Team:TorontoMaRSDiscovery/Modeling

From 2009.igem.org

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===Accumulation of Proteins and Encapsulin-eCFP complex===
===Accumulation of Proteins and Encapsulin-eCFP complex===
[[Image:uft_mod_pic1.png]]
[[Image:uft_mod_pic1.png]]
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[[Image:prod2.tif]]
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[[Image:uft_mod_pic2.png]]
===Addition of IPTG and aTc effectors===
===Addition of IPTG and aTc effectors===
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[[Image:prod3.tif]]
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[[Image:uft_mod_pic3.png]]
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[[Image:prod4.tif]]
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[[Image:uft_mod_pic4.png]]
===Sensitivity Analysis===
===Sensitivity Analysis===
=Future Work=
=Future Work=

Revision as of 18:50, 24 September 2009

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Home The Team The Project Parts Submitted to the Registry Modeling Notebook


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.

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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

Uft mod pic1.png Uft mod pic2.png

Addition of IPTG and aTc effectors

Uft mod pic3.png Uft mod pic4.png

Sensitivity Analysis

Future Work