TITLE Mod file for component: Component(id=D1_reduced_cascade2_0 type=D1_reduced_cascade2)
COMMENT
reduced speedy cascade from DA to phosphorylated target
- second version
- original cascade implemented and exported to SBML by Anu Nair; nair at kth . se
based on published cascade in Nair et al., 2016 with removed dependencies and
addition of excitable target.
- transformation from SBML to mod by Robert Lindroos; robert . lindroos at ki . se
using NeuroML and a custom made python script that searches
the xml file and replaces the ID's of the substrates for the names.
The script also shortens long names (e.g. reversable_reaction -> r_r)
the name of the mechanism has alos been manually changed from D1_LTP_cascade... to
D1_reduced_cascade2_0
This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
org.neuroml.export v1.4.2
org.neuroml.model v1.4.2
jLEMS v0.9.7.3
ENDCOMMENT
NEURON {
THREADSAFE
POINT_PROCESS D1_reduced_cascade2_0
RANGE kGaolfGTPase: parameter
RANGE kfPKA_2cAMP: parameter
RANGE krPKA_2cAMP: parameter
RANGE krPKAc_PKAr: parameter
RANGE kfPKAc_PKAr: parameter
RANGE kfPKA2cAMP_2cAMP: parameter
RANGE krPKA2cAMP_2cAMP: parameter
RANGE kactGolf: parameter
RANGE kcatPDE4_cAMP: parameter
RANGE kfPDE4_cAMP: parameter
RANGE krPDE4_cAMP: parameter
RANGE krPDE10_cAMP: parameter
RANGE kcatPDE10c_cAMP: parameter
RANGE kfPDE10_cAMP: parameter
RANGE kfcAMP_PDE10: parameter
RANGE krcAMP_PDE10: parameter
RANGE kcatcAMP_PDE10: parameter
RANGE kcatAC5GaolfGTP_ATP: parameter
RANGE kicatAC5GaolfGTP_ATP: parameter
RANGE kcatAC5_ATP: parameter
RANGE kicatAC5_ATP: parameter
RANGE kfAC5_ATP: parameter
RANGE kGolfback: parameter
RANGE kfAC5GaolfGTP_ATP: parameter
RANGE kfD1R_Golf: parameter
RANGE krD1R_Golf: parameter
RANGE kfD1RDA_Golf: parameter
RANGE krD1RDA_Golf: parameter
RANGE krAC5X_ATP: parameter
RANGE kfAC5XGaolfGTP: parameter
RANGE krAC5XGaolfGTP: parameter
RANGE krgso: parameter
RANGE kfPDE10c_cAMP: parameter
RANGE krPDE10c_cAMP: parameter
RANGE kfD1R_DA: parameter
RANGE kfD1RGolf_DA: parameter
RANGE krD1R_DA: parameter
RANGE krD1RGolf_DA: parameter
RANGE kfPP1_Target1p : parameter
RANGE krPP1_Target1p : parameter
RANGE kfPKAc_Target1 : parameter
RANGE krPKAc_Target1 : parameter
RANGE kcatPP1_Target1p : parameter
RANGE kcatPKAc_Target1 : parameter
RANGE tscale : parameter
RANGE Spine: parameter
RANGE init_GaolfGDP: parameter
RANGE init_Gbgolf: parameter
RANGE init_GaolfGTP: parameter
RANGE init_D1RDAGolf: parameter
RANGE init_Golf: parameter
RANGE init_D1RGolf: parameter
RANGE init_D1RDA: parameter
RANGE init_D1R: parameter
RANGE init_cAMP: parameter
RANGE init_AC5: parameter
RANGE init_AC5GaolfGTP: parameter
RANGE init_PDE4: parameter
RANGE init_PKA: parameter
RANGE init_PKAcAMP2: parameter
RANGE init_PKAcAMP4: parameter
RANGE init_PKAreg: parameter
RANGE init_PKAc: parameter
RANGE init_PP1: parameter
RANGE init_DA: parameter
RANGE init_AMP: parameter
RANGE init_PDE4_cAMP: parameter
RANGE init_PDE10c: parameter
RANGE init_PDE10: parameter
