210898
stoichiometry: 1.0
species: 942812
type: SpeciesReference

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

942953
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
type: Reaction

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

210573
stoichiometry: 1.0
species: 942673
type: SpeciesReference

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

210826
stoichiometry: 1.0
species: 942813
type: SpeciesReference

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

210488
stoichiometry: 1.0
species: 942833
type: SpeciesReference

210740
stoichiometry: 1.0
species: 942813
type: SpeciesReference

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

210652
stoichiometry: 1.0
species: 942673
type: SpeciesReference

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

942933
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
type: Reaction

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

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

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

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

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

210665
stoichiometry: 1.0
species: 942852
type: SpeciesReference

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

210802
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species: 942772
type: SpeciesReference

210704
stoichiometry: 1.0
species: 942812
type: SpeciesReference

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

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

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

210548
stoichiometry: 1.0
species: 942773
type: SpeciesReference

210874
stoichiometry: 1.0
species: 942793
type: SpeciesReference

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

942912
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
type: Reaction

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

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

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

210524
stoichiometry: 1.0
species: 942832
type: SpeciesReference

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

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

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

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

210790
stoichiometry: 1.0
species: 942813
type: SpeciesReference

210886
stoichiometry: 1.0
species: 942852
type: SpeciesReference

MODEL9080388197
species: 942773
name: Bhalla2004_PKC_2003
species: 942793
time units: 131570
species: 942713
species: 942832
reaction: 942893
curated: false
area units: area
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
species: 942772
is described by: http://identifiers.org/pubmed/15298882
species: 942833
species: 942733
reaction: 942953
reaction: 942873
reaction: 942932
length unit: length
species: 942693
species: 942813
species: 942812
reaction: 942912
units def: 210403
species: 942673
reaction: 942892
type: SBMLModel
rule: 942872
species: 942753
reaction: 942972
species: 942853
reaction: 942933
species: 942852
volume units: 679943
compartment: 942640
species: 942752
reaction: 942913

942972
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
type: Reaction

942892
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
type: Reaction

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

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

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

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

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

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

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

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

210585
stoichiometry: 1.0
species: 942733
type: SpeciesReference

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

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

942913
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
type: Reaction

210838
stoichiometry: 1.0
species: 942832
type: SpeciesReference

210476
stoichiometry: 1.0
species: 942813
type: SpeciesReference

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

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

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

210850
stoichiometry: 1.0
species: 942793
type: SpeciesReference

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

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

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

942952
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
type: Reaction

210777
stoichiometry: 1.0
species: 942852
type: SpeciesReference

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

210625
stoichiometry: 1.0
species: 942752
type: SpeciesReference

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

210536
stoichiometry: 1.0
species: 942673
type: SpeciesReference

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

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

942873
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
type: Reaction

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

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

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

210500
stoichiometry: 1.0
species: 942673
type: SpeciesReference

210753
stoichiometry: 1.0
species: 942753
type: SpeciesReference

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

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

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

942832
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
type: Species

210678
stoichiometry: 1.0
species: 942713
type: SpeciesReference

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

210611
stoichiometry: 1.0
species: 942773
type: SpeciesReference

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

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

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

210716
stoichiometry: 1.0
species: 942693
type: SpeciesReference

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