MODEL9080388197
type: SBMLModel
species: 942773
name: Bhalla2004_PKC_2003
species: 942793
time units: 131570
species: 942713
species: 942832
reaction: 942893
curated: false
reaction: 942952
units def: 210366
notes: This model consists of receptor-ligand interaction, G-protein activation, Adenylyl cyclase mediated formation of cAMP and activation of PKA in the neuron. Demonstration programs using this model described in Bhalla US. (2004) Biophys J. 87(2):733-44 to generate a dose-response curve using stochastic calculations are available href=http://www.ncbs.res.in/~bhalla/stochpath/demos.html>here. 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.
substance units: 210451
compartment: 942653
units def: 210451
area units: area
species: 942772
is described by: http://identifiers.org/pubmed/15298882
species: 942833
species: 942733
reaction: 942953
reaction: 942873
reaction: 942932
species: 942693
species: 942813
species: 942812
reaction: 942912
units def: 210403
species: 942673
reaction: 942892
rule: 942872
species: 942753
reaction: 942972
species: 942853
length unit: length
reaction: 942933
species: 942852
volume units: 679943
compartment: 942640
species: 942752
reaction: 942913

942773
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 8.46316666666667E-23
initial amount: NaN
in compartment: 942653

942653
type: Compartment
constant: true
size: 1.0E-12
spatial dimensions: 3.0

942793
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.16101666666667E-16
initial amount: NaN
in compartment: 942653

942713
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.75E-16
initial amount: NaN
in compartment: 942653

942832
type: Species
notes: The conc of this has been a problem. Schaecter and Benowitz use 50 uM, but Shinomura et al have < 5. So I have altered the DAG-dependent rates in the PKC model to this.
constant: true
boundary condition: true
has only substance units: false
initial concentration: 11.0
initial amount: NaN
in compartment: 942653

942893
type: Reaction
kinetic law: 210598
product: 210585
reactant: 210573
fast: false
reversible: true

210598
type: KineticLaw
local parameters: 389596
local parameters: 389595
notes: kf*PKC_slash_PKC_minus_Ca-kb*PKC_slash_PKC_minus_Ca_minus_memb_star_

389596
type: LocalParameter
units: 210366
value: 3.5026E-12

210390
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

210378
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

389595
type: LocalParameter
units: 210366
value: 1.2705E-12

210585
type: SpeciesReference
stoichiometry: 1.0
species: 942733

942733
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.3896E-17
initial amount: NaN
in compartment: 942653

210573
type: SpeciesReference
stoichiometry: 1.0
species: 942673

942673
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 3.72083333333333E-17
initial amount: NaN
in compartment: 942653

942952
type: Reaction
kinetic law: 210814
product: 210802
reactant: 210790
reactant: 210777
notes: Raise kf from 1.667e-10 to 2e-10 to get better match data.
fast: false
reversible: true

210814
type: KineticLaw
local parameters: 389606
local parameters: 389605
notes: kf*AA*PKC_slash_PKC_minus_cytosolic-kb*PKC_slash_PKC_minus_AA_star_

389606
type: LocalParameter
units: 210366
value: 1.0E-13

389605
type: LocalParameter
units: 210403
value: 1.2E-16

210439
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

210427
type: SBMLUnit
exponent: -1.0
scale: -6
multipler: 1.0
kind: MOLE

210415
type: SBMLUnit
exponent: 2.0
scale: 0
multipler: 1.0
kind: LITRE

210802
type: SpeciesReference
stoichiometry: 1.0
species: 942772

942772
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.81333333333333E-17
initial amount: NaN
in compartment: 942653

210790
type: SpeciesReference
stoichiometry: 1.0
species: 942813

942813
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: 942653

210777
type: SpeciesReference
stoichiometry: 1.0
species: 942852

942852
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: 5.0
initial amount: NaN
in compartment: 942653

210463
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

942833
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.08
initial amount: NaN
in compartment: 942653

942953
type: Reaction
kinetic law: 210862
product: 210850
reactant: 210838
reactant: 210826
notes: kf raised 10 X based on Shinomura et al PNAS 88 5149-5153 1991 closer analysis of Shinomura et al: kf now 1e-8 (was 1.66e-8). Further tweak. To get sufficient AA synergy, increase kf to 1.5e-8 26 June 1996: Corrected DAG levels: reduce kf by 15x from 1.5e-8 1e-9
fast: false
reversible: true

210862
type: KineticLaw
local parameters: 389608
local parameters: 389607
notes: kf*PKC_slash_PKC_minus_cytosolic*DAG-kb*PKC_slash_PKC_minus_DAG

389608
type: LocalParameter
units: 210366
value: 1.0E-13

389607
type: LocalParameter
units: 210403
value: 6.0E-16

210850
type: SpeciesReference
stoichiometry: 1.0
species: 942793

210838
type: SpeciesReference
stoichiometry: 1.0
species: 942832

210826
type: SpeciesReference
stoichiometry: 1.0
species: 942813

942873
type: Reaction
kinetic law: 210512
product: 210500
reactant: 210488
reactant: 210476
notes: Need est of rate of assoc of Ca and PKC. Assume it is fast The original parameter-searched kf of 439.4 has been scaled by 1/6e8 to account for change of units to n. Kf now 8.16e-7, kb=.6085 Raised kf to 1e-6 to match Ca curve, kb to .5
fast: false
reversible: true

210512
type: KineticLaw
local parameters: 389592
local parameters: 389591
notes: kf*PKC_slash_PKC_minus_cytosolic*Ca-kb*PKC_slash_PKC_minus_Ca

