Team:NTNU Trondheim/Equations

From 2012.igem.org

(Difference between revisions)
 
(12 intermediate revisions not shown)
Line 2: Line 2:
<span class="heading">Model equations<hr/></span>
<span class="heading">Model equations<hr/></span>
 +
 +
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 [https://2008.igem.org/Team:KULeuven/Model/Overview 2008 Leuven iGEM team]
 +
 +
For a discussion of the model, see [[Team:NTNU_Trondheim/Model|Model]].
{|border="1"
{|border="1"
Line 11: Line 15:
!colspan="3"|Lldr promoter
!colspan="3"|Lldr promoter
|-
|-
-
|ø -> Lldr
+
|ø &rarr; Lldr
|0.1
|0.1
|Constant production of Lldr
|Constant production of Lldr
|-
|-
-
|Lldr -> ø
+
|Lldr &rarr; ø
|0.0001
|0.0001
|Constant degradation of Lldr relative to the creation of Lldr giving a molecule number of 1000.
|Constant degradation of Lldr relative to the creation of Lldr giving a molecule number of 1000.
|-
|-
-
|2 Lldr -> Lldr2
+
|2 Lldr &rarr; Lldr2
|3
|3
|Dimerization of Lldr
|Dimerization of Lldr
|-
|-
-
|Lldr2 -> 2 Lldr
+
|Lldr2 &rarr; 2 Lldr
|100
|100
|Undimerization of Lldr giving a majority of Lldr in dimer.
|Undimerization of Lldr giving a majority of Lldr in dimer.
|-
|-
-
|Lldr2 -> Lldr
+
|Lldr2 &rarr; Lldr
|0.0001
|0.0001
|Degradation of Lldr dimer.
|Degradation of Lldr dimer.
|-
|-
-
|Lldr2 + Lact -> Lldr2Lact
+
|Lldr2 + Lact &rarr; Lldr2Lact
|0.0001
|0.0001
|Binding of lactate to Lldr dimer. Lactate is notconsumed.
|Binding of lactate to Lldr dimer. Lactate is notconsumed.
|-
|-
-
|Lldr2Lact -> Lldr2
+
|Lldr2Lact &rarr; Lldr2
|1
|1
|Unbinding of Lactate to dimer
|Unbinding of Lactate to dimer
|-
|-
-
|Lldr2Lact -> Lldr
+
|Lldr2Lact &rarr; Lldr
|0.0001
|0.0001
|Degradation of Lldr in Lldr-Lactate complex
|Degradation of Lldr in Lldr-Lactate complex
|-
|-
-
|Lldr2 + pLact -> pLactLldr2
+
|Lldr2 + pLact &rarr; pLactLldr2
|1
|1
|Binding of dimer to lld promoter
|Binding of dimer to lld promoter
|-
|-
-
|pLactLldr2 -> Lldr2 + pLact
+
|pLactLldr2 &rarr; Lldr2 + pLact
|0.1
|0.1
|Unbinding of dimer to promoter
|Unbinding of dimer to promoter
|-
|-
-
|pLactLldr2 -> Lldr + pLact
+
|pLactLldr2 &rarr; Lldr + pLact
|0.0001
|0.0001
|Degradation of Lldr bound to prooter.
|Degradation of Lldr bound to prooter.
|-
|-
-
|pLactLldr2 + Lact -> pLactLldr2Lact + Lact
+
|pLactLldr2 + Lact &rarr; pLactLldr2Lact + Lact
|0.0001
|0.0001
|Binding of lactate to promoter dimer complex.
|Binding of lactate to promoter dimer complex.
|-
|-
-
|pLactLldr2Lact -> pLactLldr2
+
|pLactLldr2Lact &rarr; pLactLldr2
|1
|1
|Release of lactate from promoter dimer complex.
|Release of lactate from promoter dimer complex.
|-
|-
-
|pLactLldr2Lact -> pLactLldr2Lact + mLuxi
+
|pLactLldr2Lact &rarr; pLactLldr2Lact + mLuxi
|0.005
|0.005
|Transcription of activated promoter gives LuxI mRNA
|Transcription of activated promoter gives LuxI mRNA
|-
|-
-
|mLuxI -> ø
+
|mLuxI &rarr; ø
|0.0025
|0.0025
|Degradation of LuxI mRNA
|Degradation of LuxI mRNA
|-
|-
-
