Team:TorontoMaRSDiscovery/Modeling
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=Objective= | =Objective= |
Revision as of 18:52, 24 September 2009
Contents |
Objective
Model
The construct that needs to be modelled is shown below. Our submission this year may/may not have all of the parts assebled.
The construct is represented by the reactions shown below Click here for excel file. The reaction framework was mainly generated using the SynBioSS Designer (a great modelling tool!), which also provides "default" parameter values. These parameter values have been gathered from various literature sources, and should be taken as approximations on the appropriate order of magnitude. All units were taken to be (1 / molarity^n-1 * s), where n is the order of the reaction. For example, for the reaction 2 lacI --> lacI2, n = 2, thus the rate constant has the units 1/molality*s.
The pathways for the expressed proteins, eCFPt and Encapsulin, need to be modelled in more detail. For example, in this basic model eCFPt is degraded via a first order reaction and Encapsulin makes a dimer complex. However, in reality fluorescent proteins have been shown to degreade via Micheales-menton kinetics and Encapsulin is thought to make a complex of about 60 monomers. These issues will be addressed in future work.
Reaction | Rate Constant |
Constitutive Expression | |
--> lacl4 | 1E-10 |
--> tetR2 | 1E-10 |
Multimerization | |
2 lacI --> lacI2 | 1.00E+09 |
lacI2 --> 2 lacI | 10 |
2 lacI2 --> lacI4 | 1.00E+09 |
lacI4 --> 2 lacI2 | 10 |
2 tetR --> tetR2 | 1.00E+09 |
tetR2 --> 2 tetR | 10 |
2 Enc --> Enc2 | 100 |
Encapsulation | |
Enc2 + eCFPt --> Enc2:eCFPt | 100 |
Transcription | |
RNAp + BBa_R0010 + LacI_binding_site --> RNAp:BBa_R0010:LacI_binding_site | 10000000 |
RNAp:BBa_R0010:LacI_binding_site --> RNAp + BBa_R0010 + LacI_binding_site | 0.057 |
RNAp:BBa_R0010:LacI_binding_site --> RNAp:BBa_R0010:LacI_binding_site* | 0.1 |
RNAp:BBa_R0010:LacI_binding_site* --> RNAp:DNA_eCFPt + BBa_R0010 + LacI_binding_site | 30 |
RNAp:DNA_eCFPt --> RNAp + mRNA_eCFPt | 0.035 |
RNAp + BBa_R0040 + TetR_1 + TetR_2 --> RNAp:BBa_R0040:TetR_1:TetR_2 | 10000000 |
RNAp:BBa_R0040:TetR_1:TetR_2 --> RNAp + BBa_R0040 + TetR_1 + TetR_2 | 0.057 |
RNAp:BBa_R0040:TetR_1:TetR_2 --> RNAp:BBa_R0040:TetR_1:TetR_2* | 0.1 |
RNAp:BBa_R0040:TetR_1:TetR_2* --> RNAp:DNA_Enc + BBa_R0040 + TetR_1 + TetR_2 | 30 |
RNAp:DNA_Enc --> RNAp + mRNA_Enc | 0.0375 |
Translation | |
