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reaction: 899776
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species: 899437
species: 899536
species: 899377
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length unit: length
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time units: 131570
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units def: 182067
species: 899417
is described by: http://identifiers.org/pubmed/11665614
species: 899297
reaction: 899557
reaction: 899697
species: 899057
units def: 182031
notes: This is a model of the canonical cAMP signaling pathway:<br">Ligand->Receptor->G-protein->Cyclase->cAMP->PKA. It also includes phosphodiesterases to balance out cAMP formation.Bhalla US Methods Enzymol. 2002;345:3-23 This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
species: 899237
species: 899177
reaction: 899677
area units: area
units def: 182103
name: Bhalla2002_cAMP_pathway
reaction: 899716
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reaction: 899757
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reaction: 899576
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curated: false
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reaction: 899556
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compartment: 898982
units def: 182199
reaction: 899656

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898997
type: Compartment
constant: true
size: 1.0E-12
spatial dimensions: 3.0

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899157
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constant: false
boundary condition: false
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initial concentration: 0.0
initial amount: NaN
in compartment: 898997

899597
type: Reaction
kinetic law: 182503
product: 182491
product: 182479
reactant: 182467
fast: false
reversible: true

182503
type: KineticLaw
local parameters: 259261
local parameters: 259260
notes: kf*PKA_slash_cAMP4_dot_R2C-kb*PKA_minus_active*PKA_slash_cAMP4_dot_R2

259261
type: LocalParameter
units: 182151
value: 1.8E-11

182187
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exponent: -1.0
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182163
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259260
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units: 182067
value: 6.0E-11

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species: 899177

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constant: false
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species: 899217

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species: 899157

899616
type: Reaction
kinetic law: 182552
product: 182540
reactant: 182527
reactant: 182515
notes: This has to be set to zero for matching the expts in vitro. In vivo we need to consider the inhibition though.
fast: false
reversible: true

182552
type: KineticLaw
local parameters: 259263
local parameters: 259262
notes: kf*PKA_minus_active*PKA_slash_PKA_minus_inhibitor-kb*PKA_slash_inhibited_minus_PKA

259263
type: LocalParameter
units: 182067
value: 1.0E-12

259262
type: LocalParameter
units: 182151
value: 6.0E-11

182540
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stoichiometry: 1.0
species: 899057

899057
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182527
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species: 899037

899037
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constant: false
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initial concentration: 0.25
initial amount: NaN
in compartment: 898997

182515
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stoichiometry: 1.0
species: 899217

899776
type: Reaction
kinetic law: 183291
modifier: 183279
product: 183267
reactant: 183255
notes: See Feinstein et al PNAS 88:10173-10177, Jacobowitz et al JBC 286(6):3829-3832 Smigel, JBC 261(4):1976-1982 (1986)
fast: false
reversible: false

183291
type: KineticLaw
local parameters: 259327
local parameters: 259326
notes: kcat*AC_slash_Gs_dot_AC*AC_slash_ATP/(Km+AC_slash_ATP)

259327
type: LocalParameter
units: 182031
value: 20.0

182055
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259326
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units: 182067
value: 1.8E-11

899337
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constant: false
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183267
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species: 899197

899197
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initial concentration: 0.0
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in compartment: 898997

183255
type: SpeciesReference
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species: 899517

899517
type: Species
notes: ATP is present in all cells between 2 and 10 mM. See Lehninger. It is assumed buffered since the metabolic activity will take care of its levels.
constant: true
boundary condition: true
has only substance units: false
initial concentration: 5000.0
initial amount: NaN
in compartment: 898997

899756
type: Reaction
kinetic law: 183207
product: 183195
reactant: 183183
reactant: 183171
notes: This form has about twice the activity of the unphosphorylated form. See Sette et al JBC 269:28 18271-18274 1994. We\'ll ignore cGMP effects for now.
fast: false
reversible: true

183207
type: KineticLaw
local parameters: 259324
local parameters: 259321
notes: k1*cAMP*AC_slash_cAMP_minus_PDE_star_-k2*AC_slash_cAMP_minus_PDE_star__slash_PDE_star__slash_PDE_star__cplx

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units: 182067
value: 8.0E-11

259321
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units: 182151
value: 5.04E-12

183195
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899317
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183183
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species: 899297