|mLuxI -> mLuxI + LuxI
+
|mLuxI &rarr; mLuxI + LuxI
|0.0167
|0.0167
|Translation of LuxI mRNA
|Translation of LuxI mRNA
|-
|-
-
|LuxI -> ø
+
|LuxI &rarr; ø
|0.0002814
|0.0002814
|Degradation of LuxI
|Degradation of LuxI
Line 82: Line 86:
!colspan="3"|Vgb promoter
!colspan="3"|Vgb promoter
|-
|-
-
|ø -> FNR
+
|ø &rarr; FNR
|1
|1
|Constant production of FNR
|Constant production of FNR
|-
|-
-
|FNR -> ø
+
|FNR &rarr; ø
|0.001
|0.001
|Constant degradation of FNR
|Constant degradation of FNR
|-
|-
-
|ø -> ArcA
+
|ø &rarr; ArcA
|1
|1
|Constant production of ArcA
|Constant production of ArcA
|-
|-
-
|ArcA -> ø
+
|ArcA &rarr; ø
|0.001
|0.001
|Constant degradation of ArcA
|Constant degradation of ArcA
|-
|-
-
|FNR + 2 O2 -> FNRO + 2 O2
+
|FNR + 2 O2 &rarr; FNRO + 2 O2
|0.0005
|0.0005
|Oxidation of FNR. Oxygen is not consumed.
|Oxidation of FNR. Oxygen is not consumed.
|-
|-
-
|FNR -> FNRO
+
|FNR &rarr; FNRO
|0.0001
|0.0001
|Reduction of oxidized FNR.
|Reduction of oxidized FNR.
|-
|-
-
|FNRO -> ø
+
|FNRO &rarr; ø
|0.001
|0.001
|Degradation of oxidized FNR.
|Degradation of oxidized FNR.
|-
|-
-
|ArcA + O2 -> ArcAO + O2
+
|ArcA + O2 &rarr; ArcAO + O2
|0.01
|0.01
|Oxidation of Arca. Oxygen is not consumed.
|Oxidation of Arca. Oxygen is not consumed.
|-
|-
-
|ArcaO -> ArcA
+
|ArcaO &rarr; ArcA
|0.001
|0.001
|Reduction of oxidized ArcA
|Reduction of oxidized ArcA
|-
|-
-
|ArcAO -> ø
+
|ArcAO &rarr; ø
|0.001
|0.001
|Degradation of oxidized ArcA
|Degradation of oxidized ArcA
|-
|-
-
|pOx + FNR -> pOxFNR
+
|pOx + FNR &rarr; pOxFNR
|0.1
|0.1
|Binding of FNR to vgb promoter
|Binding of FNR to vgb promoter
|-
|-
-
|pOxFNR -> pOx + FNR
+
|pOxFNR &rarr; pOx + FNR
|0.05
|0.05
|Unbinding of FNR and vgb promoter
|Unbinding of FNR and vgb promoter
|-
|-
-
|pOxFNR -> pOx
+
|pOxFNR &rarr; pOx
|0.001
|0.001
|Degradation of FNR bound to promoter
|Degradation of FNR bound to promoter
|-
|-
-
|pOxFNR + ArcA -> pOxFNRArcA
+
|pOxFNR + ArcA &rarr; pOxFNRArcA
|0.5
|0.5
|Binding of ArcA to FNR-promoter complex.
|Binding of ArcA to FNR-promoter complex.
|-
|-
-
|pOxFNRArcA -> pOxFNR + ArcA
+
|pOxFNRArcA &rarr; pOxFNR + ArcA
|0.02
|0.02
|Unbinding of ArcA to FNR-promoter complex.
|Unbinding of ArcA to FNR-promoter complex.
|-
|-
-
|pOxFNRArcA -> pOx + FNR
+
|pOxFNRArcA &rarr; pOx + FNR
|0.001
|0.001
|Degradation of ArcA to FNR-promoter complex.
|Degradation of ArcA to FNR-promoter complex.
|-
|-
-
|pOxFNR -> pOxFNR + mLuxR
+
|pOxFNR &rarr; pOxFNR + mLuxR
|0.005
|0.005
|Transcription of LuxR mRNA
|Transcription of LuxR mRNA
|-
|-
-
|mLuxR -> ø
+
|mLuxR &rarr; ø
|0.00227
|0.00227
|Degradation of LuxR mRNA
|Degradation of LuxR mRNA
|-
|-
-
|mLuxR -> mLuxR + LuxR
+
|mLuxR &rarr; mLuxR + LuxR
|0.0167
|0.0167
|Translation of LuxR
|Translation of LuxR
|-
|-
-
|LuxR -> ø
+
|LuxR &rarr; ø
|0.0001
|0.0001
|Degradation of LuxR
|Degradation of LuxR
|-
|-
-
!colspan="3"|Lldr promoter
+
!colspan="3"|Lux promoter
|-
|-
-
|ø -> SAM
+
|ø &rarr; SAM
|2
|2