RANGE init_PDE10_cAMP: parameter
RANGE init_PDE10c_cAMP: parameter
RANGE init_ATP: parameter
RANGE init_AC5GaolfGTP_ATP: parameter
RANGE init_AC5_ATP: parameter
RANGE init_PP1_Target1p : parameter
RANGE init_Target1p : parameter
RANGE init_PKAc_Target1 : parameter
RANGE init_Target1 : parameter
RANGE r_r_1 : derived variable
RANGE r_r_2 : derived variable
RANGE r_r_3 : derived variable
RANGE r_r_4 : derived variable
RANGE r_r_5 : derived variable
RANGE r_r_6 : derived variable
RANGE r_r_7 : derived variable
RANGE r_r_8 : derived variable
RANGE r_r_9 : derived variable
RANGE r_r_10 : derived variable
RANGE r_r_11 : derived variable
RANGE r_r_12 : derived variable
RANGE r_r_13 : derived variable
RANGE r_r_14 : derived variable
RANGE r_r_15 : derived variable
RANGE r_ir_1 : derived variable
RANGE r_ir_2 : derived variable
RANGE r_ir_3 : derived variable
RANGE r_ir_4 : derived variable
RANGE r_ir_5 : derived variable
RANGE r_ir_6 : derived variable
RANGE r_ir_7 : derived variable
RANGE r_ir_8 : derived variable
RANGE r_ir_9 : derived variable
RANGE r_ir_10 : derived variable
RANGE r_ir_11 : derived variable
RANGE r_ir_12 : derived variable
RANGE r_r_17 : derived variable
RANGE r_r_16 : derived variable
RANGE r_ir_14 : derived variable
RANGE r_ir_15 : derived variable
}
UNITS {
(nA) = (nanoamp)
(uA) = (microamp)
(mA) = (milliamp)
(A) = (amp)
(mV) = (millivolt)
(mS) = (millisiemens)
(uS) = (microsiemens)
(molar) = (1/liter)
(kHz) = (kilohertz)
(mM) = (millimolar)
(um) = (micrometer)
(umol) = (micromole)
(S) = (siemens)
}
PARAMETER {
kGaolfGTPase = 30
kfPKA_2cAMP = 0.026
krPKA_2cAMP = 350
krPKAc_PKAr = 50
kfPKAc_PKAr = 0.03
kfPKA2cAMP_2cAMP = 0.0346
krPKA2cAMP_2cAMP = 50
kactGolf = 15
kcatPDE4_cAMP = 2.5
kfPDE4_cAMP = 0.03
krPDE4_cAMP = 1
krPDE10_cAMP = 1
kcatPDE10c_cAMP = 10
kfPDE10_cAMP = 1.0E-6
kfcAMP_PDE10 = 0.1
krcAMP_PDE10 = 2
kcatcAMP_PDE10 = 3
kcatAC5GaolfGTP_ATP = 50
kicatAC5GaolfGTP_ATP = 2.55
kcatAC5_ATP = 1
kicatAC5_ATP = 0.002
kfAC5_ATP = 1.0E-4
kGolfback = 100
kfAC5GaolfGTP_ATP = 0.00255
kfD1R_Golf = 0.06
krD1R_Golf = 250
kfD1RDA_Golf = 0.06
krD1RDA_Golf = 250
krAC5X_ATP = 1
kfAC5XGaolfGTP = 10
krAC5XGaolfGTP = 1
krgso = 1
kfPDE10c_cAMP = 0.1
krPDE10c_cAMP = 2
kfD1R_DA = 0.05
kfD1RGolf_DA = 0.05
krD1R_DA = 250
krD1RGolf_DA = 250
kfPP1_Target1p = 0.001
krPP1_Target1p = 10
kfPKAc_Target1 = 0.08
krPKAc_Target1 = 10
kcatPP1_Target1p = 5
kcatPKAc_Target1 = 10
tscale = 0.001 (kHz)
Spine = 1.0E-15
init_GaolfGDP = 0.010083121
init_Gbgolf = 29.885124
init_GaolfGTP = 0.008913481
init_D1RDAGolf = 2.008902
init_Golf = 1453.0726
init_D1RGolf = 515.0334
init_D1RDA = 5.959225
init_D1R = 1476.9984
init_cAMP = 38.186016
init_AC5 = 2.6694465
init_AC5GaolfGTP = 0.118090406
init_PDE4 = 1506.8085
init_PKA = 1157.1414
init_PKAcAMP2 = 3.2824342
init_PKAcAMP4 = 0.08673742
init_PKAreg = 39.48949
init_PKAc = 3.6607807
init_PP1 = 2927.3425
init_DA = 20
init_AMP = 0
init_PDE4_cAMP = 493.19153
init_PDE10c = 0.5781013
init_PDE10 = 396.45627
init_PDE10_cAMP = 302.78168
