 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = HomoArginine 
 %  Accession Number = 73 
 %  Transcriber = Sharat J. Vayttaden and Prasoon Agarwal, NCBS 
 %  Developer = Abu-Soud HM, Wang J, Rousseau DL, and Stuehr DJ 
 %  Species = human 
 %  Tissue = Kidney cell expressing the rat brain nNOS 
 %  Cell Compartment = Cytosol 
 %  Notes = This model is taken from the <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=10493814&query_hl=10&itool=pubmed_docsum>Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51</a> This model shows kinetic binding of HomoArginine to neuronal nitric oxide synthase.<br> Model shows the substrate (Homorginine) binding to nNOS in a two-step reversible fashion. First there is rapid binding equilibrium between Im-nNOS and Homoarginine to form an intermediate that contains bound imidazole and homoarginine. This is followed by a slower conformational change in the Im-enzyme-substrate complex that is associated with release of bound imidazole and generation of a modified enzyme-substrate complex which is detected due to spectral change. Rates approximated based on data in Table 2. The rates for first reaction are not exact since only Kd known and appropriate graphs do not exist for matching the kinetic profile.
 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Thu Aug  3 21:26:09 2006
% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
global t;
global y;

% Define Tables here
tspan=[0, 0.1];
% Molecule names
molnames = {
'1 /kinetics/Im-nNOS'
'2 /kinetics/Imidazole'
'3 /kinetics/Homoarginine'
'4 /kinetics/Im-nNOS-Homoarginine'
'5 /kinetics/nNOS-Homoarginine'
};

bufnames = {
};

sumtotnames = {
};

% Initial concs of 5 molecules
y0(1) = 1;
y0(2) = 0;
y0(3) = 6000;
y0(4) = 0;
y0(5) = 0;

% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
do_plots;

function do_plots()
global t;
global y;
%plot(t,y(:,1));
%plot in matlab
temp = [t, y(:,5)];
save('/home/prasoon/models/nNOS/Files_to_upload/homo_Arg_new/plots/nNOS-Homoarg_m.dat','temp','-ASCII');
%plot(t,y(:,4));
%plot(t,y(:,3));
%plot(t,y(:,2));
plot(t,y(:,5));

% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 - 25 * y(3) * y(1) + 250000 * y(4)
 + 42 * y(4) - 0.2 * y(5) * y(2)
 - 25 * y(3) * y(1) + 250000 * y(4)
 + 25 * y(3) * y(1) - 250000 * y(4) - 42 * y(4) + 0.2 * y(5) * y(2)
 + 42 * y(4) - 0.2 * y(5) * y(2)
];

% end of model