899297
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183171
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species: 899197

899257
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899437
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in compartment: 898997

899536
type: Species
notes: Assumed buffered to 1 mM. Value is irrelevant to simulation.
constant: true
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initial amount: NaN
in compartment: 898997

899377
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constant: false
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899657
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notes: Negligible back-reaction.
fast: false
reversible: true

182794
type: KineticLaw
local parameters: 259273
local parameters: 259272
notes: kf*Gs_slash_GDP_dot_Ga*Gs_slash_Gbg-kb*Gs_slash_GDP_dot_Gabc

259273
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units: 182067
value: 0.0

259272
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units: 182151
value: 6.0E-12

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species: 899497

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899477
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constant: false
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in compartment: 898997

899137
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initial amount: NaN
in compartment: 898997

899736
type: Reaction
kinetic law: 183123
product: 183111
reactant: 183099
reactant: 183087
notes: Best rates are from Conti et al Biochem 34 7979-7987 1995. Though these are for the Sertoli cell form, it looks like they carry nicely into alternatively spliced brain form. See Sette et al JBC 269:28 18271-18274 Km ~2 uM, Vmax est ~ 10 umol/min/mg for pure form. Brain protein is 93 kD but this was 67. So k3 ~10, k2 ~40, k1 ~4.2e-6
fast: false
reversible: true

183123
type: KineticLaw
local parameters: 259318
local parameters: 259317
notes: k1*cAMP*AC_slash_cAMP_minus_PDE-k2*AC_slash_cAMP_minus_PDE_slash_PDE_slash_PDE_cplx

259318
type: LocalParameter
units: 182067
value: 4.0E-11

259317
type: LocalParameter
units: 182151
value: 2.52E-12

183111
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species: 899277

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in compartment: 898997

183099
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species: 899257

183087
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stoichiometry: 1.0
species: 899197

899596
type: Reaction
kinetic law: 182455
product: 182443
product: 182430
reactant: 182418
notes: This has to be fast, as the activation of PKA by cAMP is also fast. kf was 10
fast: false
reversible: true

182455
type: KineticLaw
local parameters: 259259
local parameters: 259258
notes: kf*PKA_slash_cAMP4_dot_R2C2-kb*PKA_minus_active*PKA_slash_cAMP4_dot_R2C

259259
type: LocalParameter
units: 182151
value: 1.8E-11

259258
type: LocalParameter
units: 182067
value: 6.0E-11

182443
type: SpeciesReference
stoichiometry: 1.0
species: 899157

182430
type: SpeciesReference
stoichiometry: 1.0
species: 899217

182418
type: SpeciesReference
stoichiometry: 1.0
species: 899137

899077
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899097
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constant: false
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has only substance units: false
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initial amount: NaN
in compartment: 898997

899617
type: Reaction
kinetic law: 182588
product: 182576
reactant: 182564
notes: The rates for this are poorly constrained. In adipocytes (probably a different PDE) the dephosphorylation is complete within 15 min, but there are no intermediate time points so it could be much faster. Identity of phosphatase etc is still unknown.
fast: false
reversible: true

182588
type: KineticLaw
local parameters: 259265
local parameters: 259264
notes: kf*AC_slash_cAMP_minus_PDE_star_-kb*AC_slash_cAMP_minus_PDE

259265
type: LocalParameter
units: 182067
value: 0.0

259264
type: LocalParameter
units: 182067
value: 1.0E-13

182576
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species: 899257

182564
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species: 899297

899637
type: Reaction
kinetic law: 182685
product: 182673
reactant: 182660
reactant: 182648
notes: Ligand binding to receptor. From Gether et al JBC 270:28268-28275 (1995) the binding to the purified receptor is at about 1 uM, but the conformational change only happens at 30 uM. We\'ll take 1 uM for this, since it is already much weaker binding than to the R.Gs complex. The time-course from this paper appears remarkably slow, based on physiological data I estimate more like 10 sec.
fast: false
reversible: true

182685
type: KineticLaw
local parameters: 259269
local parameters: 259268
notes: kf*Gs_slash_R*Gs_slash_L-kb*Gs_slash_L_dot_R

259269
type: LocalParameter
units: 182067
value: 1.0E-13

259268
type: LocalParameter
units: 182151
value: 1.00002E-13

182673
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species: 899417

899417
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initial concentration: 0.0
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in compartment: 898997

