Team:Paris Bettencourt/Modeling/Parameters
From 2011.igem.org
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<td> 0.049</td> | <td> 0.049</td> | ||
<td>molecules.s<sup>-1</sup> <br>or pops</td> | <td>molecules.s<sup>-1</sup> <br>or pops</td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
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<td>0.057</td> | <td>0.057</td> | ||
<td>molecules.s<sup>-1</sup> <br>or pops</td> | <td>molecules.s<sup>-1</sup> <br>or pops</td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
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<td>0.0028</td> | <td>0.0028</td> | ||
<td>molecules.s<sup>-1</sup> <br>or pops</td> | <td>molecules.s<sup>-1</sup> <br>or pops</td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
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<td>0.028</td> | <td>0.028</td> | ||
<td>molecules.s<sup>-1</sup> <br>or pops</td> | <td>molecules.s<sup>-1</sup> <br>or pops</td> | ||
- | <td>Is roughly one order of magnitude higher than production rate of pComK<a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td>Is roughly one order of magnitude higher than production rate of pComK<a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[4]</a></td> |
</tr> | </tr> | ||
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<td>10</td> | <td>10</td> | ||
<td>molecules <br>per cell</td> | <td>molecules <br>per cell</td> | ||
- | <td>We used the classic assumption 1nM=1 molecule per cell and <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td>We used the classic assumption 1nM=1 molecule per cell and <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[1]</a></td> |
</tr> | </tr> | ||
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<td>110</td> | <td>110</td> | ||
<td>molecules <br>per cell</td> | <td>molecules <br>per cell</td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
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<td>100</td> | <td>100</td> | ||
<td>molecules <br>per cell</td> | <td>molecules <br>per cell</td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
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<td>500</td> | <td>500</td> | ||
<td>molecules <br>per cell</td> | <td>molecules <br>per cell</td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
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<td>50</td> | <td>50</td> | ||
<td>molecules <br>per cell</td> | <td>molecules <br>per cell</td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td>2</td> | <td>2</td> | ||
<td>NA</td> | <td>NA</td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
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<td>5</td> | <td>5</td> | ||
<td>NA</td> | <td>NA</td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
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<td>1.4x10<sup>-3</sup></td> | <td>1.4x10<sup>-3</sup></td> | ||
<td>s<sup>-1</sup></td> | <td>s<sup>-1</sup></td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
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<td>1.4x10<sup>-3</sup></td> | <td>1.4x10<sup>-3</sup></td> | ||
<td>s<sup>-1</sup></td> | <td>s<sup>-1</sup></td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
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<td>2.88x10<sup>-3</sup></td> | <td>2.88x10<sup>-3</sup></td> | ||
<td>s<sup>-1</sup></td> | <td>s<sup>-1</sup></td> | ||
- | <td> | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[4]</a></td> |
</tr> | </tr> | ||
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<td>714</td> | <td>714</td> | ||
<td>s</td> | <td>s</td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[3]</a></td> |
</tr> | </tr> | ||
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<td>300</td> | <td>300</td> | ||
<td>s</td> | <td>s</td> | ||
- | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ | + | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Parameters#references">[2]</a></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
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<li><i>Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits</i>, | <li><i>Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits</i>, | ||
Çağatay, Tolga and Turcotte, Marc and Elowitz, Michael B. and Garcia-Ojalvo, Jordi and Süel, Gürol M, Cell, 2009 139 (3). pp. (Supplementary Data) </li> | Çağatay, Tolga and Turcotte, Marc and Elowitz, Michael B. and Garcia-Ojalvo, Jordi and Süel, Gürol M, Cell, 2009 139 (3). pp. (Supplementary Data) </li> | ||
