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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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Normalization curve for the determination of active site concentration from enzyme activity.X-axis represents the concentration of added TMTFA corresponding to actual enzyme concentrations after 300 times delution. Y-axis represents the difference between the initial enzyme activity and the activity at plateau caused by the presence of experimental TMTFA concentration. The concentration of the substrate in all activity determinations was 0.5 mM.
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pone-0022265-g005: Normalization curve for the determination of active site concentration from enzyme activity.X-axis represents the concentration of added TMTFA corresponding to actual enzyme concentrations after 300 times delution. Y-axis represents the difference between the initial enzyme activity and the activity at plateau caused by the presence of experimental TMTFA concentration. The concentration of the substrate in all activity determinations was 0.5 mM.

Mentions: The parameters, i.e., the rate constant k0 and the initial concentrations [E] and [I] were fitted to the experimental progress curves by the numerical solver with non-linear regression [8] implemented in ENZO. From the fitted initial TMTFA optical density (OD) values of 0.229, 0.346, 0.477 (see Evaluated Parameters in Figure 4) corresponding to three known concentrations of 0.11 µM, 0.165 µM and 0.22 µM of added TMTFA, respectively, it follows (see Figure 5 displaying the normalization curve) that if adding 0.5 mM ATCh and measuring the enzyme activity of 0.640 OD/min, then the corresponding concentration of active sites of TcAChE is 1 nM. We report here, for the first time, the second order rate constant for the binding of TMTFA to TcAChE: 47228+/−2407 M−1 s−1 as computed by ENZO.


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)

Normalization curve for the determination of active site concentration from enzyme activity.X-axis represents the concentration of added TMTFA corresponding to actual enzyme concentrations after 300 times delution. Y-axis represents the difference between the initial enzyme activity and the activity at plateau caused by the presence of experimental TMTFA concentration. The concentration of the substrate in all activity determinations was 0.5 mM.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0022265-g005: Normalization curve for the determination of active site concentration from enzyme activity.X-axis represents the concentration of added TMTFA corresponding to actual enzyme concentrations after 300 times delution. Y-axis represents the difference between the initial enzyme activity and the activity at plateau caused by the presence of experimental TMTFA concentration. The concentration of the substrate in all activity determinations was 0.5 mM.
Mentions: The parameters, i.e., the rate constant k0 and the initial concentrations [E] and [I] were fitted to the experimental progress curves by the numerical solver with non-linear regression [8] implemented in ENZO. From the fitted initial TMTFA optical density (OD) values of 0.229, 0.346, 0.477 (see Evaluated Parameters in Figure 4) corresponding to three known concentrations of 0.11 µM, 0.165 µM and 0.22 µM of added TMTFA, respectively, it follows (see Figure 5 displaying the normalization curve) that if adding 0.5 mM ATCh and measuring the enzyme activity of 0.640 OD/min, then the corresponding concentration of active sites of TcAChE is 1 nM. We report here, for the first time, the second order rate constant for the binding of TMTFA to TcAChE: 47228+/−2407 M−1 s−1 as computed by ENZO.

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