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Structure of the Model
The code can be found at EdiGEM’s github repository together with a detailed description of all made assumptions and used rates.
The MtrCAB electron transfer system from Shewanella oneidensis implemented in E. coli proved to be a challenge in terms of modelling.
To begin with, this type of electron transfer in E. Coli is relatively new idea. There is little information on periplasmic proteins, such as NapC, so many assumptions had to be made in the modelling.
Another issue of this system from the point of view of modelling is the level of detail at which it can be represented. The Kappa language offers the useful don’t care don’t write convention (DCDW), so we can simply ignore cell elements that are not involved in this process. However, even so we are left with a significant process which involves a large part of the cell. This is why we decided to divide the whole process into sub-processes. We model them separately at first and combine them at the end.
The sub-processes can roughly be described in the following way:
Sub-process: Corresponding Kappa File: 1. Glucose -> TCA cycle -> Quinol 1_TCA.ka 2. Quinol -> NapC 2_NapC.ka 3. NapC -> MtrA-> MtrB or Fe soluble 3_MtrABC.ka 4. MtrC -> Flavins -> Fe insoluble 4_UFe.ka 5. Combines 3. and 4. 5.kaThe sub-systems 1, 3 and 4 proved to be vast enough for a modelling project on their own.
