 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = PKC_turnover 
 %  Accession Number = 26 
 %  Transcriber = Upinder S. Bhalla, NCBS 
 %  Developer = Upinder S. Bhalla, NCBS 
 %  Species = Generic mammalian 
 %  Tissue = Brain - Neuronal 
 %  Cell Compartment = Cell membrane +Cytosol 
 %  Notes =  This model is a superset of the PKC model presented in <a href= http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9888852&dopt=Abstract >Bhalla US and Iyengar R. Science (1999) 283(5400):381-7</a>. The current version includes PKC turnover. This version includes the stimulating pools Ca, AA and DAG as well as the PKC activity within the synaptic signaling pathway since it is meant to be a self-contained pathway model rather than part of a network. 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Wed Feb  2 14:47:46 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 4000];
% Molecule names
molnames = {
'1 /kinetics/PKC/PKC-Ca'
'2 /kinetics/PKC/PKC-DAG-AA*'
'3 /kinetics/PKC/PKC-Ca-AA*'
'4 /kinetics/PKC/PKC-Ca-memb*'
'5 /kinetics/PKC/PKC-DAG-memb*'
'6 /kinetics/PKC/PKC-basal*'
'7 /kinetics/PKC/PKC-AA*'
'8 /kinetics/PKC/PKC-Ca-DAG'
'9 /kinetics/PKC/PKC-DAG'
'10 /kinetics/PKC/PKC-DAG-AA'
'11 /kinetics/PKC/PKC-cytosolic'
'12 /kinetics/PKC/PKC-active/PKC-enzyme-activity/PKC-enzyme-activity_cplx'
'13 /kinetics/PKC/Ca'
'14 /kinetics/PKC/AA'
'15 /kinetics/PKC/DAG'
'16 /kinetics/PKC/PKC-substrate'
'17 /kinetics/PKC/PKC-substrate*'
};

bufnames = {
'1 /kinetics/PKC/degraded-PKC'
'2 /kinetics/PKC/PKC-RNA'
};

sumtotnames = {
'1 /kinetics/PKC/PKC-active'
};

% Initial concs of 17 molecules
y0(1) = 3.72083e-17;
y0(2) = 0;
y0(3) = 0;
y0(4) = 0;
y0(5) = 0;
y0(6) = 0;
y0(7) = 0;
y0(8) = 8.46317e-23;
y0(9) = 0;
y0(10) = 2.51883e-19;
y0(11) = 1;
y0(12) = 0;
y0(13) = 0.08;
y0(14) = 5.5;
y0(15) = 11.66;
y0(16) = 0;
y0(17) = 0;
buff(1) = 0;
buff(2) = 1;
% Sumtotal eqn for /kinetics/PKC/PKC-active: sumtot(1) =  (y(2) + y(4) + y(3) + y(5) + y(6) + y(7) )
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
plot(t, (y(:,2) + y(:,4) + y(:,3) + y(:,5) + y(:,6) + y(:,7) ));
plot(t, (y(:,2) + y(:,4) + y(:,3) + y(:,5) + y(:,6) + y(:,7) ));
plot(t, (y(:,2) + y(:,4) + y(:,3) + y(:,5) + y(:,6) + y(:,7) ));
plot(t, (y(:,2) + y(:,4) + y(:,3) + y(:,5) + y(:,6) + y(:,7) ));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 + 0.6 * y(11) * y(13) - 0.5 * y(1) - 0.0079998 * y(15) * y(1) + 8.6348 * y(8) - 1.2705 * y(1) + 3.5026 * y(4) - 0.0012 * y(1) * y(14) + 0.1 * y(3)
 + 2 * y(10) - 0.2 * y(2) - 4.63e-05 * y(2)
 + 0.0012 * y(1) * y(14) - 0.1 * y(3) - 4.63e-05 * y(3)
 + 1.2705 * y(1) - 3.5026 * y(4) - 4.63e-05 * y(4)
 + 1 * y(8) - 0.1 * y(5) - 4.63e-05 * y(5)
 + 1 * y(11) - 50 * y(6) - 4.63e-05 * y(6)
 + 0.00012 * y(14) * y(11) - 0.1 * y(7) - 4.63e-05 * y(7)
 + 0.0079998 * y(15) * y(1) - 8.6348 * y(8) - 1 * y(8) + 0.1 * y(5)
 + 0.0006 * y(11) * y(15) - 0.1 * y(9) - 0.018 * y(9) * y(14) + 2 * y(10)
 + 0.018 * y(9) * y(14) - 2 * y(10) - 2 * y(10) + 0.2 * y(2)
 - 0.6 * y(11) * y(13) + 0.5 * y(1) - 1 * y(11) + 50 * y(6) - 0.00012 * y(14) * y(11) + 0.1 * y(7) - 0.0006 * y(11) * y(15) + 0.1 * y(9) + 4.1666e-06 * buff(2)
 + 6 * y(16) *  (y(2) + y(4) + y(3) + y(5) + y(6) + y(7) ) - 16 * y(12) - 4 * y(12)
 - 0.6 * y(11) * y(13) + 0.5 * y(1)
 - 0.0012 * y(1) * y(14) + 0.1 * y(3) - 0.00012 * y(14) * y(11) + 0.1 * y(7) - 0.018 * y(9) * y(14) + 2 * y(10)
 - 0.0079998 * y(15) * y(1) + 8.6348 * y(8) - 0.0006 * y(11) * y(15) + 0.1 * y(9)
 - 6 * y(16) *  (y(2) + y(4) + y(3) + y(5) + y(6) + y(7) ) + 16 * y(12)
 + 4 * y(12)
];

% end of model