rib + mRNA_eCFPt --> rib:mRNA_eCFPt | 100000 |
rib:mRNA_eCFPt --> rib:mRNA_eCFPt_1 + mRNA_eCFPt | 33 |
rib:mRNA_eCFPt_1 --> rib + eCFPt | 0.1154 |
rib + mRNA_Enc --> rib:mRNA_Enc | 100000 |
rib:mRNA_Enc --> rib:mRNA_Enc_1 + mRNA_Enc | 33 |
rib:mRNA_Enc_1 --> rib + Enc | 0.1234 |
Protein-DNA | |
lacI4 + nsDNA --> lacI4:nsDNA | 1000 |
lacI4:nsDNA --> lacI4 + nsDNA | 1.6225 |
lacI4 + LacI_binding_site --> lacI4:LacI_binding_site | 1.00E+09 |
lacI4:LacI_binding_site --> lacI4 + LacI_binding_site | 0.005 |
tetR2 + nsDNA --> tetR2:nsDNA | 1000 |
tetR2:nsDNA --> tetR2 + nsDNA | 1.6225 |
tetR2 + TetR_1 --> tetR2:TetR_1 | 1.00E+09 |
tetR2:TetR_1 --> tetR2 + TetR_1 | 0.005 |
tetR2 + TetR_2 --> tetR2:TetR_2 | 1.00E+09 |
tetR2:TetR_2 --> tetR2 + TetR_2 | 0.005 |
Protein - Effector - DNA | |
lacI4 + IPTG --> lacI4:IPTG | 50000000 |
lacI4:IPTG --> lacI4 + IPTG | 0.1 |
lacI4:IPTG + LacI_binding_site --> lacI4:IPTG:LacI_binding_site | 1.00E+09 |
lacI4:IPTG:LacI_binding_site --> lacI4:IPTG + LacI_binding_site | 0.7 |
lacI4:LacI_binding_site + IPTG --> lacI4:IPTG:LacI_binding_site | 1000000 |
lacI4:IPTG:LacI_binding_site --> lacI4:LacI_binding_site + IPTG | 0.4 |
lacI4:IPTG + nsDNA --> lacI4:IPTG:nsDNA | 1000 |
lacI4:IPTG:nsDNA --> lacI4:IPTG + nsDNA | 1.6225 |
lacI4:nsDNA + IPTG --> lacI4:IPTG:nsDNA | 1000 |
lacI4:IPTG:nsDNA --> lacI4:nsDNA + IPTG | 1.6225 |
tetR2 + aTc --> tetR2:aTc | 50000000 |
tetR2:aTc --> tetR2 + aTc | 0.1 |
tetR2:aTc + TetR_1 --> tetR2:aTc:TetR_1 | 1.00E+09 |
tetR2:aTc:TetR_1 --> tetR2:aTc + TetR_1 | 0.7 |
tetR2:TetR_1 + aTc --> tetR2:aTc:TetR_1 | 1000000 |
tetR2:aTc:TetR_1 --> tetR2:TetR_1 + aTc | 0.4 |
tetR2:aTc + TetR_2 --> tetR2:aTc:TetR_2 | 1.00E+09 |
tetR2:aTc:TetR_2 --> tetR2:aTc + TetR_2 | 0.7 |
tetR2:TetR_2 + aTc --> tetR2:aTc:TetR_2 | 1000000 |
tetR2:aTc:TetR_2 --> tetR2:TetR_2 + aTc | 0.4 |
tetR2:aTc + nsDNA --> tetR2:aTc:nsDNA | 1000 |
tetR2:aTc:nsDNA --> tetR2:aTc + nsDNA | 1.6225 |
tetR2:nsDNA + aTc --> tetR2:aTc:nsDNA | 1000 |
tetR2:aTc:nsDNA --> tetR2:nsDNA + aTc | 1.6225 |
Degredation | |
lacI4 --> | 0.000289 |
tetR2 --> | 0.000289 |
mRNA_eCFPt --> | 0.0015 |
mRNA_Enc --> | 0.0015 |
eCFPt --> | 0.000289 |
Enc2 --> | 0.000289 |
Enc2:eCFPt --> | 0.000289 |
Dilution | |
lacI4:nsDNA --> nsDNA | 0.000193 |
tetR2:nsDNA --> nsDNA | 0.000193 |
lacI4:IPTG --> IPTG | 0.000289 |
tetR2:aTc --> aTc | 0.000289 |
lacI4:IPTG:nsDNA --> IPTG + nsDNA | 0.000193 |
tetR2:aTc:nsDNA --> aTc + nsDNA | 0.000193 |