- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-07-29 16:45:32+12:00
- Desc:
- Adding stoich matrices
- Permanent Source URI:
- https://models.cellml.org/workspace/6d1/rawfile/9b3da81dfeebecdabd68d179e63fef79d8a8a395/MATLAB/kinetic_parameters.m
% PKA module
function [k_kinetic, N_cT, K_C] = kinetic_parameters(M, include_type2_reactions, num_cols)
% Set the kinetic rate constants.
% all reactions are reversible. no closed loops.
% cAMP binds to R subunit one at a time
% CONVERT TO fM
bigNum = 1e3;
fastKineticConstant = bigNum;
smallReverse = fastKineticConstant/(bigNum^2);
u_to_f = 1e9;
% [Ka, Kb, Kd, Kpki]
Km = u_to_f*[9.14, 1.64, 4.375, 2e-4];
N = length(Km);
kim = zeros(1,N);
kip = zeros(1,N);
for i=1:4
kim(i) = fastKineticConstant; % 1/s
kip(i) = kim(i) / (Km(i)*u_to_f);
end
% repeat exct reactions for type I and type II holoenzymes
% No closed loop, so no detailed balance
k_kinetic = [
kip, kip, kim, kim
]';
% CONSTRAINTS
N_cT = zeros(1,size(M,2));
% % Reaction i: [PKA:PKI] = [C][PKI] at SS big error. Not isolated reaction
% repeat for type 1 and 2
if false
N_cT(1,num_cols + 2) = 1;
N_cT(1,num_cols + 6) = 1;
N_cT(1,num_cols + 8) = -1;
end
% Gibbs free energy of L + R binding **MED_ERROR**
if false
N_cT(3,num_cols + 4) = 1; % ARC
N_cT(3,num_cols + 1) = -1; % cAMP
N_cT(3,num_cols + 3) = -1; % RC
G_0_bind = -45.1872; % kJ/mol
R = 8.314;
T = 310;
K_bind = exp(G_0_bind/(R*T))*10^6;
end
K_C = ones(1,size(N_cT,1));
return
