be incorporated into DNA. The nuclear isoform of the enzyme has been proposed as a promising novel target for anticancer chemotherapeutic strategies. The recently determined three-dimensional structure of this protein in complex with an isosteric substrate analogue allowed in-depth structural characterization of the active site. However, fundamental steps of the dUTPase enzymatic cycle have not yet been revealed. This knowledge is indispensable for a functional understanding of the molecular mechanism and can also contribute to the design of potential antagonists. Here we present detailed pre-steady-state and steady-state kinetic investigations using a single tryptophan fluorophore engineered into the active site of human dUTPase. This sensor allowed distinction of the apoenzyme, enzyme-substrate, and enzyme-product complexes. We show that the dUTP hydrolysis cycle consists of at least four distinct enzymatic steps: (i) fast substrate binding, (ii) isomerization of the enzyme-substrate complex into the catalytically competent conformation, (iii) a hydrolysis (chemical) step, and (iv) rapid, nonordered release of the products. Independent quenched-flow experiments indicate that the chemical step is the rate-limiting step of the enzymatic cycle. To follow the reaction in the quenched-flow, we devised a novel method to synthesize γ-32P-labeled dUTP. We also determined by indicator-based rapid kinetic assays that proton release is concomitant with the rate-limiting hydrolysis step. Our results led to a quantitative kinetic model of the human dUTPase catalytic cycle and to direct assessment of relative flexibilities of the C-terminal arm, critical for enzyme activity, in the enzyme-ligand complexes along the reaction pathway.

scholarly journals The Complete Pathway for ERK2-catalyzed Reaction

2007 ◽  
Vol 282 (38) ◽  
pp. 27678-27684 ◽  
Author(s):  
Zhi-Xin Wang ◽  
Jia-Wei Wu
Keyword(s):  
Steady State ◽  
Detailed Balance ◽  
Kinetic Studies ◽  
Kinetic Mechanism ◽  
Initial Reaction ◽  
Enzymatic Mechanism ◽  
Enzyme Substrate ◽  
Steady State Kinetic ◽  
Mitogen Activated Protein ◽  
State Kinetic

In the present study, the enzymatic mechanism of ERK2 is re-examined by a combination of steady-state kinetic studies in the absence and presence of viscosogenic agents. Kinetic studies carried out in various concentrations of sucrose revealed that both kcat and kcat/Km for either ATP or EtsΔ138 were highlysensitive to solvent viscosity, suggesting that the rapid equilibrium assumption is not valid for the phosphorylation of protein substrate by ERK2. Furthermore, the kinetic analysis with the minimal random Bi Bi reaction mechanism is shown to be inconsistent with the principle of the detailed balance. This inconsistent calculation strongly suggests that there is isomerization of the enzyme-substrate ternary complex. The viscosity-dependent steady-state kinetic data are combined to establish a kinetic mechanism for the ERK2-catalyzed reaction that predicts initial reaction velocities under varying concentrations of ATP and substrate. These results complement previous structure-function studies of mitogen-activated protein kinases and provide important insight for mechanistic interpretation of the kinase functions.

Kinetic studies of prothrombin activation: effect of factor Va and phospholipids on formation of the enzyme-substrate complex

Biochemistry ◽  
1984 ◽  
Vol 23 (20) ◽  
pp. 4557-4564 ◽  
Author(s):  
Jan L. M. L. Van Rijn ◽  
Jose W. P. Govers-Riemslag ◽  
Robert F. A. Zwaal ◽  
Jan Rosing
Keyword(s):  
Kinetic Studies ◽  
Activation Effect ◽  
Substrate Complex ◽  
Factor Va ◽  
Enzyme Substrate ◽  
Prothrombin Activation

Transient-Phase and Steady-State Kinetics for Enzyme Activation

1973 ◽  
Vol 51 (6) ◽  
pp. 806-814 ◽  
Author(s):  
Nasrat H. Hijazi ◽  
Keith J. Laidler
Keyword(s):  
Steady State ◽  
Kinetic Data ◽  
Enzyme Activation ◽  
Transient Phase ◽  
Time Curve ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Substrate Activation ◽  
Steady State Kinetics ◽  
Special Case

A non-steady-state analysis has been worked out for two mechanisms in which an activator Q can become attached to an enzyme–substrate complex EA, the species EAQ breaking down more rapidly than EA. It is shown that if EAQ breaks down into EQ + product there can be no steady state. If, however, EAQ breaks down into E + Q + product, the transient phase is followed by a steady state in which the product versus time curve is linear. A special case of this mechanism is when Q is the substrate (substrate activation). Some published kinetic data on carboxypeptidase are analyzed with reference to the equations derived.

