scholarly journals Control analysis applied to single enzymes: can an isolated enzyme have a unique rate-limiting step?

1993 ◽  
Vol 294 (1) ◽  
pp. 87-94 ◽  
Author(s):  
G C Brown ◽  
C E Cooper
Keyword(s):  
Rate Constants ◽  
General Assumption ◽  
Control Analysis ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Steady State Rate ◽  
Carbamate Kinase ◽  
State Rate ◽  
Rate Limiting ◽  
Control Coefficients

Control analysis is used to analyse and quantify the concept of a rate-limiting step within an enzyme. The extent to which each rate constant within the enzyme limits the steady-state rate of the enzyme and the levels of enzyme intermediate species are quantified as flux and concentration control coefficients. These coefficients are additive and obey summation theorems. The control coefficients of triose phosphate isomerase, carbamate kinase and lactate dehydrogenase are calculated from literature values of the rate constants. It is shown that, contrary to previous assumption, these enzymes do not have a unique rate-limiting step, but rather flux control is shared by several rate constants and varies with substrate, product and effector concentrations, and with the direction of the reaction. Thus the general assumption that an enzyme will have a unique rate-limiting step is unjustified.

scholarly journals Characterization of a Baculovirus-Encoded RNA 5′-Triphosphatase

1998 ◽  
Vol 72 (9) ◽  
pp. 7057-7063 ◽  
Author(s):  
Christian H. Gross ◽  
Stewart Shuman
Keyword(s):  
Steady State ◽  
Product Formation ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Mrna Capping ◽  
Steady State Rate ◽  
Rna Triphosphatase ◽  
State Rate ◽  
Nuclear Polyhedrosis ◽  
Rate Limiting

ABSTRACT Autographa californica nuclear polyhedrosis virus (AcNPV) encodes a 168-amino-acid polypeptide that contains the signature motif of the superfamily of protein phosphatases that act via a covalent cysteinyl phosphate intermediate. The sequence of the AcNPV phosphatase is similar to that of the RNA triphosphatase domain of the metazoan cellular mRNA capping enzyme. Here, we show that the purified recombinant AcNPV protein is an RNA 5′-triphosphatase that hydrolyzes the γ-phosphate of triphosphate-terminated poly(A); it also hydrolyzes ATP to ADP and GTP to GDP. The phosphatase sediments as two discrete components in a glycerol gradient: a 9.5S oligomer and 2.5S putative monomer. The 2.5S form of the enzyme releases 32Pi from 1 μM γ-32P-labeled triphosphate-terminated poly(A) with a turnover number of 52 min−1 and converts ATP to ADP with V max of 8 min−1and Km of 25 μM ATP. The 9.5S oligomeric form of the enzyme displays an initial pre-steady-state burst of ADP and Pi formation, which is proportional to and stoichiometric with the enzyme, followed by a slower steady-state rate of product formation (approximately 1/10 of the steady-state rate of the 2.5S enzyme). We surmise that the oligomeric enzyme is subject to a rate-limiting step other than reaction chemistry and that this step is either distinct from or slower than the rate-limiting step for the 2.5S enzyme. Replacing the presumptive active site nucleophile Cys-119 by alanine abrogates RNA triphosphatase and ATPase activity. Our findings raise the possibility that baculoviruses encode enzymes that cap the 5′ ends of viral transcripts synthesized at late times postinfection by a virus-encoded RNA polymerase.

scholarly journals Beyond the Active Site: Mechanistic Investigations of the Role of the Secondary Coordination Sphere and Beyond on Multi-Electron Electrocatalytic Reactions and Their Relations Between Kinetics and Thermodynamics

2020 ◽  
Author(s):  
Vincent Wang
Keyword(s):  
Thermodynamic Parameters ◽  
Coordination Sphere ◽  
Active Site ◽  
Rate Constants ◽  
Reduction Reaction ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Secondary Coordination Sphere ◽  
Catalytic Rate ◽  
Rate Limiting

