- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-08-04 16:31:51+12:00
- Desc:
- Finding BG parameters from kinetic, version 1 (incomplete)
- Permanent Source URI:
- https://models.cellml.org/workspace/6d6/rawfile/21e434d1a778b748dbd26e9e8ad894d2fe47c825/MATLAB/kinetic_parameters.m
% PLB module
% all rxn directions align with kinetic Saucerman model (Km unchanged,
% aside from dimensional scaling)
function [k_kinetic, N_cT, K_C] = kinetic_parameters(M, include_all_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;
cPP2A = 0.224; % uM (Bhalla Iyengar a on PMR) but not sure what cell type this is
% reaction IDs
% PLBph1, PLBph2,
% PLBd1 (reverse), PLBd2 (reverse)
% PKAi1 (reverse), PKAi2 (reverse)
% PP2ai1, PP2ai2
% inh
k_pka_plb = 54; %: per_sec 54
Km_pka_plb = 21; %: uM 21
k_pp1_plb = 8.5; % per_sec 8.5
Km_pp1_plb = 7; % uM 7
k_pka_i1 = 60; %: per_sec 60
Km_pka_i1 = 1; %: uM 1
Vmax_pp2a_i1 = 14; %: uM_per_sec 14
Km_pp2a_i1 = 1; %: uM 1
Ki_inhib1 = 1e-3; %: uM 1e-3
vKm = u_to_f*[Km_pka_plb, Km_pp1_plb, Km_pka_i1, Km_pp2a_i1];
vkcat = [k_pka_plb, ...
k_pp1_plb, ...
k_pka_i1, ...
Vmax_pp2a_i1/cPP2A];
N = length(vKm);
k1m = zeros(1,N);
k1p = zeros(1,N);
k2m = zeros(1,N);
k2p = zeros(1,N);
% iforward = [1,4];
for i=1:N % forward rxns
% if find(i==iforward)
k2p(i) = vkcat(i);
k1m(i) = fastKineticConstant; % 1/s
k1p(i) = (k1m(i) + k2p(i)) / (vKm(i)*u_to_f);
k2m(i) = k1p(i)*k2p(i)/k1m(i); % detailed balance
% else
% k1m(i) = vkcat(i);
% k2p(i) = fastKineticConstant; % 1/s
% k2m(i) = (k2p(i) + k1m(i)) / (vKm(i)*u_to_f);
% k1p(i) = k2m(i)*k1m(i)/k2p(i); % detailed balance
% end
end
km_inh = fastKineticConstant;
kp_inh = km_inh / (Ki_inhib1*u_to_f); % type 2
if include_all_reactions
k_kinetic = [
k1p, k2p, kp_inh, k1m, k2m, km_inh
]';
else
irr = [1 2 3];
k_kinetic = [
k1p(irr), k2p(irr), k1m(irr), k2m(irr)
]';
end
% CONSTRAINTS
N_cT = [];
% 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
