| Line 279: | Line 279: | ||
|0.0002 | |0.0002 | ||
|Degradation of holin in complex. | |Degradation of holin in complex. | ||
| + | |} | ||
| + | |||
| + | The nonzero start concentrations are given in the table below. Oxygen and lactate concentrations are variable parameters. | ||
| + | {|border="1" | ||
| + | |- | ||
| + | !Species | ||
| + | !Concentrations | ||
| + | |- | ||
|} | |} | ||
The equations and propensity parameters used in the model are given in the table below. Translation and transcription rates, as well as binding rates for the lux promoter are adapted from the 2008 Leuven iGEM team
For a discussion of the model, see Model.
| Reaction | Propensity | Comments |
|---|---|---|
| Lldr promoter | ||
| ø -> Lldr | 0.1 | Constant production of Lldr |
| Lldr -> ø | 0.0001 | Constant degradation of Lldr relative to the creation of Lldr giving a molecule number of 1000. |
| 2 Lldr -> Lldr2 | 3 | Dimerization of Lldr |
| Lldr2 -> 2 Lldr | 100 | Undimerization of Lldr giving a majority of Lldr in dimer. |
| Lldr2 -> Lldr | 0.0001 | Degradation of Lldr dimer. |
| Lldr2 + Lact -> Lldr2Lact | 0.0001 | Binding of lactate to Lldr dimer. Lactate is notconsumed. |
| Lldr2Lact -> Lldr2 | 1 | Unbinding of Lactate to dimer |
| Lldr2Lact -> Lldr | 0.0001 | Degradation of Lldr in Lldr-Lactate complex |
| Lldr2 + pLact -> pLactLldr2 | 1 | Binding of dimer to lld promoter |
| pLactLldr2 -> Lldr2 + pLact | 0.1 | Unbinding of dimer to promoter |
| pLactLldr2 -> Lldr + pLact | 0.0001 | Degradation of Lldr bound to prooter. |
| pLactLldr2 + Lact -> pLactLldr2Lact + Lact | 0.0001 | Binding of lactate to promoter dimer complex. |
| pLactLldr2Lact -> pLactLldr2 | 1 | Release of lactate from promoter dimer complex. |
| pLactLldr2Lact -> pLactLldr2Lact + mLuxi | 0.005 | Transcription of activated promoter gives LuxI mRNA |
| mLuxI -> ø | 0.0025 | Degradation of LuxI mRNA |
| mLuxI -> mLuxI + LuxI | 0.0167 | Translation of LuxI mRNA |
| LuxI -> ø | 0.0002814 | Degradation of LuxI |
| Vgb promoter | ||
| ø -> FNR | 1 | Constant production of FNR |
| FNR -> ø | 0.001 | Constant degradation of FNR |
| ø -> ArcA | 1 | Constant production of ArcA |
| ArcA -> ø | 0.001 | Constant degradation of ArcA |
| FNR + 2 O2 -> FNRO + 2 O2 | 0.0005 | Oxidation of FNR. Oxygen is not consumed. |
| FNR -> FNRO | 0.0001 | Reduction of oxidized FNR. |
| FNRO -> ø | 0.001 | Degradation of oxidized FNR. |
| ArcA + O2 -> ArcAO + O2 | 0.01 | Oxidation of Arca. Oxygen is not consumed. |
| ArcaO -> ArcA | 0.001 | Reduction of oxidized ArcA |
| ArcAO -> ø | 0.001 | Degradation of oxidized ArcA |
| pOx + FNR -> pOxFNR | 0.1 | Binding of FNR to vgb promoter |
| pOxFNR -> pOx + FNR | 0.05 | Unbinding of FNR and vgb promoter |
| pOxFNR -> pOx | 0.001 | Degradation of FNR bound to promoter |
| pOxFNR + ArcA -> pOxFNRArcA | 0.5 | Binding of ArcA to FNR-promoter complex. |
| pOxFNRArcA -> pOxFNR + ArcA | 0.02 | Unbinding of ArcA to FNR-promoter complex. |
| pOxFNRArcA -> pOx + FNR | 0.001 | Degradation of ArcA to FNR-promoter complex. |
| pOxFNR -> pOxFNR + mLuxR | 0.005 | Transcription of LuxR mRNA |
| mLuxR -> ø | 0.00227 | Degradation of LuxR mRNA |
| mLuxR -> mLuxR + LuxR | 0.0167 | Translation of LuxR |
| LuxR -> ø | 0.0001 | Degradation of LuxR |
| Lux promoter | ||
| ø -> SAM | 2 | Constant production of S-adenosylmethionine |
| SAM -> ø | 0.01 | Constant degradation of SAM |
| ø -> hex | 2 | Constant production of 3-oxo-hexanoyl-CoA |
| hex -> ø | 0.01 | Constant degradation of hex |
| LuxI + SAM -> LuxISAM | 2 | Binding of LuxI and SAM. |
| LuxISAM -> LuxI + SAM | 1 | Unbinding of LuxI and SAM |
| LuxISAM -> SAM | 0.0002814 | Degradation of LuxI in complex |
| LuxISAM + hex -> LuxISAMhex | 2 | Formation of complex of LuxI, SAM and hex |
| LuxISAMhex -> LuxISAM + hex | 1 | Complex disasembles |
| LuxISAMhex -> SAM + hex | 0.0002814 | LuxI degrades in complex |
| LuxISAMhex -> LuxI + HSL | 0.0167 | Homoserine lactone formed from SAM and hex |
| HSL -> ø | 0.1 | Diffusion of HSL |
| 2 LuxR + 2 HSL -> LuxRHSL | 0.002372 | HSL and LuxR forms a complex |
| LuxRHSL -> 2 LuxR + 2 HSL | 1 | LuxR-HSL complex disassembles |
| LuxRHSL -> LuxR + 2 HSL | 0.0001 | Degradation of LuxR in complex |
| pLux + LuxRHSL -> pLuxLuxRHSL | 1 | Binding of LuxRHSL to promoter |
| pLuxLuxRHSL -> pLux + LuxRHSL | 0.1 | Unbinding of LuxRHSL and promoter |
| pLuxLuxRHSL -> pLux + LuxR + 2 HSL | 0.0001 | Degradation of LuxR in complex |
| pLuxLuxRHSL -> pLuxLuxRHSL + mHolin | 0.005 | Transcription of holin mRNA |
| mHolin -> ø | 0.0025 | Degradation of holin mRNA |
| mHolin -> mHolin + holin | 0.0167 | Translation of holin mRNA |
| holin -> ø | 0.0002 | Degradation of holin |
| ø -> antiholin | 0.2 | Constant production of antiholin |
| antiholin -> ø | 0.0002 | Degradation of antiholin |
| holin + antiholin -> holinantiholin | 0.1 | Formation of holin-antiholin complex |
| holinantiholin -> holin + antiholin | 0.01 | Solvation of holin-antiholin complex |
| holinantiholin -> holin | 0.0002 | Degradation of antiholin in complex. |
| holinantiholin -> antiholin | 0.0002 | Degradation of holin in complex. |
The nonzero start concentrations are given in the table below. Oxygen and lactate concentrations are variable parameters.
| Species | Concentrations |
|---|
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