<p>The development of an electrocatalyst with a rapid turnover frequency, low overpotential and long-term stability is highly desired for fuel-forming reactions, such as water splitting and CO<sub>2</sub> reduction. The findings of the scaling relationships between the catalytic rate and thermodynamic parameters over a wide range of electrocatalysts in homogeneous and heterogeneous systems provide useful guidelines and predictions for designing better catalysts for those redox reactions. However, such relationships also suggest that a catalyst with a high catalytic rate is typically associated with a high overpotential for a given reaction. Inspired by enzymes, the introduction of additional interactions through the secondary coordination sphere beyond the active site, such as hydrogen-bonding or electrostatic interactions, have been shown to offer a promising avenue to disrupt these unfavorable relationships. Herein, we further investigate the influence of these cooperative interactions on the faster chemical steps, in addition to the rate-limiting step widely examined before, for molecular electrocatalysts with the structural and electronic modifications designed to facilitate the dioxygen reduction reaction, CO<sub>2</sub> reduction reaction and hydrogen evolving reaction. Based on the electrocatalytic kinetic analysis, the rate constants for faster chemical steps and their correlation with the corresponding thermodynamic parameters are evaluated. The results suggest that the effects of the secondary coordination sphere and beyond on these fuel-forming reactions are not necessarily beneficial for promoting all chemical steps and no apparent relation between rate constants and thermodynamic parameters are found in some cases studied here, which may implicate the design of electrocatalysts in the future. Finally, these analyses demonstrate that the characteristic features for voltammograms and foot-of-the-wave-analysis plots are associated with the specific kinetic phenomenon among these multi-electron electrocatalytic reactions, which provides a useful framework to probe the insights of chemical and electronic modifications on the catalytic steps quantitatively (i.e. kinetic rate constants) and to optimize some of critical steps beyond the rate-limiting step.</p>

Reactions of 1-substituted 2,4,6-trinitrobenzenes with nucleophiles

1979 ◽  
Vol 44 (5) ◽  
pp. 1453-1459 ◽  
Author(s):  
Jaromír Kaválek ◽  
Ahmad Ashfaq ◽  
Vojeslav Štěrba
Keyword(s):  
Methyl Ether ◽  
Rate Constants ◽  
Equilibrium Constants ◽  
Nucleophilic Aromatic Substitution ◽  
Aromatic Substitution ◽  
Phenyl Ester ◽  
Methyl Derivative ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Rate Limiting

Rate constants have been determined of nucleophilic aromatic substitution of 2,4,6-trinitrophenyl methyl ether (Ia), 2,4,6-trinitrophenyl ethanoate (Ic), 2,4,6-trinitrochlorobenzene (Ib), 2,4,6-trinitrodiphenyl ether (Id), 2,4,6-trinitro-4'-bromodiphenyl ether (Ie), 2,3',4,6-tetranitrodiphenyl ether (If) and 2,4,4',6-tetranitrodiphenyl ether (Ig) with methoxide, ethanoate and methyl cyanoethanoate (II) anions in methanol. For the compounds Ia,b rate and equilibrium constants of addition of the anion II(-) at positions 3 and 5 have been measured, too. In reactions of the compounds Ia to Ig with ethanoate anion the first (rate-limiting) step produces the phenyl ester Ic which reacts with a further ethanoate anion to give 2,4,6-trinitrophenol (Ih) and ethanoic anhydride. In reactions of the bromo derivative Ie and, to a still larger extent, compound Id the methyl derivative Ia is formed besides the compound Ih.

Reactions of 1,3-diacylthioureas with methoxide ion and with amines

1987 ◽  
Vol 52 (1) ◽  
pp. 120-131 ◽  
Author(s):  
Jaromír Kaválek ◽  
Josef Jirman ◽  
Vojeslav Štěrba
Keyword(s):  
Carbonyl Group ◽  
Rate Constants ◽  
Dissociation Constants ◽  
Equilibrium Constants ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Order Of Magnitude ◽  
Acetyl Group ◽  
Methoxide Ion ◽  
Rate Limiting

