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introvoyz041
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biomass

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EGF binds EGFR <--> Ra | kf=0.003, kr=0.06 | EGFR=100
Ra dimerizes <--> R2 | kf=0.01, kr=0.1
R2 is phosphorylated <--> RP | kf=1, kr=0.01
RP is dephosphorylated --> R2 | V=450, K=50
RP binds PLCg <--> RPL | kf=0.06, kr=0.2 | PLCg=105
RPL is phosphorylated <--> RPLP | kf=1, kr=0.05
RPLP is dissociated into RP and PLCgP | kf=0.3, kr=0.006
PLCgP is dephosphorylated --> PLCg | V=1, K=100
RP binds Grb2 <--> RG | kf=0.003, kr=0.05 | Grb2=85
RG binds SOS <--> RGS | kf=0.01, kr=0.06 | SOS=34
RGS is dissociated into RP and GS | kf=0.03, kr=4.5e-3
GS is dissociated into Grb2 and SOS | kf=1.5e-3, kr=1e-4
RP binds Shc <--> RSh | kf=0.09, kr=0.6 | Shc=150
RSh is phosphorylated <--> RShP | kf=6, kr=0.06
RShP is dissociated into ShP and RP | kf=0.3, kr=9e-4
ShP is dephosphorylated --> Shc | V=1.7, K=340
RShP binds Grb2 <--> RShG | kf=0.003, kr=0.1
RShG is dissociated into RP and ShG | kf=0.3, kr=9e-4
RShG binds SOS <--> RShGS | kf=0.01, kr=2.14e-2
RShGS is dissociated into ShGS and RP | kf=0.12, kr=2.4e-4
ShP binds Grb2 <--> ShG | kf=0.003, kr=0.1
ShG binds SOS <--> ShGS | kf=0.03, kr=0.064
ShGS is dissociated into ShP and GS | kf=0.1, kr=0.021
RShP binds GS <--> RShGS | kf=0.009, kr=4.29e-2
PLCgP is translocated to cytoskeletal or membrane structures <--> PLCgP_I | kf=1, kr=0.03
# Kholodenko, B. N., Demin, O. V, Moehren, G. & Hoek, J. B.
# Quantification of short term signaling by the epidermal growth factor receptor.
# J. Biol. Chem. 274, 30169–30181 (1999). https://doi.org/10.1074/jbc.274.42.30169
# observable layer
@obs Total_phosphorylated_Shc: u[RShP] + u[RShG] + u[RShGS] + u[ShP] + u[ShG] + u[ShGS]
@obs Total_Grb2_coprecipitated_with_Shc: u[RShG] + u[ShG] + u[RShGS] + u[ShGS]
@obs Total_phosphorylated_Shc_bound_to_EGFR: u[RShP] + u[RShG] + u[RShGS]
@obs Total_Grb2_bound_to_EGFR: u[RG] + u[RGS] + u[RShG] + u[RShGS]
@obs Total_SOS_bound_to_EGFR: u[RGS] + u[RShGS]
@obs ShGS_complex: u[ShGS]
@obs Total_phosphorylated_PLCg: u[RPLP] + u[PLCgP]
# simulation layer
@sim tspan: [0, 120]
@sim condition EGF20nM: init[EGF] = 680
@sim condition EGF2nM: init[EGF] = 68
@sim condition Absence_PLCgP_transloc: init[EGF] = 680; p[kf25] = 0; p[kr25] = 0
EGF + EGFR <--> Ra | kf=0.003, kr=0.06 | EGFR=100
Ra + Ra <--> R2 | kf=0.01, kr=0.1
R2 <--> RP | kf=1, kr=0.01
RP is dephosphorylated --> R2 | V=450, K=50
