- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-02-18 13:32:23+13:00
- Desc:
- Updating way cellml is written
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/6d1/rawfile/bdc41c1cc38a5bf33b62e6b5432fc23e17a15dfa/parameter_finder/kinetic_parameters_PLB.py
# 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 (k_kinetic, N_cT, K_C, W) kinetic parameters, constraints, and vector of volumes in each
# compartment (pL) (1 if gating variable, or in element corresponding to
# kappa)
import numpy as np
def 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/(pow(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 = len(vKm)
k1m = [] #np.zeros(N)
k1p = [] #np.zeros(N)
k2m = [] #np.zeros(N)
k2p = [] #np.zeros(N)
for i in range(N):
k2p.append(vkcat[i])
k1m.append(fastKineticConstant) # 1/s
k1p.append((k1m[i] + k2p[i]) / vKm[i])
k2m.append(k1p[i]*k2p[i]/k1m[i]) # detailed balance
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 = range(3)
k_kinetic = [
k1p[irr], k2p[irr], k1m[irr], k2m[irr]
]
# CONSTRAINTS
N_cT = []
# N_cT = []
# # # Reaction i: [PKA:PKI] = [C][PKI] at SS big error. Not isolated reaction
# # repeat for type 1 and 2
# if False:
# N_cT[0][num_cols + 1] = 1
# N_cT[0][num_cols + 5] = 1
# N_cT[0][num_cols + 8) = -1
#
# # Gibbs free energy of L + R binding **MED_ERROR**
# if False:
# N_cT[2][num_cols + 3] = 1 # ARC
# N_cT[2][num_cols) = -1 # cAMP
# N_cT[2][num_cols + 2] = -1 # RC
# G_0_bind = -45.1872 # kJ/mol
# R = 8.314
# T = 310
# K_bind = np.exp(G_0_bind/(R*T))*10^6
#
K_C = []
# volume vector
W = list(np.append([1] * num_cols, [V['V_myo']] * num_rows))
return (k_kinetic, [N_cT], K_C, W)