Rate constants of base-catalyzed methanolysis and dissociation constants in methanol have been determined for benzoylthiourea (II), 1,3-diacetylthiourea (III), 1,3-dibenzoylthiourea (IV), and 1-acetyl-3-benzoylthiourea (V). With the diacyl derivatives III and IV, the reaction of methoxide ion with the neutral substrate is accompanied by that of methoxide with the substrate anion (at higher alkoxide concentrations). Above 0.1 mol l-1 CH3O(-), the rate constants are also affected by medium. The rate of the reaction of neutral diacyl derivative is decreased, and that of the reaction of methoxide with the substrate anion is rapidly increased. The dissociation constant of II is higher than that of acetylthiourea (I) by about one order of magnitude, but the attack of methoxide on the carbonyl group of II is about three times slower than that in I. The benzoyl group at the N1 nitrogen exhibits a greater activating influence (in both the rate and the equilibrium constants) on the other NHCOR group than the acetyl group does. With V the ratio of methanolysis rate constants is 9 : 1 in favour of the acetyl group. The reaction of diacetyl derivative III with 1-butanamine has been followed in butanamine buffers. At the lowest butanamine concentrations, the reaction is second order in the amine, and the rate-limiting step is the proton transfer from the intermediate to the second amine molecule. At the highest butanamine concentrations the reaction becomes first order in the amine, and the rate-limiting step changes to the attack of butanamine on the carbonyl group of diacetyl derivative III.

Kinetics and mechanism of methanolysis of benzoyl derivatives of substituted phenylureas and phenylthioureas

1984 ◽  
Vol 49 (9) ◽  
pp. 2103-2110 ◽  
Author(s):  
Jaromír Kaválek ◽  
Said El Bahaie ◽  
Vojeslav Štěrba
Keyword(s):  
Nitrogen Atom ◽  
Steric Hindrance ◽  
Rate Constants ◽  
Dissociation Constants ◽  
Kinetics And Mechanism ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Order Of Magnitude ◽  
Rate Limiting ◽  
Derivatives Of

The methanolysis rate constants and dissociation constants have been measured of benzoyl derivatives of substituted phenylureas and phenylthioureas. The dissociation constants of the thio derivatives are higher by 1 order of magnitude and the rate constants are higher by 2 orders of magnitude than the respective values of the oxygen analogues. Logarithms of the rate and dissociation constants have been correlated with the Hammet σ constant; the ρ constant of the methanolysis of the oxygen derivatives is almost 2x higher than that of the thio derivatives, which is explained by a change in the rate-limiting step. Methylation of the phenyl nitrogen atom increases the acidity by almost 2 orders of magnitude. This effect is due obviously to steric hindrance to the conjugation with the adjacent carbonyl or thiocarbonyl group.

scholarly journals Metabolic Control Analysis: A Tool for Designing Strategies to Manipulate Metabolic Pathways

2008 ◽  
Vol 2008 ◽  
pp. 1-30 ◽  
Author(s):  
Rafael Moreno-Sánchez ◽  
Emma Saavedra ◽  
Sara Rodríguez-Enríquez ◽  
Viridiana Olín-Sandoval
Keyword(s):  
Metabolic Control ◽  
Metabolic Pathway ◽  
Large Scale ◽  
Metabolic Control Analysis ◽  
Metabolite Concentration ◽  
Control Analysis ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Experimental Approaches ◽  
Rate Limiting

The traditional experimental approaches used for changing the flux or the concentration of a particular metabolite of a metabolic pathway have been mostly based on the inhibition or over-expression of the presumed rate-limiting step. However, the attempts to manipulate a metabolic pathway by following such approach have proved to be unsuccessful. Metabolic Control Analysis (MCA) establishes how to determine, quantitatively, the degree of control that a given enzyme exerts on flux and on the concentration of metabolites, thus substituting the intuitive, qualitative concept of rate limiting step. Moreover, MCA helps to understand (i) the underlying mechanisms by which a given enzyme exerts high or low control and (ii) why the control of the pathway is shared by several pathway enzymes and transporters. By applying MCA it is possible to identify the steps that should be modified to achieve a successful alteration of flux or metabolite concentration in pathways of biotechnological (e.g., large scale metabolite production) or clinical relevance (e.g., drug therapy). The different MCA experimental approaches developed for the determination of the flux-control distribution in several pathways are described. Full understanding of the pathway properties when working under a variety of conditions can help to attain a successful manipulation of flux and metabolite concentration.

