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Team:Evry/Model3
From 2013.igem.org
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<td>mol^-1</td> | <td>mol^-1</td> | ||
<td>Avogadro's constant</td> | <td>Avogadro's constant</td> | ||
| - | <td> | + | <td>-</td> |
</tr> | </tr> | ||
<tr width="100%"> | <tr width="100%"> | ||
| Line 132: | Line 132: | ||
<td>min^-1</td> | <td>min^-1</td> | ||
<td>fixation rate of FeFUR</td> | <td>fixation rate of FeFUR</td> | ||
| + | <td>-</td> | ||
| + | </tr> | ||
| + | <tr width="100%"> | ||
| + | <td>Fur0</td> | ||
| + | <td>0.01</td> | ||
| + | <td>mM.min^⁻1</td> | ||
| + | <td>Fur Production</td> | ||
| + | <td>-</td> | ||
| + | </tr> | ||
| + | <tr width="100%"> | ||
| + | <td>Fur0</td> | ||
| + | <td>0.01</td> | ||
| + | <td>mM.min^⁻1</td> | ||
| + | <td>Fur Production</td> | ||
<td>-</td> | <td>-</td> | ||
</tr> | </tr> | ||
Revision as of 01:01, 5 October 2013
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
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.
| 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 | - |
| 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 | - |
| Fur0 | 0.01 | mM.min^⁻1 | Fur Production | - |
| Fur0 | 0.01 | mM.min^⁻1 | Fur Production | - |
| 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:
