Team:Evry/Model3

From 2013.igem.org

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<td>min^-1</td>
<td>min^-1</td>
<td>translation rate</td>
<td>translation rate</td>
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<td>-</td>
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<tr width="100%">
 +
<td>KT</td>
 +
<td>2.0</td>
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<td>M.min^-1</td>
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<td>transcription rate</td>
<td>-</td>
<td>-</td>
</tr>
</tr>
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<td>m^3</td>
<td>m^3</td>
<td>Volume of a call</td>
<td>Volume of a call</td>
-
<td>-</td>
 
-
</tr>
 
-
<tr width="100%">
 
-
<td>p</td>
 
-
<td>0.005</td>
 
-
<td>Value at zero of the activator</td>
 
<td>-</td>
<td>-</td>
</tr>
</tr>
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</tr>
</tr>
<tr width="100%">
<tr width="100%">
-
<td>d</td>
+
<td>Kf</td>
-
<td>10^-9</td>
+
<td>10^-4</td>
-
<td>Activator threshold</td>
+
<td>min^-1</td>
-
<td>[2]</td>
+
<td>fixation rate of FeFUR</td>
 +
<td>-</td>
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</tr>
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<tr width="100%">
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<td>Npla1</td>
 +
<td></td>
 +
<td>-</td>
 +
<td>Number of plasmides with LacI</td>
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<td>-</td>
</tr>
</tr>
</table>
</table>
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<u>Enzymatic Parameters:</u><br/>
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<table width="100%" border="1">
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<tr width="100%">
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<td>KcatA</td>
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<td>5550</td>
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<td>min^-1</td>
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<td>-</td>
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<td>-</td>
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</tr>
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<tr width="100%">
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<td>KcatB</td>
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<td>600</td>
 +
<td>min^-1</td>
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<td>-</td>
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<td>-</td>
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</tr>
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<tr width="100%">
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<td>KcatC</td>
 +
<td>173</td>
 +
<td>min^-1</td>
 +
<td>-</td>
 +
<td>-</td>
 +
</tr>
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<tr width="100%">
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<td>KmA</td>
 +
<td>300</td>
 +
<td>M</td>
 +
<td>-</td>
 +
<td>-</td>
 +
</tr>
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<tr width="100%">
 +
<td>KmB</td>
 +
<td>14.7</td>
 +
<td>M</td>
 +
<td>-</td>
 +
<td>-</td>
 +
</tr>
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<tr width="100%">
 +
<td>KmC</td>
 +
<td>14</td>
 +
<td>M</td>
 +
<td>-</td>
 +
<td>-</td>
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</tr>
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</table>
<h2>Results</h2>
<h2>Results</h2>

Revision as of 00:52, 5 October 2013

Iron coli project

Metabolic model

Overview

Enzymes regulation:
This regulation is based on two consecutives inhibitions, which, in the end, is an activator with a certain delay. The model will follow this principle.

Assumptions

Model Description

Variables:

  • [Fe] : Iron concentration inside the bacteria
  • [Fur] : FUR concentration inside the bacteria
  • [FeFur] : Iron-FUR complex concentration inside the bacteria
  • LacI : Number of inhibited LacI
  • LacO : Number of non-inhibited LacO
  • [mRNA]: mRNA (from LacO) concentration
  • [Enz] : Enzyme concentration : EntA,-B,-C,-D,-E,-F
All those concentrations are expressed in mmol/L

Parameters table:

Fe, FUR and FeFUR:
The iron-FUR complex is simply formed that way:
 
We reduced this equation to:

Which is not annoying, since we just have to divide our [FeFur] by to to get the real complex concentration.
We can easily write down both the formation (v) and the dissociation (v') speed:

We chose to model the iron input in the bacteria using a linear function of the external iron concentration Ferext, the factor p being the cell-wall permeability for iron.
The FUR on the other hand, is produced by the bacteria. It's evolution can also be considered linerar, using a mean production rate Fur0.


In this model, we only track the free Fe-FUR and not those which are attached to a FUR Binding Site. As LacI is the number of inhibited LacI, we can use this number to express how much Fe-FUR does bind to a FBS per unit of time.

Parameters:
Name Value Unite Description Reference
p 0.1 min^-1 Permeability of cell wall -
KfeFUR 0.01 M^-1.s^-1 Formation constant of FeFur complex -
Dff 0.001 min^-1 - -
Kp 0.5 min^-1 translation rate -
KT 2.0 M.min^-1 transcription rate -
milliNa 6.02.10^20 mol^-1 Avogadro's constant [1]
V 6.5.10^-16 m^3 Volume of a call -
Dmrna 0.001 min^-1 mRNA degradation rate -
Denz 0.001 min^-1 Enzyme degradation rate -
Kf 10^-4 min^-1 fixation rate of FeFUR -
Npla1 - Number of plasmides with LacI -
Enzymatic Parameters:
KcatA 5550 min^-1 - -
KcatB 600 min^-1 - -
KcatC 173 min^-1 - -
KmA 300 M - -
KmB 14.7 M - -
KmC 14 M - -

Results

Conclusion

References:

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