- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-01-19 15:52:11+13:00
- Desc:
- formatting
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/674/rawfile/2c9e21d94212bf1a53df7045b2768a1f38de0ab1/parameter_finder/kinetic_parameters.m
% cAMP module
% Return kinetic parameters, constraints, and vector of volumes in each
% compartment (pL) (1 if gating variable, or in element corresponding to
% kappa)
% includes contributions from Gs and Gi proteins - assume they act on the
% same adenylyl cyclase form
% data for Gs is from saucerman2003
% data for Gi is made up from Shelley's brain
function [k_kinetic, N_cT, K_C, W] = kinetic_parameters(M, include_type2_reactions, dims, V)
% Set the kinetic rate constants
% knowns: K_m [=] fmol/L
% kcat [=] per_sec
num_cols = dims.num_cols;
num_rows = dims.num_rows;
K1_m = 1.03e3; % uM
k1cat = 0.2; % 1/s
K2_m = 3.15e+2; % uM
k2cat = 8.5; % 1/s
K3_m = 8.60e+2; % uM
k3cat = 1e-16; % 1/s
K4_m = 1.30; % uM
k4cat = 5; % 1/s
K5_m = 30; % uM
K6_m = 0.4; % uM
K7_m = 44; % uM
KGiAC_m = 10; % made up value % uM
% initialise arrays
vkap = zeros(4,1);
vkam = zeros(4,1);
vkbp = zeros(4,1);
vkbm = zeros(4,1);
vkm2 = zeros(4,1);
vkp2 = zeros(4,1);
vK_m = [K1_m,K2_m,K3_m,K4_m,K5_m,K6_m,K7_m,KGiAC_m];
vkcat = [k1cat,k2cat,k3cat,k4cat];
kap_mult = [0.93, 0.1, 1, 1,0.1]; % finding rates from literature?
fastKineticConstant = 1e6; % 1/s
% include the Gi reaction to remove it from the system in inhibited
% form
iks = 1:4;
for i=1:4
vkap(i) = kap_mult(i)*fastKineticConstant;
vkam(i) = vkap(i)*vK_m(iks(i)) - vkcat(i);
vkbp(i) = vkcat(i);
vkbm(i) = (vkap(i)*vkbp(i))/vkam(i);
end
% reactions 1,2,3 are COUPLED as they share the same substrates and
% products, so their Keq are the same. Choose Keq(1) as the truth to
% use.
if include_type2_reactions
iks = 5:8;
for i= 1:4
vkm2(i) = fastKineticConstant;
vkp2(i) = vkm2(i)/vK_m(iks(i));
end
end
% Calculate bond graph constants from kinetic parameters
% Note: units of kappa are fmol/s, units of K are fmol^-1
k_kinetic = [vkap(1) vkbp(1) ...
vkap(2) vkbp(2) ...
vkap(3) vkbp(3) ...
vkap(4) vkbp(4) ...
vkp2(1:4)' ...
vkam(1) vkbm(1) ...
vkam(2) vkbm(2) ...
vkam(3) vkbm(3) ...
vkam(4) vkbm(4) ...
vkm2(1:4)'...
]';
% CONSTRAINTS
N_cT = zeros(2,size(M,2));
if false
% show substrate ATP is in eqlm with product cAMP
N_cT(1,num_cols + 1) = 1;
N_cT(1,num_cols + 2) = -1;
end
% constraint for equilibrium between cAMP and five_AMP
N_cT(1,num_cols + 2) = 1;
N_cT(1,num_cols + 11) = -1;
% constraint for formation of five_AMP from cAMP and PDE rxn
G_0_cAMP = -48.116; % kJ/mol
R = 8.314;
T = 310;
K_cAMP = exp(G_0_cAMP/(R*T))*10^6;
N_cT(2,num_cols+3) = 1;
N_cT(2,num_cols+1) = -1;
K_C = [1 K_cAMP];
% volume vector
W = [ones(num_cols,1); V.V_myo*ones(num_rows,1)];
return