+ | <li><i>An Introduction to Systems Biology: Design Principles of Biological Circuits</i>, Uri Alon</li> | ||
<ol> | <ol> | ||
</div> | </div> |
Latest revision as of 20:39, 21 September 2011
Parameters
Parameter | Description | Value | Unit | Reference |
---|---|---|---|---|
Concentration of X | NA | molecules per cell |
Notation convention | |
Delay due to protein X production and maturation | NA | s | Notation convention | |
Maximal production rate of pVeg promoter (constitutive) | 0.02 | molecules.s-1 or pops |
Estimated, see the justification | |
Maximal production rate of pHyperSpank promoter | 0.02 | molecules.s-1 or pops |
Estimated, see the justification | |
Maximal production rate of pT7 promoter | 0.02 | molecules.s-1 or pops |
Estimated, see the justification | |
Maximal production rate of pComK promoter | 0.049 | molecules.s-1 or pops |
[3] | |
Maximal production rate of pComS promoter | 0.057 | molecules.s-1 or pops |
[3] | |
Maximal production rate of pComG promoter | 0.02 | molecules.s-1 or pops |
Estimated, see the justification | |
Basal production rate of pComK promoter | 0.0028 | molecules.s-1 or pops |
[3] | |
Basal production rate of pComG promoter | 0.028 | molecules.s-1 or pops |
Is roughly one order of magnitude higher than production rate of pComK[4] | |
Dissociation constant for IPTG to LacI | 1200 | molecules per cell |
Aberdeen 2009 wiki | |
Dissociation constant for LacI to LacO (pLac) | 700 | molecules per cell |
Aberdeen 2009 wiki | |
Dissociation constant for T7 RNA polymerase to pT7 | 10 | molecules per cell |
We used the classic assumption 1nM=1 molecule per cell and [1] | |
Dissociation constant for ComK to pComK | 110 | molecules per cell |
[3] | |
Dissociation constant for ComK to pComS | 100 | molecules per cell |
[3] | |
ComK concentration for half maximal degradation | 500 | molecules per cell |
[3] | |
ComS concentration for half maximal degradation | 50 | molecules per cell |
[3] | |
Hill coefficient for LacI/IPTG interaction | 2 | NA | Aberdeen 2009 wiki | |
Hill coefficient for LacI/pHyperSpank interaction | 2 | NA | Aberdeen 2009 wiki | |
Hill coefficient for ComK/pComK and ComK/pComG (positive feedback) interaction | 2 | NA | [3] | |
Hill coefficient for ComK/pComS (negative feedback) interaction | 5 | NA | [3] | |
Translation rate of proteins | 0.9 | s-1 | Estimated, see the justification | |
Dilution rate in exponential phase | 2.88x10-4 | s-1 | Calculated with a 40 min generation time. See explanation | |
Unrepressed degradation rate of ComK | 1.4x10-3 | s-1 | [3] | |
Unrepressed degradation rate of ComS | 1.4x10-3 | s-1 | [3] | |
Degradation rate of mRNA | 2.88x10-3 | s-1 | [4] | |
Degradation rate of GFP | 10-4 | s-1 | BioNumbers | |
Degradation rate of RFP | 10-4 | s-1 | Estimated equal to GFP degradation rate | |
Delay due to CFP production and maturation | 360 | s | Estimated equal to GFP delay (similar molecules) | |
Delay due to YFP production and maturation | 360 | s | Estimated equal to GFP delay (similar molecules) | |
Delay due to ComK production and maturation | 300 | s | Arbitrary | |
Delay due to ComS production and maturation | 300 | s | Arbitrary | |
Delay for ComS repression by ComK | 714 | s | [3] | |
Delay due tT7 RNA polymerase production and maturation | 300 | s | [2] | |
Delay due GFP production and maturation | 360 | s | BioNumbers | |
Delay due RFP production and maturation | 360 | s | Estimated equal to GFP delay (similar molecules) | |
Delay due to mRNA production | 30 | s | BioNumbers with an approximation: all our contructs are around 1-2kb |
References
- Cytoplasmic expression of a reporter gene by co-delivery of T7 RNA polymerase and T7 promoter sequence with cationic liposomes, X Gao and L Huang, accessible here
- Molecular Biology for Masters by Dr. G. R. Kantharaj, accessible here
- An excitable gene regulatory circuit induces transient cellular differentiation, Süel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB, Nature. 2006 Mar 23;440(7083):545-50.
- Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits, Çağatay, Tolga and Turcotte, Marc and Elowitz, Michael B. and Garcia-Ojalvo, Jordi and Süel, Gürol M, Cell, 2009 139 (3). pp. (Supplementary Data)
- An Introduction to Systems Biology: Design Principles of Biological Circuits, Uri Alon