init_PDE10c_cAMP = 0.18396154
init_ATP = 5000000
init_AC5GaolfGTP_ATP = 29.748037
init_AC5_ATP = 667.4644
init_PP1_Target1p = 73.65742
init_Target1p = 377.42807
init_PKAc_Target1 = 36.82871
init_Target1 = 2515.0857
}
ASSIGNED {
r_r_1 : derived variable
r_r_2 : derived variable
r_r_3 : derived variable
r_r_4 : derived variable
r_r_5 : derived variable
r_r_6 : derived variable
r_r_7 : derived variable
r_r_8 : derived variable
r_r_9 : derived variable
r_r_10 : derived variable
r_r_11 : derived variable
r_r_12 : derived variable
r_r_13 : derived variable
r_r_14 : derived variable
r_r_15 : derived variable
r_ir_1 : derived variable
r_ir_2 : derived variable
r_ir_3 : derived variable
r_ir_4 : derived variable
r_ir_5 : derived variable
r_ir_6 : derived variable
r_ir_7 : derived variable
r_ir_8 : derived variable
r_ir_9 : derived variable
r_ir_10 : derived variable
r_ir_11 : derived variable
r_ir_12 : derived variable
r_r_17 : derived variable
r_r_16 : derived variable
r_ir_14 : derived variable
r_ir_15 : derived variable
rate_GaolfGDP (/ms)
rate_PKAreg (/ms)
rate_AC5_ATP (/ms)
rate_AC5GaolfGTP_ATP (/ms)
rate_PKAcAMP4 (/ms)
rate_AC5GaolfGTP (/ms)
rate_PP1 (/ms)
rate_Gbgolf (/ms)
rate_PDE10 (/ms)
rate_GaolfGTP (/ms)
rate_PDE10_cAMP (/ms)
rate_Target1p (/ms)
rate_PDE10c (/ms)
rate_cAMP (/ms)
rate_AC5 (/ms)
rate_PDE10c_cAMP (/ms)
rate_D1RDAGolf (/ms)
rate_D1RGolf (/ms)
rate_PKAc_Target1 (/ms)
rate_Target1 (/ms)
rate_D1R (/ms)
rate_D1RDA (/ms)
rate_PP1_Target1p (/ms)
rate_Golf (/ms)
rate_PKA (/ms)
rate_PKAc (/ms)
rate_PDE4 (/ms)
rate_PDE4_cAMP (/ms)
rate_PKAcAMP2 (/ms)
}
STATE {
GaolfGDP
Gbgolf
GaolfGTP
D1RDAGolf
Golf
D1RGolf
D1RDA
D1R
cAMP
AC5
AC5GaolfGTP
PDE4
PKA
PKAcAMP2
PKAcAMP4
PKAreg
PKAc
PP1
DA
AMP
PDE4_cAMP
PDE10c
PDE10
PDE10_cAMP
PDE10c_cAMP
ATP
AC5GaolfGTP_ATP
AC5_ATP
PP1_Target1p
Target1p
PKAc_Target1
Target1
}
INITIAL {
rates()
rates() ? To ensure correct initialisation.
GaolfGDP = init_GaolfGDP
Gbgolf = init_Gbgolf
GaolfGTP = init_GaolfGTP
D1RDAGolf = init_D1RDAGolf
Golf = init_Golf
D1RGolf = init_D1RGolf
D1RDA = init_D1RDA
D1R = init_D1R
cAMP = init_cAMP
AC5 = init_AC5
AC5GaolfGTP = init_AC5GaolfGTP
PDE4 = init_PDE4
PKA = init_PKA
PKAcAMP2 = init_PKAcAMP2
PKAcAMP4 = init_PKAcAMP4
PKAreg = init_PKAreg
PKAc = init_PKAc
PP1 = init_PP1
DA = init_DA
AMP = init_AMP
PDE4_cAMP = init_PDE4_cAMP
PDE10c = init_PDE10c
PDE10 = init_PDE10
PDE10_cAMP = init_PDE10_cAMP
PDE10c_cAMP = init_PDE10c_cAMP
ATP = init_ATP
AC5GaolfGTP_ATP = init_AC5GaolfGTP_ATP
AC5_ATP = init_AC5_ATP
PP1_Target1p = init_PP1_Target1p
Target1p = init_Target1p
PKAc_Target1 = init_PKAc_Target1
Target1 = init_Target1
}
BREAKPOINT {
SOLVE states METHOD cnexp
}
DERIVATIVE states {
rates()
GaolfGDP' = rate_GaolfGDP
PKAreg' = rate_PKAreg
AC5_ATP' = rate_AC5_ATP
AC5GaolfGTP_ATP' = rate_AC5GaolfGTP_ATP
PKAcAMP4' = rate_PKAcAMP4
AC5GaolfGTP' = rate_AC5GaolfGTP
PP1' = rate_PP1
Gbgolf' = rate_Gbgolf
PDE10' = rate_PDE10
GaolfGTP' = rate_GaolfGTP
PDE10_cAMP' = rate_PDE10_cAMP
Target1p' = rate_Target1p
PDE10c' = rate_PDE10c