182660
type: SpeciesReference
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species: 899537

899537
type: Species
notes: This ligand could be any of several which bind to the beta adrenergic receptor and other G-protein coupled receptors which activate AC. For the sake of argument, call it isoproterenol.
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.01
initial amount: NaN
in compartment: 898997

182648
type: SpeciesReference
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species: 899397

899397
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initial amount: NaN
in compartment: 898997

899696
type: Reaction
kinetic law: 182929
product: 182916
reactant: 182904
reactant: 182892
notes: Receptor binding to Gs. Scale it to the same slow rates described by Fay et al for L.R to L.R.G. From detailed balance, Kd is 50.
fast: false
reversible: true

182929
type: KineticLaw
local parameters: 259279
local parameters: 259278
notes: kf*Gs_slash_GDP_dot_Gabc*Gs_slash_R-kb*Gs_slash_R_dot_GDP_dot_Gabc

259279
type: LocalParameter
units: 182067
value: 1.0E-13

259278
type: LocalParameter
units: 182151
value: 1.99998E-13

182916
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species: 899516

899516
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in compartment: 898997

182904
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species: 899397

182892
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species: 899437

899457
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constant: false
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initial concentration: 0.0
initial amount: NaN
in compartment: 898997

899717
type: Reaction
kinetic law: 183075
product: 183062
product: 183050
reactant: 183038
fast: false
reversible: false

183075
type: KineticLaw
local parameters: 259314
notes: k3*PKA_minus_active_slash_phosph_minus_PDE_slash_phosph_minus_PDE_cplx

259314
type: LocalParameter
units: 182067
value: 9.0E-12

183062
type: SpeciesReference
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species: 899217

183050
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species: 899297

183038
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species: 899237

899237
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 898997

899577
type: Reaction
kinetic law: 182406
product: 182394
reactant: 182382
reactant: 182370
fast: false
reversible: true

182406
type: KineticLaw
local parameters: 259257
local parameters: 259256
notes: kf*cAMP*PKA_slash_cAMP3_dot_R2C2-kb*PKA_slash_cAMP4_dot_R2C2

259257
type: LocalParameter
units: 182067
value: 3.25E-11

259256
type: LocalParameter
units: 182151
value: 7.5E-11

182394
type: SpeciesReference
stoichiometry: 1.0
species: 899137

182382
type: SpeciesReference
stoichiometry: 1.0
species: 899117

899117
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 898997

182370
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species: 899197

899636
type: Reaction
kinetic law: 182636
product: 182624
reactant: 182612
reactant: 182600
notes: Half-max at around 3nM = kb/kf from fig 5 in Feinstein et al PNAS USA 88 10173-10177 1991 kf = kb/1800 = 5.56e-4 kb Ofer Jacobowitz thesis (Mount Sinai 1995) data indicates it is more like 2 nM.
fast: false
reversible: true

182636
type: KineticLaw
local parameters: 259267
local parameters: 259266
notes: kf*AC_slash_AC*GTP_dot_Ga-kb*AC_slash_Gs_dot_AC

259267
type: LocalParameter
units: 182067
value: 1.0E-12

259266
type: LocalParameter
units: 182151
value: 4.99998E-10

182624
type: SpeciesReference
stoichiometry: 1.0
species: 899337

182612
type: SpeciesReference
stoichiometry: 1.0
species: 899377

182600
type: SpeciesReference
stoichiometry: 1.0
species: 899357

899357
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.015
initial amount: NaN
in compartment: 898997

899557
type: Reaction
kinetic law: 182308
product: 182296
reactant: 182284
reactant: 182272
notes: For now let us set this to the same Km (1e-7M) as site B. This gives kf/kb = .7e-7M * 1e6 / (6e5^2) : 1/(6e5^2) = 2e-13:2.77e-12 Smith et al have better values. They say that this is cooperative, so the consts are now kf/kb =8.3e-4
fast: false
reversible: true

182308
type: KineticLaw
local parameters: 259253
local parameters: 259252
notes: kf*PKA_slash_cAMP_dot_R2C2*cAMP-kb*PKA_slash_cAMP2_dot_R2C2