The influence of pH and inhibitors on the kinetics of enzyme reactions involving two intermediates

1967 ◽  
Vol 45 (5) ◽  
pp. 539-546 ◽  
Author(s):  
Harvey Kaplan ◽  
Keith J. Laidler
Keyword(s):  
Steady State ◽  
Ph Dependence ◽  
Free Enzyme ◽  
State Equations ◽  
Enzyme Reactions ◽  
Substrate Complex ◽  
Rate Determining Step ◽  
Enzyme Substrate ◽  
Special Cases ◽  
Influence Of Ph

General steady-state equations are worked out for enzyme reactions which occur according to the scheme [Formula: see text]Equations showing the pH dependence of the kinetic parameters are developed in a form which distinguishes between essential and nonessential ionizing groups. The pK dependence of [Formula: see text], the second-order constant extrapolated to zero substrate constant, gives pK values for groups which ionize on the free enzyme, but reveals such a pK only if the corresponding group is also involved in the breakdown of the Michaelis complex. General steady-state equations are also developed for the case in which an inhibitor can combine with the free enzyme, the enzyme–substrate complex, and also a second intermediate (e.g. an acyl enzyme). The equations are given in a form that is convenient for analyzing the experimental results, and a number of special cases are considered. It is shown how the type of inhibition depends not only on the nature of the inhibitor but also on that of the substrate, an important factor being the rate-determining step of the reaction. Examples of the various kinds of behavior are given.

Kinetic characterization of a cis- and trans-acting M2+-independent DNAzyme that depends on synthetic RNaseA-like functionality — Burst-phase kinetics from the coalescence of two active DNAzyme folds

2007 ◽  
Vol 85 (4) ◽  
pp. 313-329 ◽  
Author(s):  
Richard Ting ◽  
Jason M Thomas ◽  
David M Perrin
Keyword(s):  
Steady State ◽  
Rate Constant ◽  
Acid Catalyst ◽  
Initial Population ◽  
Substrate Complex ◽  
Single Turnover ◽  
A Value ◽  
Burst Phase ◽  
Cis And Trans

This work describes the kinetics of the DNAzyme 925-11, a combinatorially selected, M2+-independent ribophosphodiesterase that is covalently modified with both cationic amines and imidazoles. At 13 °C, cis- and trans-cleaving constructs of 925-11 demonstrate the highest rate constants reported to date for any M2+-independent nucleic acid catalyst, investigated at physiological ionic strength and pH 7.5 (0.3 min–1 for self cleavage and 0.2 min–1 for intermolecular cleavage). In contrast to the cis-cleaving species, single-turnover experiments with the trans-cleaving species exhibit biphasic cleavage data, suggesting the presence of two conformations of the catalyst–substrate complex. Pulse–chase experiments demonstrate that both complexes lead to substrate cleavage. Under multiple-turnover conditions, the higher rate constant appears in a burst phase that decays to a slower steady state exhibiting a rate constant of 0.0077 min–1, a value approximating that of the slow-cleaving phase seen in single-turnover experiments. Slow product release is excluded as the source of the burst phase. An integrated rate equation is derived to describe burst-phase kinetics based on the funneling of the initial population of fast-cleaving conformation into a steady-state population composed largely of the slow-cleaving conformation.Key words: RNase mimics, DNAzymes, ribozymes, kinetics, RNA cleavage.

scholarly journals Steady-state and pre-steady kinetic studies on mitochondrial sheep liver aldehyde dehydrogenase. A comparison with the cytoplasmic enzyme

1978 ◽  
Vol 171 (3) ◽  
pp. 527-531 ◽  
Author(s):  
A K H MacGibbon ◽  
L F Blackwell ◽  
P D Buckley
Keyword(s):  
Steady State ◽  
Aldehyde Dehydrogenase ◽  
Kinetic Studies ◽  
Kinetic Properties ◽  
Protein Fluorescence ◽  
Sheep Liver ◽  
Steady State Kinetic ◽  
Wide Range ◽  
Liver Aldehyde Dehydrogenase

