Modeling is an important part of synthetic biology. With good models, one can gain insight of the biological phenomena before doing anything in the lab. Understanding the biological system allows us to make better decisions as we modify the system for our purposes. Our project consisted of quite a few different parts, and that gave us a natural way to divide our modeling to four parts.
The main goal of our project was the production of propane with E. coli, so the main task in modeling was to gain insight to the propane pathway. We made a model based on Michaelis-Menten enzyme kinetics and calculated numerical results from it with Copasi and Matlab. With these tools we found the bottlenecks and most sensitive parts of our reaction. We also got some ideas on how much propane will be produced in our system. For more information, see our page of modeling propane pathway.
One big concern in our project was the efficiency of propane production. To solve this problem we wanted to use micelles to hold enzymes together and speed up the reactions. We thought that this approach would be especially suitable for the of the last enzymes in our pathway, CAR and ADO, who have toxic butyraldehyde as a substrate between them. Since there are many butyraldehyde-consuming enzymes in a cell, the speed up we could get would be even better. We did a stochastic model of synergy with python to confirm if this approach would really work as we hope.
As mentioned above we wanted to make propane production more efficient by having enzymes together in a micelle. While we modeled the efficiency of having the enzymes close together, we also wanted to know if it was possible to form the micelles with our enzymes in the first place. That is why we made a geometrical model about micelle structure.
Our project involves creating renewable propane from cellulose, which is why we wanted to model the pathway responsible for hydrolysing cellulose. The pathway consists of three different genes that cut the cellulose to glucose which the cell can then use as an energy source for propane production. While building a beneficial model of this wasn't possible for us, see our page of modeling cellulose pathway to see what thoughts our modeling team had on this.