Difference between revisions of "Team:Stony Brook/Modeling"
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<h5 id=cow>Rate of the influx of glucose </h5> | <h5 id=cow>Rate of the influx of glucose </h5> | ||
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<h5 id=cow>Rate of EnvZ Phosphorylation</h5> | <h5 id=cow>Rate of EnvZ Phosphorylation</h5> | ||
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<h5 id=cow>Rate of EnvZ Binding to OmpR</h5> | <h5 id=cow>Rate of EnvZ Binding to OmpR</h5> | ||
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<h5 id=cow>Rate of OmpR/OmpC Binding</h5> | <h5 id=cow>Rate of OmpR/OmpC Binding</h5> | ||
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Revision as of 00:11, 19 September 2015
Modeling
Model
Model
EnvZ Model
Sensor Design
Currently our engineered cells rely on the sensory histidine kinase, EnvZ, which senses for environmental osmolarity. In high osmolarity, EnvZ phosphorylates a transcriptional regulatory protein, OmpR, which then binds to the ompC promoter to begin the transcription of our tripeptides.
Osmolarity of the blood is affected by many factors besides just sugar levels so in the future we want to implement a sensor specifically for glucose. The lac operon has the ability to sense cAMP, which has an inverse relationship to environmental glucose concentration. To use this system, we will knock out the lacI repressor and replace lacZ with a tetR repressor. Separate from the operon, the tripeptides will be located under the control of a constitutively expressing Ptet promoter. In the case of a glucose spike (or hyperglycemia), cAMP levels would fall and transcription of the tetR repressor would drop. The lack of TetR would allow the PTet promoter to transcribe the tripeptides and regulate blood sugar.
Glucose Sensor Model
Topic 4
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Topic 5
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Variable Table
| Name | Description |
|---|---|
| s | DescriptionSynthesis rate of QSP |
| δ | Degradation rate of QSP |
| R | Concentration of QSP |
| ξ | Amount of OmpC/OmpR that’s expressing peptides |
| Kon | Transcription factor activation coefficient |
| Koff | Dissociation rate of OmpR for the peptide DNA |
| φ | Concentration of the OmpC/OmpR complex |
| M | Concentration of peptide mRNA |
| Γ | Maximum transcription rate of mRNA |
| σ | Degradation rate of peptide mRNA |
| γ | Concentration of translated QSP |
| χ | Maximum translation rate of peptide |
| Ι | Concentration of incoming glucose |
| ζ | Concentration of outgoing glucose |
| Kin | Proportionality constant for the influx of glucose |
| EnvZAct | Concentration of Activated EnvZ |
| Kact | Proportionality constant for EnvZ phosphorylation |
| Z | Concentration of EnvZ-OmpR-P complex |
| OmpR | Concentration of OmpR |
| Kphosphorylated | Proportionality constant for the phosphorylation of OmpR |
| Koff | Proportionality constant for the dissociation of OmpR from EnvZ |
| ε | Concentration of cAMP bound to CRP |
| Con/Coff | Binding affinity of cAMP to CRP |
| Τ | Degradation rate of cAMP from CRP |
| P | Proportionality constant for glucose levels |
| ω | Concentration of TetR |
| Φ | Concentration of PTet |
| τ | Dissociation constant of TetR to Ptet |
| Y | Concentration of free TetR |
| cAMP-CRPdis | Concentration of unbound cAMP-CRP |
| cAMP-CRPbind | Concentration of bound cAMP-CRP |
| υ | Activation rate of TetR |
| T | Binding affinity of cAMP-CRPdis to the ABS |
| Ψ | Dissociation constant of cAMP-CRPdis to the ABS |
Equations
EnvZ Equations
Rate of the influx of glucose
Rate of EnvZ Phosphorylation
Rate of EnvZ Binding to OmpR
Rate of OmpR/OmpC Binding
Rate of Transcription for peptide mRNA
Eqs
Rate of Translation of Peptide mRNA
Eqs
Code
Synthetic Sensor Equations
Rate of cAMP Binding to CRP
Eqs
Rate of tetR Activation
Eqs
Rate of tetR Repression on pTet
Eqs
Amount of Peptides Produced Under The Sensor
Eqs
