Modelling

Intro

In an effort to understand our system and understand the dynamics behind our construct and its impact on the bacteria we decided to make a computer simulation. With this simulation we hope to be able to predict the amount of inulin produced by our bacteria and maybe get a measurement of how much sucrose is needed to meet the inulin requirements.

Disclaimer

Due to the limited characterization we’ve had with our enzymes it hasn’t been possible to make any exact modelling but we hope to display some of the basic functionality of our bacterial system. With this model we hope to show the dynamics behind the process of inulin metabolization but due to the large number of variables we have had to assume a lot of parameters.

For the modelling purpose we’ve used the program Berkeley Madonna which is a simple yet effective program to model biological systems. (http://www.berkeleymadonna.com/)

Theory

SST: is able to cleave and combines a sucrose with a fructose moiety of a cleaved sucrose molecule to make the trisaccharide 1-kestose through a beta2->1 linkage.

FFT: uses 1-kestose as a substrate and elongates this by the iterative addition of n amount of fructose moiety again through beta2->1 linkages. This enzyme also has the ability to cleave sucrose into its two constituents.

Figur 1 – In the image we can see the basic structure of inulin, with the bottom part being the first sucrose and the “arm” extending upward from the green fructose are fructose units added by FFT. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC196615/)

When making a model it is often helpful to make a simple sketch of your system to visualize it and then figuring out what goes into your system where, and what comes out. It is also essential to find bottlenecks i.e. where there might be delays in the system due to enzyme inefficiencies or transport of precursors across membranes etc. from this sketch we constructed a causality diagram which is shown below.