 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = sGC_Stone_Marletta 
 %  Accession Number = 15 
 %  Transcriber = Sudhir Sivakumaran, NCBS 
 %  Developer = Stone and Marletta, 1996. 
 %  Species = Bovine 
 %  Tissue = Lungs 
 %  Cell Compartment = Cytosol 
 %  Notes =  This features the two step binding of NO to soluble Guanylyl Cyclase as proposed by <a href= http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8573563 >Stone JR, Marletta MA. Biochemistry (1996) 35(4):1093-9</a>. There is a fast step binding scheme and a slow step binding scheme. The difference lies in the binding of a NO to a non-heme site on sGC, which may not necessarily be the same site of binding during the initial binding. The rates have been directly used from their models 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Tue Feb  1 11:55:13 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 10];
% Molecule names
molnames = {
'1 /kinetics/group/GTP'
'2 /kinetics/group/NO.sGCfast'
'3 /kinetics/group/NO.SGC_6coord'
'4 /kinetics/group/sGCfast'
'5 /kinetics/group/NO.sGC_5coord'
'6 /kinetics/group/sGCtot/kenz/kenz_cplx'
'7 /kinetics/group/NO.sGC5accord'
'8 /kinetics/group/nonhemebind_int'
'9 /kinetics/group/NO.sGC6coord'
'10 /kinetics/group/NO.sGCslow'
'11 /kinetics/group/sGCslow'
'12 /kinetics/group/cGMP'
'13 /kinetics/group/NO'
};

bufnames = {
};

sumtotnames = {
'1 /kinetics/group/sGCtot'
};

% Initial concs of 13 molecules
y0(1) = 10;
y0(2) = 0;
y0(3) = 0;
y0(4) = 3;
y0(5) = 0;
y0(6) = 0;
y0(7) = 0;
y0(8) = 0;
y0(9) = 0;
y0(10) = 0;
y0(11) = 3;
y0(12) = 0;
y0(13) = 0;
% Sumtotal eqn for /kinetics/group/sGCtot: sumtot(1) =  (y(5) + y(7) )
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
plot(t, (y(:,5) + y(:,7) ));
plot(t, (y(:,5) + y(:,7) ));
plot(t,y(:,12));
plot(t,y(:,13));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 - 6.3125 * y(1) *  (y(5) + y(7) ) + 101 * y(6)
 + 700 * y(4) * y(13) - 800 * y(2) - 850 * y(2)
 + 850 * y(2) - 20 * y(3) + 0.2 * y(5)
 - 700 * y(4) * y(13) + 800 * y(2)
 + 20 * y(3) - 0.2 * y(5)
 + 6.3125 * y(1) *  (y(5) + y(7) ) - 101 * y(6) - 25.25 * y(6)
 + 1.6 * y(8) - 0.02 * y(7)
 + 5 * y(9) * y(13) - 25 * y(8) - 1.6 * y(8) + 0.02 * y(7)
 + 850 * y(10) - 5 * y(9) * y(13) + 25 * y(8)
 + 700 * y(11) * y(13) - 800 * y(10) - 850 * y(10)
 - 700 * y(11) * y(13) + 800 * y(10)
 + 25.25 * y(6)
 - 700 * y(4) * y(13) + 800 * y(2) - 700 * y(11) * y(13) + 800 * y(10) - 5 * y(9) * y(13) + 25 * y(8)
];

% end of model
