MODEL4780181279
type: SBMLModel
reaction: 201722
units def: metaid_0000034
species: 201422
reaction: 201861
reaction: 201782
creator:
  ORG:
    orgname: DOQCS
  n:
    given: Sharat
    family: Vayttaden
reaction: 201822
reaction: 201842
modified:
  W3 CDTF: Thu Oct 08 12:52:05 BST 2009
species: 201402
notes: This model of sGC is based on the paper byKuroda S. et al. J Neurosci. (2001) 21(15):5693-702 . This models features the activation of sGC by NO, synthesis of cGMP, activity of PKG and PP2A in the synapse. The rates and concentrations have been taken from literature. It contains only the part described in figure 1B of the article. This model originates from BioModels Database: A Database of Annotated Published Models. 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: 201582
compartment: 201324
length unit: length
species: 201522
time units: 013121
creator:
  ORG:
    orgname: DOQCS
  n:
    given: Sharat
    family: Vayttaden
created:
  W3 CDTF: Wed Sep 10 10:51:47 BST 2008
modified:
  W3 CDTF: Thu Oct 08 12:52:05 BST 2009
species: 201442
substance units: metaid_0000034
reaction: 201682
species: 201662
species: 201562
units def: metaid_0000033
curated: false
species: 201502
reaction: 201742
area units: area
reaction: 201762
species: 201342
species: 201642
reaction: 201802
species: 201542
reaction: 201702
name: Kuroda2001_NO_cGMP_Pathway
volume units: metaid_0000217
modified:
  W3 CDTF: Thu Oct 08 12:52:05 BST 2009
creator:
  ORG:
    orgname: DOQCS
  n:
    given: Sharat
    family: Vayttaden
units def: metaid_0000032
is described by: http://identifiers.org/pubmed/11466441
species: 201622
species: 201462
species: 201362
species: 201602
species: 201482
reaction: 201862
species: 201382

201722
type: Reaction
kinetic law: 063566
product: 063554
reactant: 063542
reactant: 063530
notes: Kd - 0.05uM Shinya Kuroda, 2001, 21(15):5693-5702.
fast: false
reversible: true

063566
type: KineticLaw
local parameters: 106497
local parameters: 106496
notes: kf*cGMP*PKG-kb*cGMP_dot_PKG

106497
type: LocalParameter
units: metaid_0000032
value: 8.33333333333333E-19

063385
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

063373
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

106496
type: LocalParameter
units: metaid_0000033
value: 1.66666666666667E-17

063422
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

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

063397
type: SBMLUnit
exponent: 2.0
scale: 0
multipler: 1.0
kind: LITRE

063554
type: SpeciesReference
stoichiometry: 1.0
species: 201522

201522
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 201324

201324
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0

063542
type: SpeciesReference
stoichiometry: 1.0
species: 201502

201502
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.5
initial amount: NaN
in compartment: 201324

063530
type: SpeciesReference
stoichiometry: 1.0
species: 201442

201442
type: Species
constant: false
boundary condition: false
has only substance units: false
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initial amount: NaN
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063434
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

201422
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 10.0
initial amount: NaN
in compartment: 201324

201861
type: Reaction
kinetic law: 063892
product: 063880
reactant: 063867
reactant: 063855
notes: Km - 0.2 Vmax - 0.72 Shinya Kuroda, J.Neurosci, 2001, 21(15):5693-5702
fast: false
reversible: true

063892
type: KineticLaw
local parameters: 106514
local parameters: 106512
notes: k1*Gsub*cGMP_dot_PKG-k2*cGMP_dot_PKG_slash_kenz_slash_kenz_cplx

106514
type: LocalParameter
units: metaid_0000032
value: 4.8E-18

106512
type: LocalParameter
units: metaid_0000033
value: 3.0E-17

063880
type: SpeciesReference
stoichiometry: 1.0
species: 201542

201542
type: Species
constant: false
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initial concentration: 0.0
initial amount: NaN
in compartment: 201324

063867
type: SpeciesReference
stoichiometry: 1.0
species: 201522

063855
type: SpeciesReference
stoichiometry: 1.0
species: 201562

201562
type: Species
constant: false
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initial concentration: 10.7
initial amount: NaN
in compartment: 201324

201782
type: Reaction
kinetic law: 063698
product: 063686
reactant: 063674
reactant: 063662
notes: Km - 45 Vamx - 7.35 Shinya Kuroda, J.Neurosci, 2001, 21(15):5693-5702.
fast: false
reversible: true

063698
type: KineticLaw
local parameters: 106506
local parameters: 106505
notes: k1*GTP*NO_GC-k2*NO_GC_slash_kenz_slash_kenz_cplx

106506
type: LocalParameter
units: metaid_0000032
value: 4.9E-17

106505
type: LocalParameter
units: metaid_0000033
value: 1.36111666666667E-18

063686
type: SpeciesReference
stoichiometry: 1.0
species: 201382

201382
type: Species
constant: false
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initial amount: NaN
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063674
type: SpeciesReference
stoichiometry: 1.0
species: 201362

201362
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 201324

063662
type: SpeciesReference
stoichiometry: 1.0
species: 201422

201822
type: Reaction
kinetic law: 063794
product: 063782
reactant: 063770
reactant: 063758
notes: Km - 2 Vmax - 3.87 Thru personal Correspondence with Shinya Kuroda... rates initially from Turko et al., 1998, Biochem J, 329, 505-510
fast: false
reversible: true

063794
type: KineticLaw
local parameters: 106509
local parameters: 106508
notes: k1*cGMP*PDE-k2*PDE_slash_kenz_slash_kenz_cplx