scholarly journals Beyond the Active Site: Mechanistic Investigations of the Role of the Secondary Coordination Sphere and Beyond on Multi-Electron Electrocatalytic Reactions and Their Relations Between Kinetics and Thermodynamics

2020 ◽  
Author(s):  
Vincent Wang
Keyword(s):  
Thermodynamic Parameters ◽  
Coordination Sphere ◽  
Active Site ◽  
Rate Constants ◽  
Reduction Reaction ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Secondary Coordination Sphere ◽  
Catalytic Rate ◽  
Rate Limiting

<p>The development of an electrocatalyst with a rapid turnover frequency, low overpotential and long-term stability is highly desired for fuel-forming reactions, such as water splitting and CO<sub>2</sub> reduction. The findings of the scaling relationships between the catalytic rate and thermodynamic parameters over a wide range of electrocatalysts in homogeneous and heterogeneous systems provide useful guidelines and predictions for designing better catalysts for those redox reactions. However, such relationships also suggest that a catalyst with a high catalytic rate is typically associated with a high overpotential for a given reaction. Inspired by enzymes, the introduction of additional interactions through the secondary coordination sphere beyond the active site, such as hydrogen-bonding or electrostatic interactions, have been shown to offer a promising avenue to disrupt these unfavorable relationships. Herein, we further investigate the influence of these cooperative interactions on the faster chemical steps, in addition to the rate-limiting step widely examined before, for molecular electrocatalysts with the structural and electronic modifications designed to facilitate the dioxygen reduction reaction, CO<sub>2</sub> reduction reaction and hydrogen evolving reaction. Based on the electrocatalytic kinetic analysis, the rate constants for faster chemical steps and their correlation with the corresponding thermodynamic parameters are evaluated. The results suggest that the effects of the secondary coordination sphere and beyond on these fuel-forming reactions are not necessarily beneficial for promoting all chemical steps and no apparent relation between rate constants and thermodynamic parameters are found in some cases studied here, which may implicate the design of electrocatalysts in the future. Finally, these analyses demonstrate that the characteristic features for voltammograms and foot-of-the-wave-analysis plots are associated with the specific kinetic phenomenon among these multi-electron electrocatalytic reactions, which provides a useful framework to probe the insights of chemical and electronic modifications on the catalytic steps quantitatively (i.e. kinetic rate constants) and to optimize some of critical steps beyond the rate-limiting step.</p>

Mechanism of base-catalyzed cyclization of ethyl N-(substituted aminocarbonyl)glycinates

1987 ◽  
Vol 52 (1) ◽  
pp. 156-161
Author(s):  
Jaromír Mindl ◽  
Vojeslav Štěrba
Keyword(s):  
Rate Constants ◽  
Ethoxy Group ◽  
Tetrahedral Intermediate ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Acid Catalyzed ◽  
Cyclization Rate ◽  
Rate Limiting ◽  
Cyclic Intermediate

The cyclization rate constants have been measured of substituted ethyl N-(phenylaminocarbonyl)-, N-(alkylaminocarbonyl)-, and N-(phenylaminothiocarbonyl)glycinates RNHCXNHCH2CO2.C2H5 (X = O, S). Logarithms of these constants increase with decreasing basicity of the amines down to the value of pKa(RNH2) = 5.5. The rate-limiting step of the reaction is formation of the tetrahedral intermediate. With ethyl N-(phenylaminocarbonyl)glycinates (whose pKa(RNH2) values are higher) this dependence, on the contrary, slightly decreases, and the acid-catalyzed splitting off of ethoxy group from the cyclic intermediate becomes rate-limiting. The cyclization rate of a series of ethyl N-(phenylaminothiocarbonyl)glycinates is practically independent of the pKa(RNH2) values, the change in the rate-limiting step would take place at pH about 9.

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