Team:Mexico-UNAM-CINVESTAV/Modeling/Simulations

From 2010.igem.org

Cold shock response simulations

Our model was implemented in the software tool CellDesigner 4.1. And the model file can be downloaded from MEXICO_UNAM_CINVESTAV_CspA_system.zip

The estimation of the parameters has been a serious problem for the design of any model, and in our case we are not te exception. Unfortunately we were not able to obtain enough laboratory meditions and then our model is more an qualitative than quantitative approach.

The main behavior that we tried to reproduce was the induction of the expression of the CspA protein during cold shock and later the adapted state of the cell where the synthesis of the cold shock proteins is low and the rate of the synthesis of the rest of the proteins stabilizes to certain level.

Simulation 1

Simulation 2

In the Simulations 1 and 2 is represented the qualitative response of the cold shock system. From time t=0 the level of the E. coli proteins decrease until enough CspA is present in the media. The amount of CspA grows until a E. coli proteins reach a maximum level and then decays to a stable one.

Visualization of the Antifreeze protein

Software references

• Funahashi, A., Tanimura, N., Morohashi, M., and Kitano, H., CellDesigner: a process diagram editor for gene-regulatory and biochemical networks, BIOSILICO, 1:159-162, 2003 [doi:10.1016/S1478-5382(03)02370-9]

• Funahashi, A.; Matsuoka, Y.; Jouraku, A.; Morohashi, M.; Kikuchi, N.; Kitano, H."CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks" Proceedings of the IEEE Volume 96, Issue 8, Aug. 2008 Page(s):1254 - 1265 [doi 10.1109/JPROC.2008.925458]