Team:Linkoping Sweden/Modeling
Modeling
What
The modeling in this project is supposed to anticipate what shall be done in the lab, to achive the task of quantifying as much soluble protein as possible. This modeling is achived by using MATLAB with the SBtoolbox [1, 2] and base the model on FoldEco [3, 4].
Why
By having a system of connections between states of protein folding, a system with differential equetions descibing the changes to each state can be created with different parameters. The parameteres can (sometimes) be found in the literature for the state in question.
By having the differential equations for each state (including known parameters), the changes in the different states can be measured over time. If the changes in the differential equations matches changes in real life experiments, the model may be validated. The validated model can then be used to predict real life experiments, when there are changes in the model such as an increase in the conentration of a chemical compound.
How
Our model is based on the FoldEco model for protein folding [3, 4] , where we use the model to create differential equations for the states (e.g. changes in amount of misfolded protein). The created differential equations are then visualized in MATLAB using the SBtoolbox [1, 2], to obtain graphs of the changes in all states. By having data from the laboratory, we can either confirm or deny the model. If the model is confirmed, we change different parameters to try to obtain the desired task - as much folded protein as possible.
Sources
1. SBPOPPACKAGE. [Internet]. Cited 2017-06-15. URL: http://www.sbtoolbox2.org/main.php
2. Link to the toolbox, from ISB-group. URL: http://www.isbgroup.eu/files/SBPOP_PACKAGE_Rev_98.zip
3. Powers, E. T., Powers, D. L., & Gierasch, L. M. (2012). FoldEco: A Model for Proteostasis in E. coli. Cell Reports, 1(3), 265–276. http://doi.org/10.1016/j.celrep.2012.02.011
4. Link to the FoldEco website. URL: http://foldeco.scripps.edu:8080/webMathematica/foldecoindex.html