389592
type: LocalParameter
units: 210366
value: 5.0E-13

389591
type: LocalParameter
units: 210403
value: 6.0E-13

210500
type: SpeciesReference
stoichiometry: 1.0
species: 942673

210488
type: SpeciesReference
stoichiometry: 1.0
species: 942833

210476
type: SpeciesReference
stoichiometry: 1.0
species: 942813

942932
type: Reaction
kinetic law: 210728
product: 210716
reactant: 210704
notes: Assume slowish too. Schaechter Benowitz
fast: false
reversible: true

210728
type: KineticLaw
local parameters: 389602
local parameters: 389601
notes: kf*PKC_slash_PKC_minus_DAG_minus_AA-kb*PKC_slash_PKC_minus_DAG_minus_AA_star_

389602
type: LocalParameter
units: 210366
value: 2.0E-13

389601
type: LocalParameter
units: 210366
value: 2.0E-12

210716
type: SpeciesReference
stoichiometry: 1.0
species: 942693

942693
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 4.91366666666667E-18
initial amount: NaN
in compartment: 942653

210704
type: SpeciesReference
stoichiometry: 1.0
species: 942812

942812
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.51883333333333E-19
initial amount: NaN
in compartment: 942653

942912
type: Reaction
kinetic law: 210639
product: 210625
reactant: 210611
notes: Raise kb from .087 to 0.1 to match data from Shinomura et al. Lower kf from 1.155 to 1.0 to match data from Shinomura al.
fast: false
reversible: true

210639
type: KineticLaw
local parameters: 389598
local parameters: 389597
notes: kf*PKC_slash_PKC_minus_Ca_minus_DAG-kb*PKC_slash_PKC_minus_DAG_minus_memb_star_

389598
type: LocalParameter
units: 210366
value: 1.0E-13

389597
type: LocalParameter
units: 210366
value: 1.0E-12

210625
type: SpeciesReference
stoichiometry: 1.0
species: 942752

942752
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 9.43516666666667E-21
initial amount: NaN
in compartment: 942653

210611
type: SpeciesReference
stoichiometry: 1.0
species: 942773

942892
type: Reaction
kinetic law: 210560
product: 210548
reactant: 210536
reactant: 210524
notes: Need est of rate. Assume it is fast Obtained from param search kf raised 10 X : see Shinomura et al PNAS 88 5149-5153 1991. kf changed from 3.865e-7 to 2.0e-7 in line with closer analysis of Shinomura data. 26 June 1996: Corrected DAG data: reduce kf 15x from 2e-7 1.333e-8
fast: false
reversible: true

210560
type: KineticLaw
local parameters: 389594
local parameters: 389593
notes: kf*DAG*PKC_slash_PKC_minus_Ca-kb*PKC_slash_PKC_minus_Ca_minus_DAG

389594
type: LocalParameter
units: 210366
value: 8.6348E-12

389593
type: LocalParameter
units: 210403
value: 7.9998E-15

210548
type: SpeciesReference
stoichiometry: 1.0
species: 942773

210536
type: SpeciesReference
stoichiometry: 1.0
species: 942673

210524
type: SpeciesReference
stoichiometry: 1.0
species: 942832

942753
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.02
initial amount: NaN
in compartment: 942653

942972
type: Reaction
kinetic law: 210910
product: 210898
reactant: 210886
reactant: 210874
notes: Reduced kf to 0.66X to match Shinomura et al data. Initial: kf = 3.3333e-9 New: 2e-9 Newer: 2e-8 kb was 0.2 2.
fast: false
reversible: true

210910
type: KineticLaw
local parameters: 389610
local parameters: 389609
notes: kf*PKC_slash_PKC_minus_DAG*AA-kb*PKC_slash_PKC_minus_DAG_minus_AA

389610
type: LocalParameter
units: 210366
value: 2.0E-12

389609
type: LocalParameter
units: 210403
value: 1.8E-14

210898
type: SpeciesReference
stoichiometry: 1.0
species: 942812

210886
type: SpeciesReference
stoichiometry: 1.0
species: 942852

210874
type: SpeciesReference
stoichiometry: 1.0
species: 942793

942853
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.12216666666667E-16
initial amount: NaN
in compartment: 942653

942933
type: Reaction
kinetic law: 210765
product: 210753
reactant: 210740
notes: Initial basal levels were set by kf = 1, kb = 20. In model, though, the basal levels of PKC activity higher.
fast: false
reversible: true

210765
type: KineticLaw
local parameters: 389604
local parameters: 389603
notes: kf*PKC_slash_PKC_minus_cytosolic-kb*PKC_slash_PKC_minus_basal_star_

389604
type: LocalParameter
units: 210366
value: 5.0E-11

389603
type: LocalParameter
units: 210366
value: 1.0E-12

210753
type: SpeciesReference
stoichiometry: 1.0
species: 942753

210740
type: SpeciesReference
stoichiometry: 1.0
species: 942813

942640
type: Compartment
constant: true
size: 1.0E-18
spatial dimensions: 3.0

942913
type: Reaction
kinetic law: 210691
product: 210678
reactant: 210665
reactant: 210652
notes: Schaechter and Benowitz We have to increase Kf for conc scaling Changed kf to 2e-9 on Sept 19, 94. This gives better match.
fast: false
reversible: true

210691
type: KineticLaw
local parameters: 389600
local parameters: 389599
notes: kf*PKC_slash_PKC_minus_Ca*AA-kb*PKC_slash_PKC_minus_Ca_minus_AA_star_

389600
type: LocalParameter
units: 210366
value: 1.0E-13

389599
type: LocalParameter
units: 210403
value: 1.2E-15

210678
type: SpeciesReference
stoichiometry: 1.0
species: 942713

210665
type: SpeciesReference
stoichiometry: 1.0
species: 942852

210652
type: SpeciesReference
stoichiometry: 1.0
species: 942673