cAMP' = rate_cAMP
AC5' = rate_AC5
PDE10c_cAMP' = rate_PDE10c_cAMP
D1RDAGolf' = rate_D1RDAGolf
D1RGolf' = rate_D1RGolf
PKAc_Target1' = rate_PKAc_Target1
Target1' = rate_Target1
D1R' = rate_D1R
D1RDA' = rate_D1RDA
PP1_Target1p' = rate_PP1_Target1p
Golf' = rate_Golf
PKA' = rate_PKA
PKAc' = rate_PKAc
PDE4' = rate_PDE4
PDE4_cAMP' = rate_PDE4_cAMP
PKAcAMP2' = rate_PKAcAMP2
}
PROCEDURE rates() {
r_r_1 = ( Spine * ((( kfD1RGolf_DA * D1RGolf ) * DA ) - ( krD1RGolf_DA * D1RDAGolf ))) ? evaluable
r_r_2 = ( Spine * ((( kfD1R_DA * D1R ) * DA ) - ( krD1R_DA * D1RDA ))) ? evaluable
r_r_3 = ( Spine * ((( kfD1R_Golf * D1R ) * Golf ) - ( krD1R_Golf * D1RGolf ))) ? evaluable
r_r_4 = ( Spine * ((( kfD1RDA_Golf * Golf ) * D1RDA ) - ( krD1RDA_Golf * D1RDAGolf ))) ? evaluable
r_r_5 = ( Spine * ((( kfAC5XGaolfGTP * AC5 ) * GaolfGTP ) - ( krAC5XGaolfGTP * AC5GaolfGTP ))) ? evaluable
r_r_6 = ( Spine * ((( kfAC5GaolfGTP_ATP * AC5GaolfGTP ) * ATP ) - ( krAC5X_ATP * AC5GaolfGTP_ATP ))) ? evaluable
r_r_7 = ( Spine * ((( kfAC5_ATP * AC5 ) * ATP ) - ( krAC5X_ATP * AC5_ATP ))) ? evaluable
r_r_8 = ( Spine * ((( kfAC5XGaolfGTP * GaolfGTP ) * AC5_ATP ) - ( krAC5XGaolfGTP * AC5GaolfGTP_ATP ))) ? evaluable
r_r_9 = ( Spine * ((( kfPDE4_cAMP * cAMP ) * PDE4 ) - ( krPDE4_cAMP * PDE4_cAMP ))) ? evaluable
r_r_10 = ( Spine * ((( kfPDE10_cAMP * PDE10 ) * ( cAMP ^ 2.0)) - ( krPDE10_cAMP * PDE10c ))) ? evaluable
r_r_11 = ( Spine * ((( kfcAMP_PDE10 * cAMP ) * PDE10 ) - ( krcAMP_PDE10 * PDE10_cAMP ))) ? evaluable
r_r_12 = ( Spine * ((( kfPDE10c_cAMP * cAMP ) * PDE10c ) - ( krPDE10c_cAMP * PDE10c_cAMP ))) ? evaluable
r_r_13 = ( Spine * ((( kfPKA_2cAMP * cAMP ) * PKA ) - ( krPKA_2cAMP * PKAcAMP2 ))) ? evaluable
r_r_14 = ( Spine * ((( kfPKA2cAMP_2cAMP * cAMP ) * PKAcAMP2 ) - ( krPKA2cAMP_2cAMP * PKAcAMP4 ))) ? evaluable
r_r_15 = ( Spine * (( krPKAc_PKAr * PKAcAMP4 ) - (( kfPKAc_PKAr * PKAc ) * PKAreg ))) ? evaluable
r_ir_1 = (( Spine * kactGolf ) * D1RDAGolf ) ? evaluable
r_ir_2 = (( Spine * kGaolfGTPase ) * GaolfGTP ) ? evaluable
r_ir_3 = ((( Spine * kGolfback ) * GaolfGDP ) * Gbgolf ) ? evaluable
r_ir_4 = (( Spine * kcatAC5GaolfGTP_ATP ) * AC5GaolfGTP_ATP ) ? evaluable
r_ir_5 = ((( Spine * kicatAC5GaolfGTP_ATP ) * cAMP ) * AC5GaolfGTP ) ? evaluable
r_ir_6 = (( Spine * kcatAC5_ATP ) * AC5_ATP ) ? evaluable
r_ir_7 = ((( Spine * kicatAC5_ATP ) * cAMP ) * AC5 ) ? evaluable
r_ir_8 = (( Spine * krgso ) * AC5GaolfGTP ) ? evaluable
r_ir_9 = (( Spine * krgso ) * AC5GaolfGTP_ATP ) ? evaluable
r_ir_10 = (( Spine * kcatPDE4_cAMP ) * PDE4_cAMP ) ? evaluable
r_ir_11 = (( Spine * kcatcAMP_PDE10 ) * PDE10_cAMP ) ? evaluable
r_ir_12 = (( Spine * kcatPDE10c_cAMP ) * PDE10c_cAMP ) ? evaluable
r_r_17 = ( Spine * ((( kfPP1_Target1p * PP1 ) * Target1p ) - ( krPP1_Target1p * PP1_Target1p ))) ? evaluable
r_r_16 = ( Spine * ((( kfPKAc_Target1 * Target1 ) * PKAc ) - ( krPKAc_Target1 * PKAc_Target1 ))) ? evaluable
r_ir_14 = (( Spine * kcatPKAc_Target1 ) * PKAc_Target1 ) ? evaluable
