"
Team:Imperial College London/Modelling/Output/Detailed Description
From 2010.igem.org
m |
|||
| Line 31: | Line 31: | ||
<html><h3>2. Model preA: Simple production of dioxygenase</h3></html> | <html><h3>2. Model preA: Simple production of dioxygenase</h3></html> | ||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||
| + | [[Image:IC_Simple_production.JPG|300px|thumb|center|alt=A|Transcription and translation (simple production) of dioxygenase]] | ||
This model includes transcription and translation of the dioxygenase. It does not involve any amplification steps. It is our control model against which we will be comparing the results of other models. | This model includes transcription and translation of the dioxygenase. It does not involve any amplification steps. It is our control model against which we will be comparing the results of other models. | ||
| Line 46: | Line 38: | ||
<html><h3>3. Model A: Activation of Dioxygenase by TEV enzyme</h3></html> | <html><h3>3. Model A: Activation of Dioxygenase by TEV enzyme</h3></html> | ||
| - | + | [[Image:IC_1-step_amplification.JPG|300px|thumb|center|alt=A|1-step amplification]] | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
|} | |} | ||
This model consists of the basic enzymatic reaction: | This model consists of the basic enzymatic reaction: | ||
| Line 68: | Line 54: | ||
Another approach to model the amplification module would be to implement it in a program such as TinkerCell (or CellDesigner). This would be useful to check whether the Matlab model works. | Another approach to model the amplification module would be to implement it in a program such as TinkerCell (or CellDesigner). This would be useful to check whether the Matlab model works. | ||
| - | + | ||
| - | + | [[Image:IC_Tinkercell_Model_A.PNG|300px|thumb|center|alt=A|Model A implemented in TinkerCell]] | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
<html><h3>4. Model B: Activation of Dioxygenase by TEV or activated split TEV enzyme</h3></html> | <html><h3>4. Model B: Activation of Dioxygenase by TEV or activated split TEV enzyme</h3></html> | ||
| - | + | ||
| - | + | [[Image:IC_2-step_amplification.JPG|300px|thumb|center|alt=A|2-step amplification]] | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
This version includes the following features: | This version includes the following features: | ||
*2 amplification steps (TEV and split TEV) | *2 amplification steps (TEV and split TEV) | ||
Revision as of 19:32, 17 October 2010
| Temporary sub-menu: Objectives; Detailed Description; Parameters & Constants; Results & Conclusion;Download MatLab Files; |
| Output Amplification Model |
Detailed Description1. Model based on Law of Mass ActionDuring a meeting with our advisors, it was noted that our initial models (which had assumed that our system obeyed Michaelis Menten kinetics) were wrong. This is due to the fact that Michaelis Menten kinetics does not apply to our system. Click here to learn more about our models based on Michaelis Menten kinetics. In order to be able to use Michaelis Menten kinetics, there a lot of assumptions that have to be made. A few of these assumptions were not met by our system:
Since we are continuously producing enzyme, Vmax will change. Therefore the conservation E0 = E + ES does not hold for our system.
We are producing both substrate and enzyme, so we have approximately the same amount of substrate and enzyme.
Therefore, the model above is not representative of the enzymatic reaction. As we cannot use the Michaelis-Menten model we will have to solve from first principle (which involves writing down all of the biochemical equations and solving for these in Matlab). Change of output During our literature research, we came across a better output, so we abandoned the idea of using GFP as an output. Instead, we are using catechol. An enzyme, dioxygenase, will be acting on the catechol, which will then result in a coloured output. Catechol will be added to the bacteria manually (i.e. the bacteria will not produce catechol). Hence, in our models dioxygenase will be treated as an output as this enzyme is the only activator of catechol in our system. This means that the change of catechol into its colourful form is dependent on the dioxygenase concentration.
2. Model preA: Simple production of dioxygenase This model includes transcription and translation of the dioxygenase. It does not involve any amplification steps. It is our control model against which we will be comparing the results of other models. 3. Model A: Activation of Dioxygenase by TEV enzyme |
This model consists of the basic enzymatic reaction:
This is a simple enzymatic reaction, where TEV is the enzyme, Dioxygenase the product and split Dioxygenase the substrate. Choosing k1, k2, k3 as reaction constants, the reaction can be rewritten in these four sub-equations:
These four equations were implemented in Matlab, using a built-in function (ode45) which solves ordinary differential equations.
Implementation in TinkerCell
Another approach to model the amplification module would be to implement it in a program such as TinkerCell (or CellDesigner). This would be useful to check whether the Matlab model works.
4. Model B: Activation of Dioxygenase by TEV or activated split TEV enzyme
This version includes the following features:
- 2 amplification steps (TEV and split TEV)
- Split TEV is specified to have a and b parts
- TEVa is forbidden to interact with TEVa (though in reality there could be some affinity between the two). Same for the interaction between Tevb and Tevb
- Both TEV and TEVs are allowed to activate dioxygenase
- Dioxygenase is assumed to be active as a monomer
- Activate split TEV (TEVs) is not allowed to activate sTEVa or sTEVb (this kind of interaction is accounted for in the next model version)
- This model does not include any specific terms for time delays
5. Model C: Further improvements
This model has not been implemented because of the conclusions that we reached from Models A and B. It would include the following features:
- activated split TEV (TEVs) is allowed to activate not only sD but sTEVa and sTEVb
|}
