- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-09-07 10:58:21+12:00
- Desc:
- Adding MATLAB files
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/700/rawfile/2e8de21e3aa250ec6b5a6c083a57eb04946dbfce/MATLAB2/BG_LRGbinding/kinetic_parameters.m
% LRGbinding module - for iancu Muscarinic 2 as GPCR
% Return kinetic parameters, constraints, and vector of volumes in each
% compartment (pL) (1 if gating variable, or in element corresponding to
% kappa)
function [k_kinetic, N_cT, K_C, W] = kinetic_parameters(M, include_type2_reactions, dims, V)
% 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
num_cols = dims.num_cols;
num_rows = dims.num_rows;
% concentration of BARK = 0.6uM (crude approx from litsearch, for GRK)
bigNum = 1e6;
fastKineticConstant = bigNum;
Ksig1 = 30; % uM Kc
Ksig2 = 0.16; % uM Kh
Ksig4 = 11; % uM Kl
ksig1p = fastKineticConstant;
ksig1m = ksig1p*Ksig1;
ksig2p = fastKineticConstant;
ksig2m = ksig2p*Ksig2;
ksig4p = fastKineticConstant;
ksig4m = ksig4p*Ksig4;
ksig3p = fastKineticConstant;
% find ksig4m using detailed balance
ksig3m = ksig1m*ksig2m*ksig3p*ksig4p/(ksig1p*ksig2p*ksig4m);
k_kinetic = [
ksig1p, ksig2p, ksig3p, ksig4p,...
ksig1m, ksig2m, ksig3m, ksig4m
]';
% CONSTRAINTS
N_cT = [];
if false
N_cT = zeros(1,size(M,2));
% substrate B1ARp is in eqlm with product B1ARtot
N_cT(1,num_cols + 1) = 1;
N_cT(1,num_cols + 2) = -1;
end
K_C = ones(1,size(N_cT,1));
% volume vector
W = [ones(num_cols,1); V.V_myo*ones(num_rows,1)];
return
