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Team:Bielefeld-CeBiTec/Results/Modelling/sourcecode
From 2014.igem.org
Source Code
main
function dy_dt = main_new(t, y, kcat, conc, km)
dy_dt = zeros(6,1);
%Michaelis-Menten kinetic
v1 = (kcat(1) * conc(1) * y(1)) / (km(1) + y(1)); %alsS
v2 = (kcat(2) * conc(2) * y(2)) / (km(2) + y(2)); %ilvC
v3 = (kcat(3) * conc(3) * y(3)) / (km(3) + y(3)); %ilvD
v4 = (kcat(4) * conc(4) * y(4)) / (km(4) + y(4)); %kivD
v5 = (kcat(5) * conc(5) * y(5)) / (km(5) + y(5)); %adhA
v6 = (kcat(6) * conc(6) * y(6)) / (km(6) + y(6)); %pyruvatase
v7 = (kcat(6) * conc(6) * y(6)) / (km(6) + y(6)); %pyruvatase
%differentiation systems
dy_dt(1) = -v1; %pyruvate
dy_dt(2) = v1 - 2*v2; %2-acetolactate
dy_dt(3) = v2 - v3; %2,3-dihydroxisovalerate
dy_dt(4) = v3 - v4; %2-ketoisovalerate
dy_dt(5) = v4 - v5; %isobutyraldehyde
dy_dt(6) = v5; %isobutanol
dy_dt(7) = v6 - v7; %pyruvate derivatives
solve
%%%%%%%%%% INPUT %%%%%%%%%%%%%
%timespan of the calculation [h]
timespan=[0,20];
%starting conentrations [mM]:
sc = [10 0.0 0.0 0.0 0.06 0.0, 0.0];
%kcat values [molecules per second]:
kcat = [8.9 3.6 185 10 10 150];
%km values [mM]:
km = [13.6 0.25 1.5 5.02 9.1 0.1];
%enzyme concentrations
conc = [1 0.9 0.8 0.7 0.6 0.5];
%improved enzyme concentrations
%conc = [1 0.9 0.8 3 4 0.5];
%metabolites:
%1= pyruvate
%2= 2-acetolactate
%3= 2,3-dihydroxyisovalerate
%4= 2-ketoisovalerate
%5= isobutyraldehyde
%6= isobutanol
%7= pyruvate derivatives
%%%%%%%%%%%%%% CALCULATION %%%%%%%%%%%%%%%
[T,Y] = ode45(@main_kcat, timespan, sc, [], kcat, conc, km);
%%%%%%%%%%%%%%% PLOTTING %%%%%%%%%%%%%%%%%%
plot(T,Y)
xlabel('time [h]')
ylabel('conzentraion [mM]')
legend('pyruvate','2-acetolactate','2,3-dihydroxyisovalerate','2-ketoisovalerate','isobutyraldehyde','isobutanol','pyruvate-derivatives')
