Team:BOKU-Vienna/Model
Modeling Overview
Introduction
Since mathematical models are a very important part to help figuring out if our idea is theoretically
possible, we started very early to dive into this topic. After considering Matlab we decided to do our
model in Copasi which is an open-source software application for creating and solving mathematical
models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks,
infectious diseases, and many others.[1]
In the first weeks of July, we started to build the whole system in Copasi. From the binding of
Mycolactone to the riboswitch over the production of AHL and the amplification of it to the production
of blue Chromoprotein.
This is our general Idea:
Here are the Constructs as we have put them together.
Modeling Reactions
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Modeling Reactions
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Species Overview
| Species | Description |
|---|---|
| Mycolactone | Is a polyketide-derived macrolide produced and secreted by a group of very closly related pathogenic Mycobacteria. |
| Theophyllin | A inducer molecule for a specific Aptamer. |
| Aptamer | An oligonucleotide or peptide molecule that binds to a specific target molecule. |
| T7-Polymerase | is an RNA polymerase from the T7 bacteriophage that catalyzes the formation of RNA from DNA in the 5'→ 3' direction. |
| T7-Promotor | Specific T7 bacteriophage derived sequence for binding and initiation of the transcription. |
| mRNA-LuxI | mRNA of the LuxI-Enzyme being transcribed by the Lux Promotor and by the T7-Promotor |
| LuxI | Ezyme that catalyses the Reaktion from Precursors to AHL |
| AHL | 30C6-HSL is an acyl homoserine lactone which diffuses into the cell and mainly binds to LuxR.[2] |
| LuxR | Constitutively expressed regulator protein that can bind LuxAHL and stimulate transcription of Bxb1.[2] |
| AHL/LuxR-Komplex | Komplex formed by 2 AHL and 2 LuxR |
| mRNA-amilCP | mRNA of the amilCP-protein being transcribed by the Lux Promotor |
| amilCP | The blue Chromoprotein we used. |
| T7-Promotor | Promoter for the Lux-System |
Parameter Overview
| Parameter | Description | value | |
|---|---|---|---|
| k0 | Transcription rate of LuxI | 2,5 1/min | Literature value [4] |
| k1 | Translation rate of LuxI | 0,868 1/min | Literature value [4] |
| k2 | Rate of AHL-synthese | 0,04 1/min | Literature value [4] |
| k3 | Rate of Komplexassociation | 10-5 mL3/(mmol3*min) | Estimated by our self |
| k4 | rate of Promoter activation | 0,16 mL/(mmol*min) | Estimated by our self |
| k5 | Transcription rate of mRNA- AmilCP | 4300 1/min | Estimated by our self |
| k6 | Translation rate of mRNA-AmilCP | 1075 1/min | Estimated by our self |
| r1 | Diffusionrate of AHL outside of the cell | 13,24 mL/min | Literature value [3] |
| r2 | Diffusionrate of AHL into the cell | 11,04 mL/min | Estimated by our self |
| c1 | Constant flux of LuxR | 0,0005 mmol/(mL*min) | Estimated by our self |
| c2 | Constant flux of pAHL | 0,01 mmol/(mL*min) | Estimated by our self |
| d1 | Degradation rate of LuxR | 0,0231 1/min | Literature value [3] |
| d2 | Degradation rate of AHL inside the cell | 0,004 1/min | Literature value [5] |
| d3 | Degradation rate of AHL in the media | 0,0004 1/min | Literature value [5] |
| d4 | Mycolacton degradation rate | 3,33*10-7 1/min | Estimated by our self |
Modellation Results:
Our main goal concerning the system was to determine after what time the production of blue Chromoprotein will start.
According to the Diagram the blue Chromoprotein production will start at about 50 minutes and will reach a peak after 100 minutes.
