Team:SydneyUni Australia/Modelling Results

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Revision as of 04:14, 28 September 2013

Running the Model

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 = nop450(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

Raw MATLAB code for the pathway not involving p450

function dy = p450(t,y)
 
dy=zeros(5,1);

dy(1)= -6*(10^12)*0.0463067*(y(1)-y(2));
dy(2)= 6*(10^12)*0.0463067*(y(1)-y(2))-89.8*0.1*(y(2)/(7.2+y(2)));
dy(3)= 89.8*0.1*(y(2)/(7.2+y(2)))-0.6*0.1*(y(3)/(0.16+y(3)));
dy(4)= 0.6*0.1*(y(3)/(0.16+y(3))) - 25.4*0.1*(y(4)/(20+y(4)));
dy(5)= 25.4*0.1*(y(4)/(20+y(4)));

end

Raw MATLAB code for the pathway involving p450

Output:

The output of the raw MATLAB code for the pathway not involving p450 which depict how the concentrations of each metabolite change over time. The 't=0 min' time point is the point where the engineered cells are instantaneously introduced (and evenly homogenised) to a solution of DCA with an initial concentratioN OF 0.1Mm.

Regarding the figure legends with in the graphs themselves data 1, data 2, data 3, data 4, data 5 * data 6, represents the concentration of the metabolites αin, αout, β, γ, δ & ε respectively. The bottom graph is a rescaled version of the top graph so as to achieve a higher resolution the dynamics of the metabolites.

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