- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-04-26 11:12:51+12:00
- Desc:
- Adding matlab curve and gate fitting files from Pan
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/827/rawfile/d7007fe58bc5d140b6d6299ee7d059f01b15c7e7/matlab_parameter_fitting/NaK_fitting_vcyc.m
function v_cyc_nak = NaK_fitting_vcyc(params,struct_input)
% Calculate cycling velocity of the updated model from parameters
F = 96485; % unit C/mol
R = 8.314; % unit J/mol/K
T = struct_input.T; % unit K
G_MgATP_0 = 11900;
T_body = 310;
K_MgATP_hyd = exp(-G_MgATP_0/R/T_body)*10^6;
Vm = struct_input.V; % Unit volts
% Concentrations in mM
MgATP = struct_input.MgATP;
Pi_total = struct_input.Pi_total;
Nai = struct_input.Nai;
Nae = struct_input.Nae;
Ke = struct_input.Ke;
Ki = struct_input.Ki;
H_conc = struct_input.H_conc;
MgADP = struct_input.MgADP;
K0d_nak_nai= params(1); %K0d_nak_nai (mM)
K0d_nak_nae= params(2); %K0d_nak_nae (mM)
Kd_nak_nai2= params(3); %Kd_nak_nai2 (mM)
Kd_nak_nae2= params(4); %Kd_nak_nae2 (mM)
Kd_nak_ke= params(5); %Kd_nak_ke (mM)
Kd_nak_MgATP= params(6); %K_nak_mgatp (mM)
rate_f_nak_1= params(7); %rate_f_1 (s-1)
rate_f_nak_2= params(8); %rate_f_2 (s-1)
rate_f_nak_3= params(9); %rate_f_3 (s-1)
rate_f_nak_4= params(10); %rate_f_4 (s-1)
rate_r_nak_1= rate_f_nak_1/6.3; %rate_r_1 (s-1 mM-1)
rate_r_nak_2= params(11); %rate_r_2 (s-1 mM-1)
rate_r_nak_3= params(12); %rate_r_3 (s-1)
rate_r_nak_4= params(13); %rate_r_4 (s-1)
Kd_nak_ki= sqrt(rate_r_nak_1*rate_r_nak_2*rate_r_nak_3*rate_r_nak_4/...
rate_f_nak_1/rate_f_nak_2/rate_f_nak_3/rate_f_nak_4*...
K0d_nak_nai*Kd_nak_nai2^2*Kd_nak_ke^2*Kd_nak_MgATP*K_MgATP_hyd/...
K0d_nak_nae/Kd_nak_nae2^2); %Kd_nak_ki (mM)
factor_nak_del= params(14); %factor_nak_del
pKd_nak_hpi = 6.77d0; %pKd_nak_hpi
Kd_nak_kpi = 292.0d0; %Kd_nak_kpi (mM)
Kd_nak_napi = 224.0d0; %Kd_nak_napi (mM)
Kd_nak_nae1 = K0d_nak_nae*exp((1.0d0 ...
+factor_nak_del)*F*Vm/(R*T));
Kd_nak_nai1 = K0d_nak_nai*exp(factor_nak_del*...
F*Vm/(R*T));
Nae_bound1 = Nae/Kd_nak_nae1;
Nai_bound1 = Nai/Kd_nak_nai1;
Nae_bound2 = Nae/Kd_nak_nae2;
Nai_bound2 = Nai/Kd_nak_nai2;
Ke_bound = Ke/Kd_nak_ke;
Ki_bound = Ki/Kd_nak_ki;
MgATP_bound = MgATP/Kd_nak_MgATP;
Pi = Pi_total/(1.0d0+(Ki/Kd_nak_kpi)+ ...
(H_conc/(10^(3.0-pKd_nak_hpi)))+(Nai/...
Kd_nak_napi));
%Forward rate constants
alpha_f_nak_1 = rate_f_nak_1*Nai_bound1*...
(Nai_bound2^2.0d0)/(Nai_bound1*Nai_bound2^2 + ...
((1.0d0+Nai_bound2)^2.0d0)+...
((1.0d0+Ki_bound)^2.0d0)-1.0d0);
alpha_f_nak_2 = rate_f_nak_2;
alpha_f_nak_3 = rate_f_nak_3*(Ke_bound^2.0d0)/...
(Nae_bound1*Nae_bound2^2+...
((1.0d0+Nae_bound2)^2.0d0)+...
((1.0d0+Ke_bound)^2.0d0)-1.0d0);
alpha_f_nak_4 = rate_f_nak_4*MgATP_bound/...
(1.0d0+MgATP_bound);
%Reverse rate constants
alpha_r_nak_1 = rate_r_nak_1*MgADP;
alpha_r_nak_2 = rate_r_nak_2*Nae_bound1*...
((Nae_bound2)^2.0d0)/...
(Nae_bound1*Nae_bound2^2 +...
(1.0d0+Nae_bound2)^2.0d0+...
((1.0d0+Ke_bound)^2.0d0)-1.0d0);
alpha_r_nak_3 = rate_r_nak_3*Pi*H_conc/...
(1.0d0+MgATP_bound);
alpha_r_nak_4 = rate_r_nak_4*(Ki_bound^2.0d0)/...
(Nai_bound1*Nai_bound2^2+...
((1.0d0+Nai_bound2)^2.0d0)+...
((1.0d0+Ki_bound)^2.0d0)-1.0d0);
sig_nak = alpha_r_nak_1*alpha_r_nak_2*alpha_r_nak_3 + ...
alpha_r_nak_1*alpha_r_nak_2*alpha_f_nak_4 + ...
alpha_r_nak_1*alpha_f_nak_3*alpha_f_nak_4 + ...
alpha_f_nak_2*alpha_f_nak_3*alpha_f_nak_4 + ...
alpha_r_nak_2*alpha_r_nak_3*alpha_r_nak_4 + ...
alpha_f_nak_1*alpha_r_nak_2*alpha_r_nak_3 + ...
alpha_f_nak_1*alpha_r_nak_2*alpha_f_nak_4 + ...
alpha_f_nak_1*alpha_f_nak_3*alpha_f_nak_4 + ...
alpha_r_nak_1*alpha_r_nak_3*alpha_r_nak_4 + ...
alpha_f_nak_2*alpha_r_nak_3*alpha_r_nak_4 + ...
alpha_f_nak_1*alpha_f_nak_2*alpha_r_nak_3 + ...
alpha_f_nak_1*alpha_f_nak_2*alpha_f_nak_4 + ...
alpha_r_nak_1*alpha_r_nak_2*alpha_r_nak_4 + ...
alpha_r_nak_1*alpha_f_nak_3*alpha_r_nak_4 + ...
alpha_f_nak_2*alpha_f_nak_3*alpha_r_nak_4 + ...
alpha_f_nak_1*alpha_f_nak_2*alpha_f_nak_3;
v_cyc_nak = (alpha_f_nak_1*alpha_f_nak_2*alpha_f_nak_3*...
alpha_f_nak_4-alpha_r_nak_1*alpha_r_nak_2*...
alpha_r_nak_3*alpha_r_nak_4)/sig_nak;
end
