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Team:Colorado State/Modeling
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| - | We are currently working on modeling the reaction between the enzyme Kumamolisin and the protein responsible for causing a | + | We are currently working on modeling the reaction between the enzyme Kumamolisin and the protein responsible for causing a immune response 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 bound enzyme breaking down the protein is treated as it's own reaction. |
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3. Protein breakdown Bound Kumamolisin and Gluten -> Kumamolisin + Broken-down gluten | 3. Protein breakdown Bound Kumamolisin and Gluten -> Kumamolisin + Broken-down gluten | ||
| - | This simulation can be run on the | + | 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). | 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 we are hoping to include this in modeling reactions 1 and 2. | Our focus is on determining accurate values for these reaction rates. Smoldyn also allows for inclusions of binding site simulations, and we are hoping to include this in modeling reactions 1 and 2. | ||
Revision as of 19:37, 9 July 2012
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We are currently working on modeling the reaction between the enzyme Kumamolisin and the protein responsible for causing a immune response 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 bound enzyme breaking down the protein is 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 we are hoping to include this in modeling reactions 1 and 2.
