Team:Stony Brook/Modeling

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
      ω Degradation rate of QSP
      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

      EQUATIONS

    Rate of EnvZ Phosphorylation

      Eqs

    Rate of EnvZ Binding to OmpR

      Eqs

    Rate of OmpR/OmpC Binding

      Eqs

    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