scholarly journals Identification of the kinetic mechanism of succinyl-CoA synthetase

2013 ◽  
Vol 33 (1) ◽  
Author(s):  
Xin Li ◽  
Fan Wu ◽  
Daniel A. Beard
Keyword(s):  
Experimental Data ◽  
Catalytic Mechanism ◽  
Model Simulation ◽  
Tricarboxylic Acid Cycle ◽  
Kinetic Mechanism ◽  
Product Inhibition ◽  
Catalysed Reaction ◽  
Dead End ◽  
Haem Biosynthesis ◽  
Parameter Values

The kinetic mechanism of SCS [succinyl-CoA (coenzyme A) synthetase], which participates in the TCA (tricarboxylic acid) cycle, ketone body metabolism and haem biosynthesis, has not been fully characterized. Namely, a representative catalytic mechanism and associated kinetic parameters that can explain data on the enzyme-catalysed reaction kinetics have not been established. To determine an accurate model, a set of putative mechanisms of SCS, proposed by previous researchers, were tested against experimental data (from previous publication) on SCS derived from porcine myocardium. Based on comparisons between model simulation and the experimental data, an ordered ter–ter mechanism with dead-end product inhibition of succinate against succinyl-CoA is determined to be the best candidate mechanism. A thermodynamically constrained set of parameter values is identified for this candidate mechanism.

Kinetic mechanism of a recombinant Arabidopsis glyoxylate reductase: studies of initial velocity, dead-end inhibition and product inhibition

2007 ◽  
Vol 85 (9) ◽  
pp. 896-902 ◽  
Author(s):  
Gordon J. Hoover ◽  
Gerald A. Prentice ◽  
A. Rod Merrill ◽  
Barry J. Shelp
Keyword(s):  
Initial Velocity ◽  
Kinetic Mechanism ◽  
Competitive Inhibitor ◽  
Product Inhibition ◽  
Succinic Semialdehyde ◽  
In Planta ◽  
Dead End ◽  
Arabidopsis Protein ◽  
Enzyme Functions ◽  
Glyoxylate Reductase

Kinetic analysis of substrate specificity revealed that a recombinant Arabidopsis protein catalyzes the conversion of glyoxylate to glycolate (Km,glyoxylate = 4.5 μmol·L–1) and succinic semialdehyde (SSA) to γ-hydroxybutyrate (Km, SSA = 0.87 mmol·L–1) via an essentially irreversible, NADPH-based mechanism. In this report, the enzyme was further characterized via initial-velocity, dead-end inhibition and product inhibition studies. The kinetic mechanism was ordered Bi Bi, involving the complexation of NADPH to the enzyme before glyoxylate or SSA, and the release of NADP+ before glycolate or γ-hydroxybutyrate, respectively. It can be concluded that the enzyme functions as a NADPH-dependent glyoxylate reductase (EC 1.1.1.79) or possibly an aldehyde reductase (EC 1.1.1.2), and the kinetic mechanism involved is consistent with that found in members of both the aldo-keto reductase and 3-hydroxyisobutyrate dehydrogenase-related superfamilies of enzymes. Since NADP+ was an effective competitive inhibitor with respect to NADPH (Ki = 1–3 µmol·L–1), it is proposed that the ratio of NADPH/NADP+ regulates enzymatic activity in planta.

scholarly journals Human glutamic-γ-semialdehyde dehydrogenase. Kinetic mechanism

1989 ◽  
Vol 261 (3) ◽  
pp. 935-943 ◽  
Author(s):  
C Forte-McRobbie ◽  
R Pietruszko
Keyword(s):  
Kinetic Mechanism ◽  
Product Inhibition ◽  
Maximal Velocity ◽  
Semialdehyde Dehydrogenase ◽  
Rate Limiting Step ◽  
Dead End ◽  
Inhibition Studies ◽  
Rate Limiting ◽  
Competitive Pattern ◽  
Pattern Versus

