Modeling

Our main goal was to estimate how the EnvZ concentration correlates with the signal from GFP production. For that we decided to divide our system into four main models:

• OmpR production and phosphorylation beginning with the EnvZ receptor
• OmpC translation
• Release of quorum sensing (QS) molecules
• GFP expression for detection.

Parts 1 & 2: OmpR Phosphorylation and OmpC Translation

We wanted to insert the EnvZ receptor into a bacterial cell to activate a signal cascade including four main parts (OmpR production, OmpC translation, quorum sensing and GFP expression). For the first two parts, OmpR and OmpC production, we used various published research to find equations describing the main reactions and their rate constants. With the help of SimBiology software, a plug-in installed in MatLab, we designed these models by drawing them qualitatively, choosing the kinetics and adding all the constants. We then put the two parts together. Down below is the OmpC production-reduction EnvZ switch depending on the osmolarity level. The way to design a model is to define each compartment, in this case the cell membrane and the cytoplasm. Each reactant is a substance and the reactant molecules connect them. The substances are given their corresponding initial values. The kinetic law Mass Action is selected if the kinetics is unknown.

Figure 1:Modell for OmpF production starting from the EnvZ receptor (left image) at low osmolarity levels. EnvZ phosphorylates OmpR (OmpR-P, right image) and activates OmpF production upon reacting with the binding sites F1, F1F2 and F1F2F3.

Figure 2: Modell for OmpC production starting from the EnvZ receptor (left image) at high osmolarity levels. EnvZ phosphorylates OmpR (right image) and activates OmpC production upon reacting with the binding sites C1, C1C2 and C1C2C3. OmpF is degraded simultaneously when the osmolarity is high.

Since we wanted our final product to be OmpC and not OmpF, we chose to make two models for each scenario to get a better understanding of how the osmolarity changes the endpoint, in our case being the osmolarity-dependent GFP expression.