|Constant production of S-adenosylmethionine
|Constant production of S-adenosylmethionine
|-
|-
-
|SAM -> ø
+
|SAM &rarr; ø
|0.01
|0.01
|Constant degradation of SAM
|Constant degradation of SAM
|-
|-
-
|ø -> hex
+
|ø &rarr; hex
|2
|2
|Constant production of 3-oxo-hexanoyl-CoA
|Constant production of 3-oxo-hexanoyl-CoA
|-
|-
-
|hex -> ø
+
|hex &rarr; ø
|0.01
|0.01
|Constant degradation of hex
|Constant degradation of hex
 +
|-
 +
|LuxI + SAM &rarr; LuxISAM
 +
|2
 +
|Binding of LuxI and SAM.
 +
|-
 +
|LuxISAM &rarr; LuxI + SAM
 +
|1
 +
|Unbinding of LuxI and SAM
 +
|-
 +
|LuxISAM &rarr; SAM
 +
|0.0002814
 +
|Degradation of LuxI in complex
 +
|-
 +
|LuxISAM + hex &rarr; LuxISAMhex
 +
|2
 +
|Formation of complex of LuxI, SAM and hex
 +
|-
 +
|LuxISAMhex &rarr; LuxISAM + hex
 +
|1
 +
|Complex disasembles
 +
|-
 +
|LuxISAMhex &rarr; SAM + hex
 +
|0.0002814
 +
|LuxI degrades in complex
 +
|-
 +
|LuxISAMhex &rarr; LuxI + HSL
 +
|0.0167
 +
|Homoserine lactone formed from SAM and hex
 +
|-
 +
|HSL &rarr; ø
 +
|0.1
 +
|Diffusion of HSL
 +
|-
 +
|2 LuxR + 2 HSL &rarr; LuxRHSL
 +
|0.002372
 +
|HSL and LuxR forms a complex
 +
|-
 +
|LuxRHSL &rarr; 2 LuxR + 2 HSL
 +
|1
 +
|LuxR-HSL complex disassembles
 +
|-
 +
|LuxRHSL &rarr; LuxR + 2 HSL
 +
|0.0001
 +
|Degradation of LuxR in complex
 +
|-
 +
|pLux + LuxRHSL &rarr; pLuxLuxRHSL
 +
|1
 +
|Binding of LuxRHSL to promoter
 +
|-
 +
|pLuxLuxRHSL &rarr; pLux + LuxRHSL
 +
|0.1
 +
|Unbinding of LuxRHSL and promoter
 +
|-
 +
|pLuxLuxRHSL &rarr; pLux + LuxR + 2 HSL
 +
|0.0001
 +
|Degradation of LuxR in complex
 +
|-
 +
|pLuxLuxRHSL &rarr; pLuxLuxRHSL + mHolin
 +
|0.005
 +
|Transcription of holin mRNA
 +
|-
 +
|mHolin &rarr; ø
 +
|0.0025
 +
|Degradation of holin mRNA
 +
|-
 +
|mHolin &rarr; mHolin + holin
 +
|0.0167
 +
|Translation of holin mRNA
 +
|-
 +
|holin &rarr; ø
 +
|0.0002
 +
|Degradation of holin
 +
|-
 +
|ø &rarr; antiholin
 +
|0.2
 +
|Constant production of antiholin
 +
|-
 +
|antiholin &rarr; ø
 +
|0.0002
 +
|Degradation of antiholin
 +
|-
 +
|holin + antiholin &rarr; holinantiholin
 +
|0.1
 +
|Formation of holin-antiholin complex
 +
|-
 +
|holinantiholin &rarr; holin + antiholin
 +
|0.01
 +
|Solvation of holin-antiholin complex
 +
|-
 +
|holinantiholin &rarr; holin
 +
|0.0002
 +
|Degradation of antiholin in complex.
 +
|-
 +
|holinantiholin &rarr; 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.
 +
 +
{|border="1"
 +
|-
 +
!Species
 +
!Concentrations
 +
|-
 +
|Lldr
 +
|1000
 +
|-
 +
|FNR
 +
|1000
 +
|-
 +
|ArcA
 +
|1000
 +
|-
 +
|pLact
 +
|100
 +
|-
 +
|pOx
 +
|100
 +
|-
 +
|pLux
 +
|100
 +
|-
 +
|SAM
 +
|200
 +
|-
 +
|hex
 +
|200
 +
|-
 +
|antiholin
 +
|1000
|}
|}

Latest revision as of 09:27, 14 August 2012

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

Model equations

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
Lldr 1000
FNR 1000
ArcA 1000
pLact 100
pOx 100
pLux 100
SAM 200
hex 200
antiholin 1000
Retrieved from "http://2012.igem.org/Team:NTNU_Trondheim/Equations"