259253
type: LocalParameter
units: 182067
value: 3.3E-11

259252
type: LocalParameter
units: 182151
value: 5.4E-11

182296
type: SpeciesReference
stoichiometry: 1.0
species: 899097

182284
type: SpeciesReference
stoichiometry: 1.0
species: 899197

182272
type: SpeciesReference
stoichiometry: 1.0
species: 899077

899697
type: Reaction
kinetic law: 182977
product: 182965
reactant: 182953
reactant: 182941
notes: See Fay et al Biochem 30 5066-5075 1991. kf is 0.01/sec but does not account for Gs levels. kb is 0.0001/sec. The fraction of RG is about 50%, so we can estimate Kd at about the same as for Gs basal levels. This rate has to be faster since it has to feed GTP.Ga into the system faster than the GTPase. Waldhoer et al Mol Pharmacol 53:808-818 1988 say affinity for A1adenosine/Gi is 10 nM.
fast: false
reversible: true

182977
type: KineticLaw
local parameters: 259306
local parameters: 259304
notes: kf*Gs_slash_GDP_dot_Gabc*Gs_slash_L_dot_R-kb*Gs_slash_L_dot_R_dot_GDP_dot_Gabc

259306
type: LocalParameter
units: 182067
value: 1.0E-13

259304
type: LocalParameter
units: 182151
value: 1.00002E-11

182965
type: SpeciesReference
stoichiometry: 1.0
species: 899457

182953
type: SpeciesReference
stoichiometry: 1.0
species: 899417

182941
type: SpeciesReference
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species: 899437

899677
type: Reaction
kinetic law: 182880
product: 182868
reactant: 182855
reactant: 182842
notes: From Seifert et al Mol. Pharmacol 56:348-358 (1999) The EC50 for ISO is about 20 nM.
fast: false
reversible: true

182880
type: KineticLaw
local parameters: 259277
local parameters: 259276
notes: kf*Gs_slash_L*Gs_slash_R_dot_GDP_dot_Gabc-kb*Gs_slash_L_dot_R_dot_GDP_dot_Gabc

259277
type: LocalParameter
units: 182067
value: 1.0E-13

259276
type: LocalParameter
units: 182151
value: 4.99998E-12

182868
type: SpeciesReference
stoichiometry: 1.0
species: 899457

182855
type: SpeciesReference
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species: 899516

182842
type: SpeciesReference
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species: 899537

182139
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

182127
type: SBMLUnit
exponent: -2.0
scale: -6
multipler: 1.0
kind: MOLE

182115
type: SBMLUnit
exponent: 3.0
scale: 0
multipler: 1.0
kind: LITRE

899716
type: Reaction
kinetic law: 183026
product: 183014
reactant: 183002
reactant: 182990
notes: See Bramson et al CRC crit rev Biochem 15:2 93-124. The rates there are for peptide substrates and too fast. Scaled down by a factor of 3 as per Cohen et al FEBS Lett 76:182-86 (1977).
fast: false
reversible: true

183026
type: KineticLaw
local parameters: 259311
local parameters: 259309
notes: k1*AC_slash_cAMP_minus_PDE*PKA_minus_active-k2*PKA_minus_active_slash_phosph_minus_PDE_slash_phosph_minus_PDE_cplx

259311
type: LocalParameter
units: 182067
value: 3.6E-11

259309
type: LocalParameter
units: 182151
value: 6.0E-12

183014
type: SpeciesReference
stoichiometry: 1.0
species: 899237

183002
type: SpeciesReference
stoichiometry: 1.0
species: 899217

182990
type: SpeciesReference
stoichiometry: 1.0
species: 899257

899017
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.5
initial amount: NaN
in compartment: 898997

899757
type: Reaction
kinetic law: 183243
product: 183231
reactant: 183219
fast: false
reversible: false

183243
type: KineticLaw
local parameters: 259325
notes: k3*AC_slash_cAMP_minus_PDE_star__slash_PDE_star__slash_PDE_star__cplx

259325
type: LocalParameter
units: 182067
value: 2.0E-11

183231
type: SpeciesReference
stoichiometry: 1.0
species: 899297

183219
type: SpeciesReference
stoichiometry: 1.0
species: 899317

899576
type: Reaction
kinetic law: 182357
product: 182345
reactant: 182333
reactant: 182320
fast: false
reversible: true