The kinetic mechanism of homogeneous human glutamic-gamma-semialdehyde dehydrogenase (EC 1.5.1.12) with glutamic gamma-semialdehyde as substrate was determined by initial-velocity, product-inhibition and dead-end-inhibition studies to be compulsory ordered with rapid interconversion of the ternary complexes (Theorell-Chance). Product-inhibition studies with NADH gave a competitive pattern versus varied NAD+ concentrations and a non-competitive pattern versus varied glutamic gamma-semialdehyde concentrations, whereas those with glutamate gave a competitive pattern versus varied glutamic gamma-semialdehyde concentrations and a non-competitive pattern versus varied NAD+ concentrations. The order of substrate binding and release was determined by dead-end-inhibition studies with ADP-ribose and L-proline as the inhibitors and shown to be: NAD+ binds to the enzyme first, followed by glutamic gamma-semialdehyde, with glutamic acid being released before NADH. The Kia and Kib values were 15 +/- 7 microM and 12.5 microM respectively, and the Ka and Kb values were 374 +/- 40 microM and 316 +/- 36 microM respectively; the maximal velocity V was 70 +/- 5 mumol of NADH/min per mg of enzyme. Both NADH and glutamate were product inhibitors, with Ki values of 63 microM and 15,200 microM respectively. NADH release from the enzyme may be the rate-limiting step for the overall reaction.

scholarly journals Steady-state kinetics of malonyl-CoA synthetase from Bradyrhizobium japonicum and evidence for malonyl-AMP formation in the reaction

1994 ◽  
Vol 297 (2) ◽  
pp. 327-333 ◽  
Author(s):  
Y S Kim ◽  
S W Kang
Keyword(s):  
Steady State ◽  
Bradyrhizobium Japonicum ◽  
Initial Velocity ◽  
Catalytic Mechanism ◽  
Kinetic Mechanism ◽  
Product Inhibition ◽  
Steady State Kinetics ◽  
Malonyl Coa ◽  
Michaelis Constants ◽  
Inhibition Studies

Malonyl-CoA synthetase catalyses the formation of malonyl-CoA directly from malonate and CoA with hydrolysis of ATP into AMP and PP1. The catalytic mechanism of malonyl-CoA synthetase from Bradyrhizobium japonicum was investigated by steady-state kinetics. Initial-velocity studies and the product-inhibition studies with AMP and PPi strongly suggested ordered Bi Uni Uni Bi Ping Pong Ter Ter system as the most probable steady-state kinetic mechanism of malonyl-CoA synthetase. Michaelis constants were 61 microM, 260 microM and 42 microM for ATP, malonate and CoA respectively, and the value for Vmax, was 11.2 microM/min. The t.l.c. analysis of the 32P-labelled products in a reaction mixture containing [gamma-32P]ATP in the absence of CoA showed that PPi was produced after the sequential addition of ATP and malonate. Formation of malonyl-AMP, suggested as an intermediate in the kinetically deduced mechanism, was confirmed by the analysis of 31P-n.m.r. spectra of an AMP product isolated from the 18O-transfer experiment using [18O]malonate. The 31P-n.m.r. signal of the AMP product appeared at 0.024 p.p.m. apart from that of [16O4]AMP, indicating that one atom of 18O transferred from [18O]malonate to AMP through the formation of malonyl-AMP. Formation of malonyl-AMP was also confirmed through the t.l.c. analysis of reaction mixture containing [alpha-32P]ATP. These results strongly support the ordered Bi Uni Uni Bi Pin Pong Ter Ter mechanism deduced from initial-velocity and product-inhibition studies.

scholarly journals Kinetic studies of rat liver hexokinase D (glucokinase) in non-co-operative conditions show an ordered mechanism with MgADP as the last product to be released

