# Minnesota/24 June 2009

(Difference between revisions)
 Revision as of 15:37, 28 July 2009 (view source)Bswiniar (Talk | contribs) (New page: {|style="align:left" width="965" |- |''' Back to Notebook Home''' |- |'''Go to Previous Day (June 23)'''|| width=158|'''[[Minnesota/...)← Older edit Revision as of 15:36, 29 July 2009 (view source)Bswiniar (Talk | contribs) Newer edit → Line 4: Line 4: |- |- |'''[[Minnesota/23 June 2009|Go to Previous Day (June 23)]]'''|| width=158|'''[[Minnesota/25 June 2009|Go to Next Day (June 25)]]''' |'''[[Minnesota/23 June 2009|Go to Previous Day (June 23)]]'''|| width=158|'''[[Minnesota/25 June 2009|Go to Next Day (June 25)]]''' + |} + Since there are several problems with the first TNN model, we are deciding to focus on them one at a time. The first thing to work on is the leakiness problem. In order to deal with this issue, we are including a reaction that allows for the binding of the RNA polymerase to the operator site even if the site is occupied by a tetR. This will allow for some expression at an aTc concentration of 0, because at this point tetR is almost always bound to the tetO operator. + + Here is the model we are working on: + {| class="wikitable" style="text-align:center" border = "1" + |- + ! Reaction + ! Forward Kinetic Constant + ! Reverse Kinetic Constant + |- + | RNAp + lacP + lacI4:lacO1 ->  RNAp:lacP||6.23E+05|| + |- + | RNAp + lacP + lacO1 ↔ RNAp:lacP||1E+07|| 1 + |- + |RNA:lacP -> RNAp:lacP* || .01 || + |- + |RNAp:lacP* -> lacP + lacO1 + RNAp:DNAgfp||30|| + |- + |RNAp:DNAgfp -> RNAp + gfp_mRNA||30|| + |- + |gfp_mRNA + rib -> rib:gfp_mRNA||100000|| + |- + |rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA||33|| + |- + |rib:gfp_mRNA_1 -> rib + gfp||33|| + |- + |tetR2 + aTc ↔ tetR2:aTc||2E+09||4E-04 + |- + |tetR2:aTc + aTc  ↔ tetR2:aTc2||1E+08||1E-03 + |- + |tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc||1E+08||1 + |- + |tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2||1E+08||1E+05 + |- + |tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc||1E+08||1E-03 + |- + |tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc2||1E+08||1E-03 + |- + |tetR2 -> Ø||2.89E-04|| + |- + |tetR2:aTc -> aTc||2.89E-04|| + |- + |tetR2:aTc2 -> 2 aTc||2.89E-04|| + |- + |tetR2 + nsDNA ↔  tetR2:nsDNA||1000||3.2409 + |- + |tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA||1000||3.2409 + |- + |tetR2:aTc:nsDNA -> aTc + nsDNA||1.93E-04|| + |- + |tetR2:nsDNA -> nsDNA||1.93E-04|| + |- + |Ø -> tetR2||1E-11|| + |- + |Ø -> aTc||3.3E-04|| + |- + |gfp_mRNA -> Ø||1.16E-03|| + |- + |gfp -> Ø||3.21E-05|| |} |}

## Revision as of 15:36, 29 July 2009

Since there are several problems with the first TNN model, we are deciding to focus on them one at a time. The first thing to work on is the leakiness problem. In order to deal with this issue, we are including a reaction that allows for the binding of the RNA polymerase to the operator site even if the site is occupied by a tetR. This will allow for some expression at an aTc concentration of 0, because at this point tetR is almost always bound to the tetO operator.

Here is the model we are working on:

Reaction Forward Kinetic Constant Reverse Kinetic Constant
RNAp + lacP + lacI4:lacO1 -> RNAp:lacP6.23E+05
RNAp + lacP + lacO1 ↔ RNAp:lacP1E+07 1
RNA:lacP -> RNAp:lacP* .01
RNAp:lacP* -> lacP + lacO1 + 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