Team:SydneyUni Australia/Modelling Results

From 2013.igem.org

Revision as of 04:02, 28 September 2013 by HZFord (Talk | contribs)

SydneyUniversity Top Banner.jpg SydneyUniversity Bottom Banner.jpg


Running the Model

The model was run using MATLAB’s ODE45.

All enzyme concentrations were given a value of 0.1 mM. The temperature was set as T=298K. A plasma membrane distance of d=2nm was given. The cell concentration was given as 1E8 cells/mL. No cellular growth rate was implemented. Glycolate, ε, was left ‘unprocessed’, i.e. it is left to simply accumulate.

Using the constants above the flux took the value:


Igem J=0.04.png

Assumptions

  • All enzymes follow MM kinetics as described in the literature.
  • The enzymes and metabolites are homogeneously distributed within the cell.
  • The metabolites in the pathway are processed only by the proposed enzymes.
  • The enzyme concentrations remain constant.
  • The partition coefficient for DCA in octanol and water is approximately the same as the partition coefficient for the cell membrane.
  • The cells only grow/divide through DCA-derived-glycolate.
  • Diffusion can accurately follow
  • All cells are of the same size (ie equal membrane surface area)

Raw MATLAB code:


function dy = DCA(t,y)
 
dy=zeros(6,1);
 
dy(1)= -6*(10^4)*0.0463067*(y(1)-y(2));
dy(2)= 6*(10^4)*0.0463067*(y(1)-y(2))-3.3*0.1*(y(2)/(0.53+y(2)));
dy(3)= 3.3*0.1*(y(2)/(0.53+y(2)))-0.0871*0.1*(y(3)/(0.94+y(3)));
dy(4)= .0871*0.1*(y(3)/(0.94+y(3)))- 0.6*0.1*(y(4)/(0.16+y(4)));
dy(5)= 0.6*0.1*(y(4)/(0.16+y(4))) - 25.4*0.1*(y(5)/(20+y(5)));
dy(6)= 25.4*0.1*(y(5)/(20+y(5)));
 
end

Output:

graphs representing the model of the pathway not involving p450

Igem regraph 1.jpg

Igem regraph 2.jpg


Regarding the figure legends in the graphs themselves, "data 1" - "data 6" represents the concentration of the metabolites αin,αout, β, γ, δ & ε

References:

[1] Krooshof, G. H., I. S. Ridder, et al. (1998). "Kinetic Analysis and X-ray Structure of Haloalkane Dehalogenase with a Modified Halide-Binding Site†." Biochemistry 37(43): 15013-15023.

[2] Janecki, D. J., K. G. Bemis, et al. (2007). "A multiple reaction monitoring method for absolute quantification of the human liver alcohol dehydrogenase ADH1C1 isoenzyme." Analytical Biochemistry 369(1): 18-26.

[3] Pandey, A. V. and C. E. Flück (2013). "NADPH P450 oxidoreductase: Structure, function, and pathology of diseases." Pharmacology & Therapeutics 138(2): 229-254.

[4] van der Ploeg, J., Shmidt, M. P., Landa, A. S., and Janssen, D. B. (1994). "Identification of Chloroacetaldehyde Dehydrogenase Involved in 1,2-Dichloroethane Degradation." Applied Environmental Microbiology (60(5): 1699-1605.

[5] van der Ploeg, J., van Hall, G., Janssen, D. B. (1991) "Characterization of the haloacid dehalogenase from Xanthobacter autotrophicus GJ10 and sequencing of the dhlB gene." Journal of Bacteriology 173(24):7925-33.

[6] Sinensky, Mi “Homeoviscous Adaption – A Homeostatic Process that Regulates the Viscosity of Membrane Lipids in Escheria coli” Proceedings from the National Academy of Science 71(2): 522-525.

[7] CyberCell Database


With thanks to:



Retrieved from "http://2013.igem.org/Team:SydneyUni_Australia/Modelling_Results"