2003 ◽  
Vol 371 (1) ◽  
pp. 29-38 ◽  
Author(s):  
Octavio MONASTERIO ◽  
María Luz CÁRDENAS
Keyword(s):  
Rat Liver ◽  
Kinetic Studies ◽  
Kinetic Mechanism ◽  
Product Inhibition ◽  
Nitrobenzoic Acid ◽  
Binary Complexes ◽  
Dead End ◽  
Straight Line ◽  
Inactivation Constant ◽  
Reciprocal Value

The kinetic mechanism of rat liver hexokinase D ('glucokinase') was studied under non-co-operative conditions with 2-deoxyglucose as substrate, chosen to avoid uncertainties derived from the co-operativity observed with the physiological substrate, glucose. The enzyme shows hyperbolic kinetics with respect to both 2-deoxyglucose and MgATP2-, and the reaction follows a ternary-complex mechanism with Km = 19.2±2.3mM for 2-deoxyglucose and 0.56±0.05mM for MgATP2-. Product inhibition by MgADP- was mixed with respect to MgATP2- and was largely competitive with respect to 2-deoxyglucose, suggesting an ordered mechanism with 2-deoxyglucose as first substrate and MgADP- as last product. Dead-end inhibition by N-acetylglucosamine, AMP and the inert complex CrATP [the complex of ATP with chromium in the 3+ oxidation state, i.e. Cr(III)—ATP], studied with respect to both substrates, also supports an ordered mechanism with 2-deoxyglucose as first substrate. AMP appears to bind both to the free enzyme and to the E·dGlc complex. Experiments involving protection against inactivation by 5,5′-dithiobis-(2-nitrobenzoic acid) support the existence of the E·MgADP- and E·AMP complexes suggested by the kinetic studies. MgADP-, AMP, 2-deoxyglucose, glucose and mannose were strong protectors, supporting the existence of binary complexes with the enzyme. Glucose 6-phosphate failed to protect, even at concentrations as high as 100mM, and MgATP2- protected only slightly (12%). The inactivation results support the postulated ordered mechanism with 2-deoxyglucose as first substrate and MgADP- as last product. In addition, the straight-line dependence observed when the reciprocal value of the inactivation constant was plotted against the sugar-ligand concentration supports the view that there is just one sugar-binding site in hexokinase D.

scholarly journals d-3-Hydroxybutyrate dehydrogenase from Rhodopseudomonas spheroides. Kinetic mechanism from steady-state kinetics of the reaction catalysed by the enzyme in solution and covalently attached to diethylaminoethylcellulose

1973 ◽  
Vol 133 (1) ◽  
pp. 133-157 ◽  
Author(s):  
M. J. Preuveneers ◽  
D. Peacock ◽  
E. M. Crook ◽  
J. B. Clark ◽  
K. Brocklehurst
Keyword(s):  
Rate Constants ◽  
Specific Activity ◽  
Deae Cellulose ◽  
Kinetic Mechanism ◽  
Product Inhibition ◽  
Covalent Attachment ◽  
Soluble Enzyme ◽  
Steady State Kinetics ◽  
Dead End ◽  
Rhodopseudomonas Spheroides

1. The reversible NAD+-linked oxidation of d-3-hydroxybutyrate to acetoacetate in 0.1m-sodium pyrophosphate buffer, pH8.5, at 25.0°C, catalysed by d-3-hydroxybutyrate dehydrogenase (d-3-hydroxybutyrate–NAD+ oxidoreductase, EC 1.1.1.30), was studied by initial-velocity, dead-end inhibition and product-inhibition analysis. 2. The reactions were carried out on (a) the soluble enzyme from Rhodopseudomonas spheroides and (b) an insoluble derivative of this enzyme prepared by its covalent attachment to DEAE-cellulose by using 2-amino-4,6-dichloro-s-triazine as coupling agent. 3. The insolubilized enzyme preparation contained 5mg of protein/g wet wt. of total material, and when freshly prepared its specific activity was 1.2μmol/min per mg of protein, which is 67% of that of the soluble dialysed enzyme. 4. The reactions catalysed by both the enzyme in solution and the insolubilized enzyme were shown to follow sequential pathways in which the nicotinamide nucleotides bind obligatorily first to the enzyme. Evidence is presented for kinetically significant ternary complexes and that the rate-limiting step(s) of both catalyses probably involves isomerization of the enzyme–nicotinamide nucleotide complexes and/or dissociation of the nicotinamide nucleotides from the enzyme. Both catalyses therefore are probably best described as ordered Bi Bi mechanisms, possibly with multiple enzyme–nicotinamide nucleotide complexes. 5. The kinetic parameters and the calculable rate constants for the catalysis by the soluble enzyme are similar to the corresponding parameters and rate constants for the catalysis by the insolubilized enzyme.

