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We are currently working on modeling the reaction between the enzyme Kumamolisin and the protein responsible for causing a reaction in Celiac patients. Our model is based on Michaelis-Menten kinetics which treat enzyme kinetics as a two step reaction. First, the enzyme must bind to the protein, which is a reversible reaction. Then, the enzyme breaking down the protein is then treated as it's own reaction.

Smoldyn is a biochemical reaction modeling software we've chosen to carry out these models in. Currently, we have working a simulation based on the Michealis-Menten model. Our model includes three reactions:

1. Forward binding Kumamolisin + Gluten -> Bound Kumamolisin and Gluten

2. Reverse binding Bound Kumamolisin and Gluten -> Kumamolisin + Gluten

3. Protein breakdown Bound Kumamolisin and Gluten -> Kumamolisin + Broken-down gluten

This simulation can be run on the igem laptop by entering the Unix command python /home/local_admin/igem/pythonScripts/bittersweeper.py Currently, this simulation sweeps over different reaction rates for each of the 3 above reactions. These parameters can be edited by any member of the CSU iGEM team, by opening the python file with a text editor (i.e. gedit /home/local_admin/igem/pythonScripts/bittersweeper.py).

Our focus is on determining accurate values for these reaction rates. Smoldyn also allows for inclusions of binding site simulations, and this is also an area were looking into including for modeling reactions 1 and 2.