106509
type: LocalParameter
units: metaid_0000032
value: 2.58E-17

106508
type: LocalParameter
units: metaid_0000033
value: 1.6125E-17

063782
type: SpeciesReference
stoichiometry: 1.0
species: 201482

201482
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 201324

063770
type: SpeciesReference
stoichiometry: 1.0
species: 201462

201462
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 5.0
initial amount: NaN
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063758
type: SpeciesReference
stoichiometry: 1.0
species: 201442

201842
type: Reaction
kinetic law: 063843
product: 063831
product: 063819
reactant: 063806
fast: false
reversible: false

063843
type: KineticLaw
local parameters: 106510
notes: k3*PDE_slash_kenz_slash_kenz_cplx

106510
type: LocalParameter
units: metaid_0000032
value: 6.45E-18

063831
type: SpeciesReference
stoichiometry: 1.0
species: 201462

063819
type: SpeciesReference
stoichiometry: 1.0
species: 201642

201642
type: Species
constant: false
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initial amount: NaN
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063806
type: SpeciesReference
stoichiometry: 1.0
species: 201482

201402
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 201324

201582
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 201324

201682
type: Reaction
kinetic law: 063482
product: 063470
reactant: 063458
reactant: 063446
notes: Kd 250 nM (Stone and Marletta, 1996).. kf - 0.01 kb - 0.0025 Shinya Kuroda, J.Neurosci, 2001, ...
fast: false
reversible: true

063482
type: KineticLaw
local parameters: 106493
local parameters: 106492
notes: kf*NO*GC-kb*NO_GC

106493
type: LocalParameter
units: metaid_0000032
value: 4.16666666666667E-21

106492
type: LocalParameter
units: metaid_0000033
value: 1.66666666666667E-20

063470
type: SpeciesReference
stoichiometry: 1.0
species: 201362

063458
type: SpeciesReference
stoichiometry: 1.0
species: 201662

201662
type: Species
notes: Guanylyl Cyclase ... Intracellular concentration is around 3 uM, as sGC is enrcihed in the Purkinje cells (Shinya Kuroda, personal corresspondence).. Conc assumed on the basis of reported data in Ariano et al., PNAS,79:297-300.
constant: true
boundary condition: true
has only substance units: false
initial concentration: 3.0
initial amount: NaN
in compartment: 201324

063446
type: SpeciesReference
stoichiometry: 1.0
species: 201342

201342
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.1
initial amount: NaN
in compartment: 201324

201742
type: Reaction
kinetic law: 063614
product: 063602
reactant: 063590
reactant: 063578
notes: Kd - 0.27 uM Shinya Kuroda, J.Neurosci, 21(15):5693-5702.
fast: false
reversible: true

063614
type: KineticLaw
local parameters: 106501
local parameters: 106499
notes: kf*PP2A*Gsub_star_-kb*PP2A_Gsub_star_

106501
type: LocalParameter
units: metaid_0000032
value: 4.5E-19

106499
type: LocalParameter
units: metaid_0000033
value: 1.66666666666667E-18

063602
type: SpeciesReference
stoichiometry: 1.0
species: 201622

201622
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 201324

063590
type: SpeciesReference
stoichiometry: 1.0
species: 201582

063578
type: SpeciesReference
stoichiometry: 1.0
species: 201602

201602
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.7
initial amount: NaN
in compartment: 201324

201762
type: Reaction
kinetic law: 063650
product: 063638
reactant: 063626
notes: kf - 0.0001/sec Shinya Kuroda, J.Neurosci, 2001, 21(15):5693-5702 ... and thru personal ...
fast: false
reversible: true

063650
type: KineticLaw
local parameters: 106504
local parameters: 106503
notes: kf*Gsub_star_-kb*Gsub

106504
type: LocalParameter
units: metaid_0000032
value: 0.0

106503
type: LocalParameter
units: metaid_0000032
value: 1.66666666666667E-22

063638
type: SpeciesReference
stoichiometry: 1.0
species: 201562

063626
type: SpeciesReference
stoichiometry: 1.0
species: 201582

201802
type: Reaction
kinetic law: 063746
product: 063734
product: 063722
reactant: 063710
fast: false
reversible: false

063746
type: KineticLaw
local parameters: 106507
notes: k3*NO_GC_slash_kenz_slash_kenz_cplx

106507
type: LocalParameter
units: metaid_0000032
value: 1.225E-17

063734
type: SpeciesReference
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species: 201362

063722
type: SpeciesReference
stoichiometry: 1.0
species: 201442

063710
type: SpeciesReference
stoichiometry: 1.0
species: 201382

201702
type: Reaction
kinetic law: 063518
product: 063506
reactant: 063494
notes: degradation of NO ... kf - 0.673 / sec .... Shinya Kuroda, J.Neurosci, 2001, 21(15):5693-5702
fast: false
reversible: true

063518
type: KineticLaw
local parameters: 106495
local parameters: 106494
notes: kf*NO-kb*NOdegrade

106495
type: LocalParameter
units: metaid_0000032
value: 0.0

106494
type: LocalParameter
units: metaid_0000032
value: 1.12166666666667E-18

063506
type: SpeciesReference
stoichiometry: 1.0
species: 201402

063494
type: SpeciesReference
stoichiometry: 1.0
species: 201342

201862
type: Reaction
kinetic law: 063941
product: 063929
product: 063917
reactant: 063904
fast: false
reversible: false

063941
type: KineticLaw
local parameters: 106516
notes: k3*cGMP_dot_PKG_slash_kenz_slash_kenz_cplx

106516
type: LocalParameter
units: metaid_0000032
value: 1.2E-18

063929
type: SpeciesReference
stoichiometry: 1.0
species: 201522

063917
type: SpeciesReference
stoichiometry: 1.0
species: 201582

063904
type: SpeciesReference
stoichiometry: 1.0
species: 201542