Team:NDC-HighRiverAB/Model
Modelling
The goal of our modelling is to help our team get a better understanding of what our system and protein does.
We modeled in MATLAB using SimBiology.
We modelled both translation and transcription rates to get the protein amount for the overnight cultures we tested in our spectrophotometry lab.
To do this we made the model in figure 1, using rates from the 2017 Ediburgh_UG team (https://2017.igem.org/Team:Edinburgh_UG/Model.) and pSB1C3 copy number from the iGEM registry http://parts.igem.org/Part:pSB1C3 .
Our results showed that we got approximately 1x1011 proteins in the final sample.
This result is based on the absorbance values in the spectrophotometry lab for the nitrophenyl octanoate (0.75 in 1500 seconds) as well as the reference from Gupta et. al. (2014). This was converted to a 40µM concentration of 4-nitrophenyl octanoate, which is 3.13x1016 4-nitrophenyl octanoate molecules in our system.
This gave us a reaction rate of approximately 208 4-nitrophenyl octanoate molecules produced per second.
Figure 1: Our model of transcription and translation rates in our E.coli modelled through MATLAB using SimBiology.
Figure 2: Average absorbances for the breakdown of 4-nitrophenyl octanoate and 4-nitrophenyl palmitate graphed from our spectrophotometry lab.