Minnesota/8 June 2009

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Line 14: Line 14:
! Reverse Kinetic Constant
! Reverse Kinetic Constant
|-
|-
-
| RNAp + lacP + lacI4:lacO1 ->  RNAp:lacP||6.23E+05||  
+
| RNAp + lacP + tetR2:tetO1 ->  RNAp:lacP||6.23E+05||  
|-
|-
-
| RNAp + lacP + lacO1 ↔ RNAp:lacP||1E+07|| 1
+
| RNAp + lacP + tetO1 ↔ RNAp:lacP||1E+07|| 1
|-
|-
|RNA:lacP -> RNAp:lacP* || .01 ||
|RNA:lacP -> RNAp:lacP* || .01 ||
|-
|-
-
|RNAp:lacP* -> lacP + lacO1 + RNAp:DNAgfp||30||
+
|RNAp:lacP* -> lacP + tetO1 + RNAp:DNAgfp||30||
|-
|-
|RNAp:DNAgfp -> RNAp + gfp_mRNA||30||
|RNAp:DNAgfp -> RNAp + gfp_mRNA||30||
Line 36: Line 36:
|tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc||1E+08||1
|tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc||1E+08||1
|-
|-
-
|tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2||1E+08||1E+5
+
|tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2||1E+08||1E+05
|-
|-
|tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc||1E+08||1E-03
|tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc||1E+08||1E-03
Line 58: Line 58:
|Ø -> tetR2||1E-11||
|Ø -> tetR2||1E-11||
|-
|-
-
|Ø -> aTc||n||
+
|Ø -> aTc||3.3E-04||
|-
|-
|gfp_mRNA -> Ø||1.16E-03||
|gfp_mRNA -> Ø||1.16E-03||

Latest revision as of 18:43, 29 July 2009

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Today the first model of the TNN system was created. In order to do this, the previous work of the Kaznessis group was used to provide a basis for a a lot of the reactions. This allowed us to easily obtain reasonable kinetic constants for almost all the reactions in the model. Here is the first incarnation of the model (many future models will simply change this one):

Reaction Forward Kinetic Constant Reverse Kinetic Constant
RNAp + lacP + tetR2:tetO1 -> RNAp:lacP6.23E+05
RNAp + lacP + tetO1 ↔ RNAp:lacP1E+07 1
RNA:lacP -> RNAp:lacP* .01
RNAp:lacP* -> lacP + tetO1 + RNAp:DNAgfp30
RNAp:DNAgfp -> RNAp + gfp_mRNA30
gfp_mRNA + rib -> rib:gfp_mRNA100000
rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA33
rib:gfp_mRNA_1 -> rib + gfp33
tetR2 + aTc ↔ tetR2:aTc2E+094E-04
tetR2:aTc + aTc ↔ tetR2:aTc21E+081E-03
tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc1E+081
tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc21E+081E+05
tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc1E+081E-03
tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc21E+081E-03
tetR2 -> Ø2.89E-04
tetR2:aTc -> aTc2.89E-04
tetR2:aTc2 -> 2 aTc2.89E-04
tetR2 + nsDNA ↔ tetR2:nsDNA10003.2409
tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA10003.2409
tetR2:aTc:nsDNA -> aTc + nsDNA1.93E-04
tetR2:nsDNA -> nsDNA1.93E-04
Ø -> tetR21E-11
Ø -> aTc3.3E-04
gfp_mRNA -> Ø1.16E-03
gfp -> Ø3.21E-05
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