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Team:TorontoMaRSDiscovery/Modeling
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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 [http://synbioss.sourceforge.net/ SynBioSS Designer (a great modelling tool!)], which also provides "default" parameter values. These parameter values have been gathered from various literature [http://neptune.cems.umn.edu/designer/designer_defaults.pdf 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 |
Simulations
Accumulation of Proteins and Encapsulin-eCFP complex
File:Uft mod pic1.bmp File:Prod2.tif