RP + PLCg <--> RPL | kf=0.06, kr=0.2 | PLCg=105
RPL <--> RPLP | kf=1, kr=0.05
RPLP <--> RP + PLCgP | kf=0.3, kr=0.006
PLCgP is dephosphorylated --> PLCg | V=1, K=100
RP + Grb2 <--> RG | kf=0.003, kr=0.05 | Grb2=85
RG + SOS <--> RGS | kf=0.01, kr=0.06 | SOS=34
RGS <--> RP + GS | kf=0.03, kr=4.5e-3
GS <--> Grb2 + SOS | kf=1.5e-3, kr=1e-4
RP + Shc <--> RSh | kf=0.09, kr=0.6 | Shc=150
RSh <--> RShP | kf=6, kr=0.06
RShP <--> ShP + RP | kf=0.3, kr=9e-4
ShP is dephosphorylated --> Shc | V=1.7, K=340
RShP + Grb2 <--> RShG | kf=0.003, kr=0.1
RShG <--> RP + ShG | kf=0.3, kr=9e-4
RShG + SOS <--> RShGS | kf=0.01, kr=2.14e-2
RShGS <--> ShGS + RP | kf=0.12, kr=2.4e-4
ShP + Grb2 <--> ShG | kf=0.003, kr=0.1
ShG + SOS <--> ShGS | kf=0.03, kr=0.064
ShGS <--> ShP + GS | kf=0.1, kr=0.021
RShP + GS <--> RShGS | kf=0.009, kr=4.29e-2
PLCgP <--> PLCgP_I | kf=1, kr=0.03
# Kholodenko, B. N., Demin, O. V, Moehren, G. & Hoek, J. B.
# Quantification of short term signaling by the epidermal growth factor receptor.
# J. Biol. Chem. 274, 30169–30181 (1999). https://doi.org/10.1074/jbc.274.42.30169
# observable layer
@obs Total_phosphorylated_Shc: u[RShP] + u[RShG] + u[RShGS] + u[ShP] + u[ShG] + u[ShGS]
@obs Total_Grb2_coprecipitated_with_Shc: u[RShG] + u[ShG] + u[RShGS] + u[ShGS]
@obs Total_phosphorylated_Shc_bound_to_EGFR: u[RShP] + u[RShG] + u[RShGS]
@obs Total_Grb2_bound_to_EGFR: u[RG] + u[RGS] + u[RShG] + u[RShGS]
@obs Total_SOS_bound_to_EGFR: u[RGS] + u[RShGS]
@obs ShGS_complex: u[ShGS]
@obs Total_phosphorylated_PLCg: u[RPLP] + u[PLCgP]
# simulation layer
@sim tspan: [0, 120]
@sim condition EGF20nM: init[EGF] = 680
@sim condition EGF2nM: init[EGF] = 68
@sim condition Absence_PLCgP_transloc: init[EGF] = 680; p[kf25] = 0; p[kr25] = 0
A + B <--> AB
AB + C <--> ABC
ABC <--> A + BC
BC <--> B + C
A + B <--> AB
AB <--> A + B
@rxn ERKc --> pERKc: p[V1] * p[a] * u[ppMEKc] * u[ERKc] / ( p[K1] * (1 + u[pERKc] / p[K2]) + u[ERKc] ) || ERKc=9.60e02
@rxn pERKc --> ppERKc: p[V2] * p[a] * u[ppMEKc] * u[pERKc] / ( p[K2] * (1 + u[ERKc] / p[K1]) + u[pERKc] ) | const V2=2.20e-01, const K2=3.50e02
@rxn pERKc --> ERKc: p[V3] * u[pERKc] / ( p[K3] * (1 + u[ppERKc] / p[K4]) + u[pERKc] ) | const V3=7.20e-01, const K3=1.60e02
@rxn ppERKc --> pERKc: p[V4] * u[ppERKc] / ( p[K4]* (1 + u[pERKc] / p[K3]) + u[ppERKc] ) | const V4=6.48e-01, const K4=6.00e01
@rxn pERKn --> ERKn: p[V5] * u[pERKn] / ( p[K5] * (1 + u[ppERKn] / p[K6]) + u[pERKn] )
@rxn ppERKn --> pERKn: p[V6] * u[ppERKn] / ( p[K6] * (1 + u[pERKn] / p[K5]) + u[ppERKn] ) |5|