scholarly journals Kinetic mechanism of the glycogen-phosphorylase-catalysed reaction in the direction of glycogen synthesis: co-operative interactions of AMP and glucose 1-phosphate during catalysis

1997 ◽  
Vol 328 (1) ◽  
pp. 83-91 ◽  
Author(s):  
A. Eduard SERGIENKO ◽  
D. K. SRIVASTAVA
Keyword(s):  
Experimental Data ◽  
Glycogen Phosphorylase ◽  
Equilibrium Constants ◽  
Glycogen Synthesis ◽  
Kinetic Mechanism ◽  
Competitive Inhibitor ◽  
Hill Coefficient ◽  
Minimal Models ◽  
Dimeric Unit ◽  
Catalysed Reaction

We employed our newly developed, continuous, spectrophotometric method [Sergienko and Srivastava (1994) Anal. Biochem. 221, 348-355] for measuring the glycogen-phosphorylase-catalysed reaction in the direction of glycogen synthesis, utilizing varied concentrations of AMP (2-400 μM) and glucose 1- phosphate (G1P; 4 μM to 41 mM). The experimental data revealed that the enzyme catalysis exhibits sigmoidal dependence on both AMP and G1P concentrations, with Hill coefficient and EC50 values (mutually) affected by the concentrations of the above substrates. A detailed kinetic analysis of the substrate-dependent activation, as well as glucose-inhibition data, lead us to propose the following mechanistic features of the glycogen-phosphorylase-catalysed reaction. (1) The enzyme exhibits catalytic activity when two molecules of AMP and two molecules of G1P are bound to the dimeric unit. (2) The binding of one molecule of glucose (the competitive inhibitor of G1P) per dimeric unit results into a complete loss of the enzyme activity. (3) There is no restriction of binding of AMP or G1P when one of the dimeric subunits is already bound with the other ligand. For example, one or two G1P molecules can bind to the enzyme dimer when zero, one or two molecules of AMP are already bound. The magnitudes of rate and equilibrium constants for the glycogen-phosphorylase-catalysed reaction, derived from analyses of the experimental data in the light of a few selected minimal models, are presented.

scholarly journals CO2 Induced Foaming Behavior of Polystyrene near the Glass Transition

2017 ◽  
Vol 2017 ◽  
pp. 1-15
Author(s):  
Salah Al-Enezi
Keyword(s):  
Experimental Data ◽  
High Pressure ◽  
Glass Transition ◽  
Dissolved Gas ◽  
Foaming Process ◽  
Foaming Behavior ◽  
Potential Applications ◽  
Model C ◽  
Parameter Values ◽  
Good Agreement

This paper examines the effect of high-pressure carbon dioxide on the foaming process in polystyrene near the glass transition temperature and the foaming was studied using cylindrical high-pressure view cell with two optical windows. This technique has potential applications in the shape foaming of polymers at lower temperatures, dye impregnation, and the foaming of polystyrene. Three sets of experiments were carried out at operating temperatures of 50, 70, and 100°C, each over a range of pressures from 24 to 120 bar. Foaming was not observed when the polymer was initially at conditions below Tg but was observed above Tg. The nucleation appeared to occur randomly leading to subsequent bubble growth from these sites, with maximum radius of 0.02–0.83 mm. Three models were applied on the foaming experimental data. Variable diffusivity and viscosity model (Model C) was applied to assess the experimental data with the WLF equation. The model shows very good agreement by using realistic parameter values. The expansion occurs by diffusion of a dissolved gas from the supersaturated polymer envelope into the bubble.

