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ENZO: a web tool for derivation and evaluation of kinetic models of enzyme catalyzed reactions.

Bevc S, Konc J, Stojan J, Hodošček M, Penca M, Praprotnik M, Janežič D - PLoS ONE (2011)

Bottom Line: We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions.ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme.ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Chemistry, Ljubljana, Slovenia.

ABSTRACT
We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions. ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme. These differential equations are processed by a numerical solver and a regression algorithm which fits the coefficients of differential equations to experimentally observed time course curves. ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics. It is freely available as a web tool, at http://enzo.cmm.ki.si.

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Converged results of parameter fitting for inhibition of cholinesterase.Fitted rate constants k1, k3, k4, k5, k10, k11, k12 are displayed under the Evaluated Parameters. k0 is fixed at 8.8·106 s−1. ENZO allows, if necessary, for constraining several rate constants, thus simplifying the fitting and speeding up the evaluation process (k14 = k8 = k6 = k0, k15 = k9 = k7 = k2 = k1, k13 = k3, k10 = 2k4, k11 = 50k5, where k14, k8, k6, k0 are second order while others are first order rate constants). For all progress curves, the initial concentrations of SES, SE, EAS, ES, SEAS, P, ES, SEA are fixed to zero and not fitted. E is fixed to 2.6 nM as independently determined by active site titration. For the progress curves chst1.dat to chst14.dat, S is fixed to 2 µM, 5 µM, 10 µM, 20 µM, 4.35 µM, 7.63 µM, 0.16 mM, 0.5 mM, 1 mM, 2 mM, 5 mM, 10 mM, 20 mM and 5 mM respectively. P is the measured species. Y-axis shows the product in molar concentration and X-axis shows the time in seconds.
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pone-0022265-g009: Converged results of parameter fitting for inhibition of cholinesterase.Fitted rate constants k1, k3, k4, k5, k10, k11, k12 are displayed under the Evaluated Parameters. k0 is fixed at 8.8·106 s−1. ENZO allows, if necessary, for constraining several rate constants, thus simplifying the fitting and speeding up the evaluation process (k14 = k8 = k6 = k0, k15 = k9 = k7 = k2 = k1, k13 = k3, k10 = 2k4, k11 = 50k5, where k14, k8, k6, k0 are second order while others are first order rate constants). For all progress curves, the initial concentrations of SES, SE, EAS, ES, SEAS, P, ES, SEA are fixed to zero and not fitted. E is fixed to 2.6 nM as independently determined by active site titration. For the progress curves chst1.dat to chst14.dat, S is fixed to 2 µM, 5 µM, 10 µM, 20 µM, 4.35 µM, 7.63 µM, 0.16 mM, 0.5 mM, 1 mM, 2 mM, 5 mM, 10 mM, 20 mM and 5 mM respectively. P is the measured species. Y-axis shows the product in molar concentration and X-axis shows the time in seconds.

Mentions: In the conventional colorimetric cholinesterase detection method [10], a thio analogue of a substrate is used and the first product (P) is thiocholine. Its reaction with the thio reagent dithio-bis-nitrobenzoic acid (DTNB) yields a yellow color in stochiometric proportion with the released product. The time course of production of the yellow color in the butyrylthiocholine hydrolysis by horse BChE was measured at 14 different initial substrate concentrations, from 2 µmol to 50 mM in a 20 mM phosphate buffer solution, at pH 7 and 25°C. To avoid further complications resulting from newly formed products and/or DTNB depletion from its initial 0.6 mM concentration, the reaction was followed until a 60–80 µM concentration of thiocholine appeared. Under these conditions, all substrate is hydrolyzed at low concentrations giving rise to the plateaus in five of the curves and mainly linear product formation occurs at all other concentrations as seen in Figure 9.


ENZO: a web tool for derivation and evaluation of kinetic models of enzyme catalyzed reactions.

Bevc S, Konc J, Stojan J, Hodošček M, Penca M, Praprotnik M, Janežič D - PLoS ONE (2011)

Converged results of parameter fitting for inhibition of cholinesterase.Fitted rate constants k1, k3, k4, k5, k10, k11, k12 are displayed under the Evaluated Parameters. k0 is fixed at 8.8·106 s−1. ENZO allows, if necessary, for constraining several rate constants, thus simplifying the fitting and speeding up the evaluation process (k14 = k8 = k6 = k0, k15 = k9 = k7 = k2 = k1, k13 = k3, k10 = 2k4, k11 = 50k5, where k14, k8, k6, k0 are second order while others are first order rate constants). For all progress curves, the initial concentrations of SES, SE, EAS, ES, SEAS, P, ES, SEA are fixed to zero and not fitted. E is fixed to 2.6 nM as independently determined by active site titration. For the progress curves chst1.dat to chst14.dat, S is fixed to 2 µM, 5 µM, 10 µM, 20 µM, 4.35 µM, 7.63 µM, 0.16 mM, 0.5 mM, 1 mM, 2 mM, 5 mM, 10 mM, 20 mM and 5 mM respectively. P is the measured species. Y-axis shows the product in molar concentration and X-axis shows the time in seconds.
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Related In: Results  -  Collection

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pone-0022265-g009: Converged results of parameter fitting for inhibition of cholinesterase.Fitted rate constants k1, k3, k4, k5, k10, k11, k12 are displayed under the Evaluated Parameters. k0 is fixed at 8.8·106 s−1. ENZO allows, if necessary, for constraining several rate constants, thus simplifying the fitting and speeding up the evaluation process (k14 = k8 = k6 = k0, k15 = k9 = k7 = k2 = k1, k13 = k3, k10 = 2k4, k11 = 50k5, where k14, k8, k6, k0 are second order while others are first order rate constants). For all progress curves, the initial concentrations of SES, SE, EAS, ES, SEAS, P, ES, SEA are fixed to zero and not fitted. E is fixed to 2.6 nM as independently determined by active site titration. For the progress curves chst1.dat to chst14.dat, S is fixed to 2 µM, 5 µM, 10 µM, 20 µM, 4.35 µM, 7.63 µM, 0.16 mM, 0.5 mM, 1 mM, 2 mM, 5 mM, 10 mM, 20 mM and 5 mM respectively. P is the measured species. Y-axis shows the product in molar concentration and X-axis shows the time in seconds.
Mentions: In the conventional colorimetric cholinesterase detection method [10], a thio analogue of a substrate is used and the first product (P) is thiocholine. Its reaction with the thio reagent dithio-bis-nitrobenzoic acid (DTNB) yields a yellow color in stochiometric proportion with the released product. The time course of production of the yellow color in the butyrylthiocholine hydrolysis by horse BChE was measured at 14 different initial substrate concentrations, from 2 µmol to 50 mM in a 20 mM phosphate buffer solution, at pH 7 and 25°C. To avoid further complications resulting from newly formed products and/or DTNB depletion from its initial 0.6 mM concentration, the reaction was followed until a 60–80 µM concentration of thiocholine appeared. Under these conditions, all substrate is hydrolyzed at low concentrations giving rise to the plateaus in five of the curves and mainly linear product formation occurs at all other concentrations as seen in Figure 9.

Bottom Line: We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions.ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme.ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Chemistry, Ljubljana, Slovenia.

ABSTRACT
We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions. ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme. These differential equations are processed by a numerical solver and a regression algorithm which fits the coefficients of differential equations to experimentally observed time course curves. ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics. It is freely available as a web tool, at http://enzo.cmm.ki.si.

Show MeSH
Related in: MedlinePlus