Location: BG_PLB @ 863bf28f7e00 / MATLAB / kinetic_parameters.m

Author:

Shelley Fong <s.fong@auckland.ac.nz>

Date:

2021-09-07 13:41:40+12:00

Desc:

adding Pub: out

Permanent Source URI:

https://models.cellml.org/workspace/6d1/rawfile/863bf28f7e00066dbc721ea41dc374bdf1f4ce3c/MATLAB/kinetic_parameters.m

% PLB module
% all rxn directions align with kinetic Saucerman model (Km unchanged,
% aside from dimensional scaling)

% 5 AUG PLB separated into PLB and Inhib1 submodules
% (parameter error was large with both submodules together)
% Use [Ip_S1] where [Ip] = [Ip_s1] + [Ip_S2]

% 25 Aug
% 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_all_reactions, dims, V)
    % Set the kinetic rate constants.
    % all reactions are reversible. no closed loops.
    % cAMP binds to R subunit one at a time
    
    num_cols = dims.num_cols;
    num_rows = dims.num_rows;

    % CONVERT TO fM 
    bigNum = 1e3;
    fastKineticConstant = bigNum;
    smallReverse = fastKineticConstant/(bigNum^2);
    
    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)
%         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 = [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);

    for i=1:N 
        k2p(i) = vkcat(i);
        k1m(i) = fastKineticConstant; % 1/s
        k1p(i) = (k1m(i) + k2p(i)) / vKm(i);
        k2m(i) = k1p(i)*k2p(i)/k1m(i); % detailed balance
    end
    km_inh = fastKineticConstant;
    kp_inh = km_inh / Ki_inhib1; % 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));
    
    % volume vector
    W = [ones(num_cols,1); V.V_myo*ones(num_rows,1)];

    return