r_ir_15 = (( Spine * kcatPP1_Target1p ) * PP1_Target1p ) ? evaluable
rate_AC5GaolfGTP = tscale * ( r_r_5 - r_r_6 + r_ir_4 - r_ir_5 - r_ir_8 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_Gbgolf = tscale * ( r_ir_1 - r_ir_3 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PDE4_cAMP = tscale * ( r_r_9 - r_ir_10 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_AC5GaolfGTP_ATP = tscale * ( r_r_6 + r_r_8 - r_ir_4 + r_ir_5 - r_ir_9 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PP1 = tscale * (-1* r_r_17 + r_ir_15 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PDE4 = tscale * (-1* r_r_9 + r_ir_10 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PKAreg = tscale * ( r_r_15 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_GaolfGDP = tscale * ( r_ir_2 - r_ir_3 + r_ir_8 + r_ir_9 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_AC5 = tscale * (-1* r_r_5 - r_r_7 + r_ir_6 - r_ir_7 + r_ir_8 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_cAMP = tscale * (-1* r_r_9 - r_r_10 * 2.0 - r_r_11 - r_r_12 - r_r_13 - r_r_14 + r_ir_4 - r_ir_5 + r_ir_6 - r_ir_7 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_GaolfGTP = tscale * (-1* r_r_5 - r_r_8 + r_ir_1 - r_ir_2 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PDE10_cAMP = tscale * ( r_r_11 - r_ir_11 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PKAcAMP4 = tscale * ( r_r_14 - r_r_15 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PDE10c = tscale * ( r_r_10 - r_r_12 + r_ir_12 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PDE10c_cAMP = tscale * ( r_r_12 - r_ir_12 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PDE10 = tscale * (-1* r_r_10 - r_r_11 + r_ir_11 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_Target1 = tscale * (-1* r_r_16 + r_ir_15 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_Target1p = tscale * (-1* r_r_17 + r_ir_14 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_D1RDA = tscale * ( r_r_2 - r_r_4 + r_ir_1 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_D1R = tscale * (-1* r_r_2 - r_r_3 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_Golf = tscale * (-1* r_r_3 - r_r_4 + r_ir_3 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PKA = tscale * (-1* r_r_13 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PKAc_Target1 = tscale * ( r_r_16 - r_ir_14 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PKAc = tscale * ( r_r_15 - r_r_16 + r_ir_14 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PP1_Target1p = tscale * ( r_r_17 - r_ir_15 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_PKAcAMP2 = tscale * ( r_r_13 - r_r_14 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_D1RDAGolf = tscale * ( r_r_1 + r_r_4 - r_ir_1 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_D1RGolf = tscale * (-1* r_r_1 + r_r_3 ) / Spine ? Note units of all quantities used here need to be consistent!
rate_AC5_ATP = tscale * ( r_r_7 - r_r_8 - r_ir_6 + r_ir_7 + r_ir_9 ) / Spine ? Note units of all quantities used here need to be consistent!
}