- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-07-15 17:29:04+12:00
- Desc:
- Making various adjustments for thermodynamic consistency which are not part of original kinetic model
- Permanent Source URI:
- https://models.cellml.org/workspace/6ba/rawfile/209c5d96543a21996fdc1dd0038da700a2bbdcd6/MATLAB/kinetic_parameters.m
% B1AR module
function [k_kinetic, N_cT] = 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
% oncentration of BARK = 0.6uM (crude approx from litsearch, for GRK)
bigNum = 1e6;
fastKineticConstant = bigNum;
smallReverse = fastKineticConstant/(bigNum^2);
u_to_f = 1e9;
cBARK = 0.6*u_to_f; %fM
cPKACI = 0.0587898478276673*u_to_f; %fM
% creation of LRG - Type 2 reactions
% [K_C, K_L, K_R, K_L]
vK_mSig = [33*u_to_f, 0.285*u_to_f, 1/(0.062*u_to_f), 1/(0.285*u_to_f)]; % fM
% for detailed balance, let Km3 = 1/(Km1*Km2*Km4). Source paper values are
% thermo inconsistent
vK_mSig(2) = 1/(vK_mSig(1)*vK_mSig(3)*vK_mSig(4));
vkSigm = zeros(1,4);
vkSigp = zeros(1,4);
for i= 1:4
vkSigm(i) = fastKineticConstant; %1/s for Sig1, Sig2. 1/fM.s for Sig 3, Sig4
vkSigp(i) = vkSigm(i)/vK_mSig(i); %1/s
end
% detailed balance for last reverse ksigm(4)
vkSigm(4) = vkSigp(1)*vkSigp(2)*vkSigp(3)*vkSigp(4)/vkSigm(1)*vkSigm(2)*vkSigm(3);
% old_kSigm4 = vkSigp(1)*vkSigm(2)*vkSigm(3)*vkSigp(4)/vkSigm(1)*vkSigp(2)*vkSigp(3);
kB11p = 1.1e-3 / cBARK; % 1/fM.s
kB11m = 2.2e-3; % 1/s
kB12p = fastKineticConstant;%1/s
kB12m = smallReverse; % 1/fM.s
kB21p = kB11p; % 1/fM.s
kB21m = kB11m; % 1/s
kB22p = fastKineticConstant;%1/s
kB22m = smallReverse; % 1/fM.s
kP1p = 2.2e-3/ cPKACI; % 1/fM.s (kp_kam)
kP1m = smallReverse; % 1/s
kP2p = fastKineticConstant; % 1/s
kP2m = 3.6e-3/u_to_f; % 1/fM.s (kp_kap)
kAct1p = 16; % 1/s
kAct1m = smallReverse; % 1/fM.s
kAct2m = 16; % 1/s
kAct2p = 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
% detailed balance for kP2p
kP2p = kP2m*kP1m/kP1p;
k_kinetic = [
kB11p, kB12p, kB21p, kB22p, kP1p, kP2p, kAct1p, kAct2p, kHydp, kReassocp, vkSigp...
kB11m, kB12m, kB21m, kB22m, kP1m, kP2m, kAct1m, kAct2m, kHydm, kReassocm, vkSigm
]';
% CONSTRAINTS
N_cT = zeros(2,size(M,2));
% substrate LR/LRG is in eqlm with product B1ARd
N_cT(1,num_cols + 1) = 1;
N_cT(1,num_cols + 2) = -1;
N_cT(2,num_cols + 5) = 1;
N_cT(2,num_cols + 2) = -1;
% substrate B1ARp is in eqlm with product B1ARtot
N_cT(3,num_cols + 7) = 1;
N_cT(3,num_cols + 8) = -1;
return
