 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = CO_activation_of_GC 
 %  Accession Number = 28 
 %  Transcriber = Sudhir Sivakumaran, NCBS 
 %  Developer = Sudhir Sivakumaran, NCBS 
 %  Species = Bovine 
 %  Tissue = Lungs 
 %  Cell Compartment = Cytosol 
 %  Notes = Carbon Monoxide is an activator of soluble Guanylyl Cyclase and has been implicated as a neuronal messenger [<a href= http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8608001 >Ingi T. et al. Neuron (1996) 16(4):835-42</a>].<br>CO binds to the heme group on sGC, similar to NO binding. Exogenous CO at similar conc. to endogenous levels were used to study the extent of activation of GC. Olfactory receptor neurons were used by Ingi et al., to investigate the relationship of CO to cGMP levels, as these cells have high levels of HO activity but no NOS activity. <br><a href= http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=7708686&dopt=Abstract >Kharitonov VG. et al. Proc Natl Acad Sci U S A. (1995) 92(7):2568-71</a> and <br><a href= http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10451364 >Kharitonov VG. et al. Biochemistry (1999) 38(33):10699-706</a> report the presence of a six coordinate and a five coordinate intermediate of carboxy GC, induced by CO. Considering that activation of sGC by CO is similar in almost all tissues, some rates have been taken from original published works cited as references in Kharitonov et al., and Ingi et al., the primary datasources, this model is based on. 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Wed Feb  2 15:21:54 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 600];
% Molecule names
molnames = {
'1 /kinetics/sGC/cGMP'
'2 /kinetics/sGC/sGC'
'3 /kinetics/sGC/Heme'
'4 /kinetics/sGC/CO'
'5 /kinetics/sGC/Hemeoxyg2'
'6 /kinetics/sGC/Hemeoxyg2/HOXY/HOXY_cplx'
'7 /kinetics/sGC/GC6-CO'
'8 /kinetics/sGC/GC5_CO'
'9 /kinetics/sGC/PDE'
'10 /kinetics/sGC/PDE/kenz/kenz_cplx'
'11 /kinetics/sGC/5prime_GMP'
'12 /kinetics/sGC/Ery_HbO2'
'13 /kinetics/sGC/COHb'
};

bufnames = {
'1 /kinetics/sGC/GTP'
'2 /kinetics/sGC/dissoCO'
};

sumtotnames = {
};

% Initial concs of 13 molecules
y0(1) = 0;
y0(2) = 3;
y0(3) = 11.3;
y0(4) = 0;
y0(5) = 2;
y0(6) = 0;
y0(7) = 0;
y0(8) = 0;
y0(9) = 5;
y0(10) = 0;
y0(11) = 0;
y0(12) = 5;
y0(13) = 0;
buff(1) = 1000;
buff(2) = 0.1142;
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
plot(t,y(:,1));
plot(t,y(:,4));
plot(t,y(:,8));
plot(t,y(:,7));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 + 54.54 * y(8) * buff(1) / ( 0.5 + buff(1) ) - 9.675 * y(1) * y(9) + 15.48 * y(10)
 - 0.12 * y(2) * y(4) + 28 * y(7)
 - 0.46789 * y(3) * y(5) + 1.4224 * y(6)
 + 0.3556 * y(6) - 0.12 * y(2) * y(4) + 28 * y(7)
 - 0.46789 * y(3) * y(5) + 1.4224 * y(6) + 0.3556 * y(6)
 + 0.46789 * y(3) * y(5) - 1.4224 * y(6) - 0.3556 * y(6)
 + 0.12 * y(2) * y(4) - 28 * y(7) - 0.95 * y(7)
 + 0.95 * y(7) - 1000 * y(8)
 - 9.675 * y(1) * y(9) + 15.48 * y(10) + 3.87 * y(10)
 + 9.675 * y(1) * y(9) - 15.48 * y(10) - 3.87 * y(10)
 + 3.87 * y(10)
 - 0.17 * buff(2) * y(12) + 0.0078 * y(13)
 + 0.17 * buff(2) * y(12) - 0.0078 * y(13)
];

% end of model
