Team:Bielefeld-Germany/Modell

From 2012.igem.org

(Difference between revisions)
(The reaction)
(The reaction)
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The normal michaelis menten cinetic (1) can be adaptet for low substrate concentrations. In order to do this formula (2) replaces [ES] in formula (3). The result is formula (4). The velocity of this reaction describes the cange of the substrate concentration over time (5). Formula (6) and (7) steps to solve the integral. (8) is the resulting formula to determine the time dependent substrate concentration by a given startconcentration A.
The normal michaelis menten cinetic (1) can be adaptet for low substrate concentrations. In order to do this formula (2) replaces [ES] in formula (3). The result is formula (4). The velocity of this reaction describes the cange of the substrate concentration over time (5). Formula (6) and (7) steps to solve the integral. (8) is the resulting formula to determine the time dependent substrate concentration by a given startconcentration A.
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This transformation of the michaelis menten cinetic can be found in "Stryer biochemie". This formula is suitable for very low substrate concentrations. In this case we can estimate degradation of initial substrate [https://2012.igem.org/wiki/index.php?title=Team:Bielefeld-Germany/Project/Background/Concentrations concentrations] below  0.1 µg L<sup>-1</sup>.
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This transformation of the michaelis menten cinetic can be found in "Stryer biochemie". The resulting formula is suitable for very low substrate concentrations. In this case we can estimate degradation of initial substrate [https://2012.igem.org/wiki/index.php?title=Team:Bielefeld-Germany/Project/Background/Concentrations concentrations] below  0.1 µg L<sup>-1</sup>.
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Because we can not find any information about the K<sub>cat</sub> K<sub>M</sub><sup>-1</sup> quotient for the degradation of [https://2012.igem.org/Team:Bielefeld-Germany/Project/Background#Estradiol: estradiol] in the enzyme database [http://www.brenda-enzymes.info Brenda] we decided to use different K<sub>cat</sub> K<sub>M</sub><sup>-1</sup> quotients for the degradation of [http://www.sigmaaldrich.com/catalog/product/sigma/a1888?lang=de&region=DE ABTS], a redox mediator of the laccase. In the following picture we show a few possible reactions of our laccase.  
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Because we can not find any information about the K<sub>cat</sub> K<sub>M</sub><sup>-1</sup> quotient for the degradation of [https://2012.igem.org/Team:Bielefeld-Germany/Project/Background#Estradiol: estradiol] in the enzyme database [http://www.brenda-enzymes.info Brenda] we decided to use the K<sub>cat</sub> K<sub>M</sub><sup>-1</sup> quotients for the degradation of [http://www.sigmaaldrich.com/catalog/product/sigma/a1888?lang=de&region=DE ABTS], a redox mediator of the laccase. In the following picture we show a few possible reactions of our laccase.  
[[File:Bielefeld2012_model.jpg|center|800px|thumb|Our Model with different K<sub>cat</sub> K<sub>M</sub><sup>-1</sup> values. The span differs from 0.07 seconds to 1500 seconds.]]
[[File:Bielefeld2012_model.jpg|center|800px|thumb|Our Model with different K<sub>cat</sub> K<sub>M</sub><sup>-1</sup> values. The span differs from 0.07 seconds to 1500 seconds.]]
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We use K<sub>cat</sub> K<sub>M</sub><sup>-1</sup> values fro 11 to 643500 and get degradation time points from 0.07s to 1500s. Furthermore we try to integrate different temperatures to our model. In a span from 10°C to 30°C and a K<sub>cat</sub> K<sub>M</sub><sup>-1</sup> value of 1, the degradation differs from 40s to 100s.
+
We use K<sub>cat</sub> K<sub>M</sub><sup>-1</sup> values from 11 to 643500 that result in degradation time points from 0.07s to 1500s. Furthermore we try to integrate different temperatures to our model. In a span from 10°C to 30°C and a K<sub>cat</sub> K<sub>M</sub><sup>-1</sup> value of 1, the degradation differs from 40s to 100s.
==Extend the model with sewageplant data==
==Extend the model with sewageplant data==

Revision as of 00:27, 27 September 2012

Modelling

Contents

Model of a fixed-bed reactor

In our project we plan to construct a fixed-bed reactor, where immobilized laccases degrade synthetic estrogen and other harmful substances. As a small selection we plan to characterize our different laccases for three estrogens, three analgesics, four PAH´s, one insecticide and three possible redox mediators. If we could model the degradation of one substrate by one laccase, we could easily replace the specific Kcat KM-1 quotient of other laccases and the amounts of the other substrates.

We ignore the possible cofactors ABTS, syringaldazine and viuloric acid, because on the one hand using these cofactors would increase the costs, and on the other hand they are harmful substances. As shown by Team Substrate Analytic TVEL0 degrades ethinyl estradiol without a redox mediator. So the reaction should follow the michaelis menten kinetics.

The reaction

Bielefeld2012 MMnew.png

The normal michaelis menten cinetic (1) can be adaptet for low substrate concentrations. In order to do this formula (2) replaces [ES] in formula (3). The result is formula (4). The velocity of this reaction describes the cange of the substrate concentration over time (5). Formula (6) and (7) steps to solve the integral. (8) is the resulting formula to determine the time dependent substrate concentration by a given startconcentration A.

This transformation of the michaelis menten cinetic can be found in "Stryer biochemie". The resulting formula is suitable for very low substrate concentrations. In this case we can estimate degradation of initial substrate concentrations below 0.1 µg L-1.

Because we can not find any information about the Kcat KM-1 quotient for the degradation of estradiol in the enzyme database [http://www.brenda-enzymes.info Brenda] we decided to use the Kcat KM-1 quotients for the degradation of [http://www.sigmaaldrich.com/catalog/product/sigma/a1888?lang=de&region=DE ABTS], a redox mediator of the laccase. In the following picture we show a few possible reactions of our laccase.

Our Model with different Kcat KM-1 values. The span differs from 0.07 seconds to 1500 seconds.

We use Kcat KM-1 values from 11 to 643500 that result in degradation time points from 0.07s to 1500s. Furthermore we try to integrate different temperatures to our model. In a span from 10°C to 30°C and a Kcat KM-1 value of 1, the degradation differs from 40s to 100s.

Extend the model with sewageplant data

Sewageplant data from Schloss Holte. Temperature minimum: 8.1 °C, maximum: 20,8 °C and average temperature 14.4 °C; pH minimum: 6.6, maximum: 7.2 and average 6.9; flow minimum: 39.2 L s-1, maximum 232.8 L s-1 and avarage 76.8 L s-1

We got discharge water data from Schloss Holte about the water tempreture, pH value and flowrate. The temperature and pH value have a direct influence of enzymatic activity. Dependent on the enzymatic activity we want to calculate the time our fixed-bed reactor will need to degrdate 80 % of the substrates. This will be the dewll time. Combined with the actual flowrate we can determine the reactorsize. To estimate the feasibility we wart to know how much enzyme has to be produced for a wewage plant. A 3D model of the requirde enzme amount dependent of Kcat KM-1 values and flowrate.

The required enzyme amount for a sewageplant is dependent on Kcat KM-1 and the flow rate



Outlook

The next step will be, to add more substrates an different laccases to our model. Therefore we will need mot data about laccases. Kcat KM-1 values has to be determined and wich laccase preferes wich substrate. Additionaly we have the opportunity to work with a Lab-scale water treatment system. So we´re going to test our model in defined conditions.

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