Team:NTNU Trondheim/Equations

From 2012.igem.org

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|Degradation of holin mRNA
|Degradation of holin mRNA
|-
|-
-
|mHolin -> mHolin + Holin
+
|mHolin -> mHolin + holin
|0.0167
|0.0167
|Translation of holin mRNA
|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.
|}
|}

Revision as of 12:15, 13 August 2012

NTNU IS B.A.C.K.
Bacterial Anti-Cancer-Kamikaze

Model equations
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.
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