Statistical Design of Fatigue Experiments

1952 ◽  
Vol 19 (1) ◽  
pp. 109-113
Author(s):  
Waloddi Weibull
Keyword(s):  
Experimental Data ◽  
Statistical Design ◽  
Testing Time ◽  
Optimum Distribution ◽  
Analytical Expression ◽  
Optimum Choice ◽  
Stress Levels ◽  
Parameter Values ◽  
Applied Stresses

Abstract An analytical expression connecting fatigue lives with applied stresses, and methods for computing the values of its parameters from experimental data are given. Formulas for estimating the uncertainty of computed parameter values, caused by scatter of loads and fatigue lives, for optimum distribution of specimens, and for optimum choice of stress levels, are deduced. Testing time and costs may be reduced by more than 40 per cent by using the formulas.

Combustion Simulation of Propane/Oxygen (With Nitrogen/Argon) Mixtures Using Rate-Controlled Constrained-Equilibrium

2018 ◽  
Vol 141 (2) ◽  
Author(s):  
Guangying Yu ◽  
Hameed Metghalchi ◽  
Omid Askari ◽  
Ziyu Wang
Keyword(s):  
Experimental Data ◽  
Energy System ◽  
Kinetic Mechanism ◽  
Chemical Kinetic ◽  
Oxygen Mixture ◽  
Free Valence ◽  
Wide Range ◽  
Constrained Equilibrium ◽  
Rate Controlled ◽  
Good Agreement

The rate-controlled constrained-equilibrium (RCCE), a model order reduction method, has been further developed to simulate the combustion of propane/oxygen mixture diluted with nitrogen or argon. The RCCE method assumes that the nonequilibrium states of a system can be described by a sequence of constrained-equilibrium states subject to a small number of constraints. The developed new RCCE approach is applied to the oxidation of propane in a constant volume, constant internal energy system over a wide range of initial temperatures and pressures. The USC-Mech II (109 species and 781 reactions, without nitrogen chemistry) is chosen as chemical kinetic mechanism for propane oxidation for both detailed kinetic model (DKM) and RCCE method. The derivation for constraints of propane/oxygen mixture starts from the eight universal constraints for carbon-fuel oxidation. The universal constraints are the elements (C, H, O), number of moles, free valence, free oxygen, fuel, and fuel radicals. The full set of constraints contains eight universal constraints and seven additional constraints. The results of RCCE method are compared with the results of DKM to verify the effectiveness of constraints and the efficiency of RCCE. The RCCE results show good agreement with DKM results under different initial temperature and pressures, and RCCE also reduces at least 60% CPU time. Further validation is made by comparing the experimental data; RCCE shows good agreement with shock tube experimental data.

Information content of data with respect to models

1983 ◽  
Vol 245 (5) ◽  
pp. R620-R623
Author(s):  
M. Berman ◽  
P. Van Eerdewegh
Keyword(s):  
Experimental Data ◽  
Data Collection ◽  
Information Content ◽  
Mathematical Framework ◽  
Statistical Measures ◽  
Parameter Values ◽  
Collection Strategies

A measure is proposed for the information content of data with respect to models. A model, defined by a set of parameter values in a mathematical framework, is considered a point in a hyperspace. The proposed measure expresses the information content of experimental data as the contribution they make, in units of information bits, in defining a model to within a desired region of the hyperspace. This measure is then normalized to conventional statistical measures of uncertainty. It is shown how the measure can be used to estimate the information of newly planned experiments and help in decisions on data collection strategies.

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