Kinetic studies were carried out on mitochondrial aldehyde dehydrogenase (EC 1.2.1.3) isolated from sheep liver. Steady-state studies over a wide range of acetaldehyde concentrations gave a non-linear double-reciprocal plot. The dissociation of NADH from the enzyme was a biphasic process with decay constants 0.6s-1 and 0.09s-1. Pre-steady-state kinetic data with propionaldehyde as substrate could be fitted by using the same burst rate constant (12 +/- 3s-1) over a wide range of propionaldehyde concentrations. The quenching of protein fluorescence on the binding of NAD+ to the enzyme was used to estimate apparent rate constants for binding (2 × 10(4) litre.mol-1.s-1) and dissociation (4s-1). The kinetic properties of the mitochondrial enzyme, compared with those reported for the cytoplasmic aldehyde dehydrogenase from sheep liver, show significant differences, which may be important in the oxidation of aldehydes in vivo.

scholarly journals Allosteric Enzyme-Based Biosensors—Kinetic Behaviours of Immobilised L-Lysine-α-Oxidase from Trichoderma viride: pH Influence and Allosteric Properties

Biosensors ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 145
Author(s):  
Antonio Guerrieri ◽  
Rosanna Ciriello ◽  
Giuliana Bianco ◽  
Francesca De Gennaro ◽  
Silvio Frascaro
Keyword(s):  
Trichoderma Viride ◽  
Kinetic Studies ◽  
Pt Electrode ◽  
Allosteric Enzyme ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Ph Influence ◽  
Ph Dependent ◽  
Kinetics Of ◽  
Allosteric Properties

The present study describes the kinetics of L-lysine-α-oxidase (LO) from Trichoderma viride immobilised by co-crosslinking onto the surface of a Pt electrode. The resulting amperometric biosensor was able to analyse L-lysine, thus permitting a simple but thorough study of the kinetics of the immobilised enzyme. The kinetic study evidenced that LO behaves in an allosteric fashion and that cooperativity is strongly pH-dependent. Not less important, experimental evidence shows that cooperativity is also dependent on substrate concentration at high pH and behaves as predicted by the Monod-Wyman-Changeux model for allosteric enzymes. According to this model, the existence of two different conformational states of the enzyme was postulated, which differ in Lys species landing on LO to form the enzyme–substrate complex. Considerations about the influence of the peculiar LO kinetics on biosensor operations and extracorporeal reactor devices will be discussed as well. Not less important, the present study also shows the effectiveness of using immobilised enzymes and amperometric biosensors not only for substrate analysis, but also as a convenient tool for enzyme kinetic studies.

Mechanism of Collagen: Glucosyl-transferase and its Relation to Platelet: Collagen Adhesion

1975 ◽  
Author(s):  
D. F. Smith ◽  
D. P. Kosow ◽  
G. A. Jamieson
Keyword(s):  
Steady State ◽  
Cell Surface ◽  
Platelet Function ◽  
Kinetic Data ◽  
Soluble Form ◽  
Physiological Conditions ◽  
Substrate Complex ◽  
Enzymatic Mechanism ◽  
Enzyme Substrate ◽  
Induced Aggregation

Elucidation of the enzymatic mechanism of collagen: glucosyltransferase is essential to an understanding of its role in platelet function. A soluble form of the enzyme has been purified 100-fold and a sensitive new assay system developed. Studies with effectors such as UDP, ADP and ristocetin under steady state conditions have shown that only two of the possible sequential mechanisms are consistent with the kinetic data. Inhibition by UDP and ADP is competitive with UDPG but non-competitive with galactosylhydroxylysine. They would not, therefore, be expected to inhibit the formation of an enzyme-substrate complex with collagen. Under physiological conditions, their presence would be expected to increase the affinity of the cell surface enzyme for its acceptor on collagen in the case of the ordered mechanism, or not to affect it in the case of the random mechanism. These data are consistent with the potentiation of collagen-induced aggregation by ADP, and the lack of effect of UDP on the adherence of platelets to collagen.(Supported, in part, by USPHS.)

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