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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 enzyme active site titration experiment.Initial concentrations of enzyme E and inhibitor I for progress curve files tfk1.dat, tfk2.dat, tfk3.dat (Experimental Data panel shows tfk1.dat) are fitted in the interval of [0, 1020]; the initial concentration of EI is zero and fixed; the checkbox “E” is checked under Measured Species, which signifies that E is the measured quantity and the progress curves below represent the time course of its residual activity. The respective units of the residual activity in the Y-axis are OD/min and the units of time in X-axis are seconds. Fitted rate constant k0 and initial values of E and I at three different concentrations of I are displayed under the Evaluated Parameters in the upper right corner panel, the experimental progress curves are blue and the fitted curves are red as shown in Time Course of the Reaction chart at the bottom panel of the screen. The arrows mark the difference between the inital value and the plateau.
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pone-0022265-g004: Converged results of parameter fitting for enzyme active site titration experiment.Initial concentrations of enzyme E and inhibitor I for progress curve files tfk1.dat, tfk2.dat, tfk3.dat (Experimental Data panel shows tfk1.dat) are fitted in the interval of [0, 1020]; the initial concentration of EI is zero and fixed; the checkbox “E” is checked under Measured Species, which signifies that E is the measured quantity and the progress curves below represent the time course of its residual activity. The respective units of the residual activity in the Y-axis are OD/min and the units of time in X-axis are seconds. Fitted rate constant k0 and initial values of E and I at three different concentrations of I are displayed under the Evaluated Parameters in the upper right corner panel, the experimental progress curves are blue and the fitted curves are red as shown in Time Course of the Reaction chart at the bottom panel of the screen. The arrows mark the difference between the inital value and the plateau.

Mentions: Once the reaction scheme is established, the Set Parameters tab is used to define the initial conditions and estimates of rate constants with rational limits. The measured time course data are then uploaded as progress curves. One can select and upload multiple progress curves or alternatively, it is possible to upload a compressed .zip file containing multiple progress curves. When uploaded, these are shown as blue curves in the Time Course of the Reaction chart (e.g., Figure 4 bottom). The initial concentration and the identity of the measured species corresponding to each uploaded data file are defined. The initial values of rate constants and species concentrations can also be set to a constant value, in which case the server will perform a first approximation without any fitting of the proposed kinetic model.


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 enzyme active site titration experiment.Initial concentrations of enzyme E and inhibitor I for progress curve files tfk1.dat, tfk2.dat, tfk3.dat (Experimental Data panel shows tfk1.dat) are fitted in the interval of [0, 1020]; the initial concentration of EI is zero and fixed; the checkbox “E” is checked under Measured Species, which signifies that E is the measured quantity and the progress curves below represent the time course of its residual activity. The respective units of the residual activity in the Y-axis are OD/min and the units of time in X-axis are seconds. Fitted rate constant k0 and initial values of E and I at three different concentrations of I are displayed under the Evaluated Parameters in the upper right corner panel, the experimental progress curves are blue and the fitted curves are red as shown in Time Course of the Reaction chart at the bottom panel of the screen. The arrows mark the difference between the inital value and the plateau.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3139599&req=5

pone-0022265-g004: Converged results of parameter fitting for enzyme active site titration experiment.Initial concentrations of enzyme E and inhibitor I for progress curve files tfk1.dat, tfk2.dat, tfk3.dat (Experimental Data panel shows tfk1.dat) are fitted in the interval of [0, 1020]; the initial concentration of EI is zero and fixed; the checkbox “E” is checked under Measured Species, which signifies that E is the measured quantity and the progress curves below represent the time course of its residual activity. The respective units of the residual activity in the Y-axis are OD/min and the units of time in X-axis are seconds. Fitted rate constant k0 and initial values of E and I at three different concentrations of I are displayed under the Evaluated Parameters in the upper right corner panel, the experimental progress curves are blue and the fitted curves are red as shown in Time Course of the Reaction chart at the bottom panel of the screen. The arrows mark the difference between the inital value and the plateau.
Mentions: Once the reaction scheme is established, the Set Parameters tab is used to define the initial conditions and estimates of rate constants with rational limits. The measured time course data are then uploaded as progress curves. One can select and upload multiple progress curves or alternatively, it is possible to upload a compressed .zip file containing multiple progress curves. When uploaded, these are shown as blue curves in the Time Course of the Reaction chart (e.g., Figure 4 bottom). The initial concentration and the identity of the measured species corresponding to each uploaded data file are defined. The initial values of rate constants and species concentrations can also be set to a constant value, in which case the server will perform a first approximation without any fitting of the proposed kinetic model.

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