- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-07-26 08:45:13+12:00
- Desc:
- Adding MATLAB script to call function to find kinetic parameters. One for each module.
- Permanent Source URI:
- https://models.cellml.org/workspace/6f9/rawfile/388451396a719f4944f3bdbc3b121ce2855589df/MATLAB/kinetic_parameters.m
% GPCR module. From Dupont Sneyd, simple GPCR model.
function [k_kinetic, N_cT, K_C] = kinetic_parameters(M, include_type2_reactions, num_cols)
% Set the kinetic rate constants.
% original model had reactions that omitted enzymes as substrates e.g. BARK
% convert unit from 1/s to 1/uM.s by dividing by conc of enzyme
% all reactions were irreversible, made reversible by letting kr ~= 0
% CONVERT TO fM
bigNum = 1e3;
fastKineticConstant = bigNum;
smallReverse = fastKineticConstant/(bigNum^2);
u_to_f = 1e9;
c_G = 3.83*u_to_f; % fM
kbindm = fastKineticConstant; % 1/s
kbindp = kbindm / (0.285*u_to_f); % 1/fM.s
kActp = 16/c_G; % 1/fM.s
kActm = smallReverse; % 1/fM.s
kHydp = 0.8; % 1/s
kHydm = smallReverse; % 1/s
kReassocp = 1.21e3/u_to_f; % 1/fM.s
kReassocm = kReassocp/bigNum; % 1/s
% No closed loop, so no detailed balance
k_kinetic = [
kbindp, kActp, kHydp, kReassocp...
kbindm, kActm, kHydm, kReassocm
]';
% CONSTRAINTS
N_cT = zeros(1,size(M,2));
% Reaction BIND: equal portions of L + derivatives (L == LR) **SMALL_ERROR**
N_cT(1,num_cols + 1) = -1;
% N_cT(1,num_cols + 2) = -1; % this must be present, like Mg reaction in SERCA
N_cT(1,num_cols + 4) = 1;
if false
% Reaction BIND: equal portions of R == LR
% error 10(2): this reaction is already in use?
N_cT(2,num_cols + 2) = -1;
N_cT(2,num_cols + 4) = 1;
end
% Reaction HYD: substrate aGTP is in eqlm with product aGDP
% error 10(2): a-G is present in other reactions
if false
N_cT(2,num_cols + 5) = 1;
N_cT(2,num_cols + 7) = -1;
end
% Reaction ACT:
% a-GTP == betaGamma **SMALL_ERROR**
if false
N_cT(2,num_cols + 5) = 1;
N_cT(2,num_cols + 6) = -1;
end
% or LR.G = aGTP.betaGamma
if false
N_cT(2,num_cols + 3) = 1;
N_cT(2,num_cols + 4) = 1;
N_cT(2,num_cols + 5) = -1;
N_cT(2,num_cols + 6) = -1;
end
% [a-GTP] + [a-GDP] = [beta.gamma] **SMALL_ERROR**
if true % could be acceptable !!!!!!!!!!!!!!!!!!!!!!!!!!
N_cT(2,num_cols + 6) = 1; % beta_gamma
N_cT(2,num_cols + 5) = -1; % a_GTP
N_cT(2,num_cols + 7) = -1; % a_GDP
end
% Gibbs free energy of L + R binding **MED_ERROR**
if true
N_cT(3,num_cols + 4) = 1; % RL
N_cT(3,num_cols + 1) = -1; % L
N_cT(3,num_cols + 2) = -1; % R
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 = [1 1 K_bind];
return