182357
type: KineticLaw
local parameters: 259255
local parameters: 259254
notes: kf*PKA_slash_cAMP2_dot_R2C2*cAMP-kb*PKA_slash_cAMP3_dot_R2C2

259255
type: LocalParameter
units: 182067
value: 1.1E-10

259254
type: LocalParameter
units: 182151
value: 7.5E-11

182345
type: SpeciesReference
stoichiometry: 1.0
species: 899117

182333
type: SpeciesReference
stoichiometry: 1.0
species: 899197

182320
type: SpeciesReference
stoichiometry: 1.0
species: 899097

899676
type: Reaction
kinetic law: 182830
product: 182818
reactant: 182806
notes: From Brandt and Ross JBC 261(4):1656-1664, rate is 4/min and is agonist independent. I treat this as irreversible.
fast: false
reversible: true

182830
type: KineticLaw
local parameters: 259275
local parameters: 259274
notes: kf*GTP_dot_Ga-kb*Gs_slash_GDP_dot_Ga

259275
type: LocalParameter
units: 182067
value: 0.0

259274
type: LocalParameter
units: 182067
value: 6.6667E-14

182818
type: SpeciesReference
stoichiometry: 1.0
species: 899477

182806
type: SpeciesReference
stoichiometry: 1.0
species: 899377

182211
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

899737
type: Reaction
kinetic law: 183159
product: 183147
reactant: 183135
fast: false
reversible: false

183159
type: KineticLaw
local parameters: 259320
notes: k3*AC_slash_cAMP_minus_PDE_slash_PDE_slash_PDE_cplx

259320
type: LocalParameter
units: 182067
value: 1.0E-11

183147
type: SpeciesReference
stoichiometry: 1.0
species: 899257

183135
type: SpeciesReference
stoichiometry: 1.0
species: 899277

899556
type: Reaction
kinetic law: 182259
product: 182247
reactant: 182235
reactant: 182223
notes: Hasler et al FASEB J 6:2734-2741 1992 say Kd =1e-7M for type II, 5.6e-8 M for type I. Take mean which comes to 2e-13 #/cell Smith et al PNAS USA 78:3 1591-1595 1981 have better data. First kf/kb=2.1e7/M = 3.5e-5 (#/cell). Ogreid and Doskeland Febs Lett 129:2 287-292 1981 have figs suggesting time course of complete assoc is < 1 min.
fast: false
reversible: true

182259
type: KineticLaw
local parameters: 259251
local parameters: 259250
notes: kf*PKA_slash_R2C2*cAMP-kb*PKA_slash_cAMP_dot_R2C2

259251
type: LocalParameter
units: 182067
value: 3.3E-11

259250
type: LocalParameter
units: 182151
value: 5.4E-11

182247
type: SpeciesReference
stoichiometry: 1.0
species: 899077

182235
type: SpeciesReference
stoichiometry: 1.0
species: 899197

182223
type: SpeciesReference
stoichiometry: 1.0
species: 899017

898982
type: Compartment
constant: true
size: 1.0E-18
spatial dimensions: 3.0

899656
type: Reaction
product: 182709
reactant: 182697
notes: This step combines several stages in GTP.Galpha release. From Berstein et al activation is at .35 - 0.7/min From Fay et al Biochem 30 5066-5075 1991 kf = .01/sec. From Brandt and Ross JBC 261(4):1656-1664 (1986) and Ransan et al Biochem J 283(2):519-524 (1992) rates around 2.5/min to 1.5/min are better.
product: 182721
reversible: true
fast: false
kinetic law: 182746
product: 182734

182709
type: SpeciesReference
stoichiometry: 1.0
species: 899497

182697
type: SpeciesReference
stoichiometry: 1.0
species: 899457

182721
type: SpeciesReference
stoichiometry: 1.0
species: 899417

182746
type: KineticLaw
local parameters: 259271
local parameters: 259270
notes: kf*Gs_slash_L_dot_R_dot_GDP_dot_Gabc-kb*Gs_slash_Gbg*Gs_slash_L_dot_R*GTP_dot_Ga

259271
type: LocalParameter
units: 182103
value: 0.0

259270
type: LocalParameter
units: 182067
value: 2.5E-14

182734
type: SpeciesReference
stoichiometry: 1.0
species: 899377