MODEL9086628127
type: SBMLModel
compartment: 698533
species: 698732
species: 698712
reaction: 698873
species: 698673
species: 698653
reaction: 698933
reaction: 698813
reaction: 699013
area units: area
reaction: 698932
reaction: 698852
species: 698793
time units: 131570
compartment: 698553
notes: This is a highly simplified model of the AMPAR trafficking cycle that exhibits bistability. It is model 2 from Hayer and Bhalla, PLoS 2005. Its main purpose it to illustrate how the bistability arises. 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.
reaction: 698833
reaction: 698872
reaction: 698952
species: 698633
units def: 310966
reaction: 699012
compartment: 698499
species: 698733
species: 698713
species: 698693
units def: 310918
is described by: http://identifiers.org/pubmed/16110334
reaction: 698853
species: 698772
length unit: length
curated: false
species: 698613
units def: 310882
reaction: 698832
reaction: 698972
reaction: 698992
species: 698773
species: 698753
name: Hayer2005_simple_AMPAR_traff_model2
reaction: 698812
reaction: 698892
species: 698792
substance units: 310966
compartment: 698513
volume units: 679943
reaction: 698912
species: 698593
species: 698573

698533
type: Compartment
constant: true
size: 9.0E-17
spatial dimensions: 3.0

698732
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698533

698712
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698533

698873
type: Reaction
kinetic law: 311331
product: 311319
reactant: 311307
reactant: 311295
notes: Note halving of Km from 2 to 1. See also notes for internal-PKA-act. Basically, the enzyme must act on two substrate subunits which are lumped in the current simplification of the original detailed model. We thank an anonymous reviewer for pointing this out.
fast: false
reversible: true

311331
type: KineticLaw
local parameters: 178632
local parameters: 178630
notes: k1*Membrane_slash_MR_star__star_*Membrane_slash_PP1_minus_active-k2*Membrane_slash_PP1_minus_active_slash_PP1_sbo_1_sbc__slash_PP1_sbo_1_sbc__cplx

178632
type: LocalParameter
units: 310882
value: 1.4E-17

310906
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

310894
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

178630
type: LocalParameter
units: 310918
value: 1.75002E-17

310954
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

310942
type: SBMLUnit
exponent: -1.0
scale: -6
multipler: 1.0
kind: MOLE

310930
type: SBMLUnit
exponent: 2.0
scale: 0
multipler: 1.0
kind: LITRE

311319
type: SpeciesReference
stoichiometry: 1.0
species: 698613

698613
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698553

698553
type: Compartment
constant: true
size: 1.0E-17
spatial dimensions: 3.0

311307
type: SpeciesReference
stoichiometry: 1.0
species: 698573

698573
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.333333333333333
initial amount: NaN
in compartment: 698553

311295
type: SpeciesReference
stoichiometry: 1.0
species: 698673

698673
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698553

698653
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698553

698933
type: Reaction
kinetic law: 311533
product: 311521
reactant: 311509
reactant: 311497
notes: Note that Km is halved from the main model, from 7.5 to 3.75. This is because here we lump two subunits into one, thus double the effective substrate conc that the enzyme must deal with. We thank an anonymous reviewer for pointing this out.
fast: false
reversible: true

311533
type: KineticLaw
local parameters: 178639
local parameters: 178638
notes: k1*Internal_slash_IR*PKA_minus_active-k2*PKA_minus_active_slash_internal_minus_PKA_minus_act_slash_internal_minus_PKA_minus_act_cplx

178639
type: LocalParameter
units: 310882
value: 2.16E-15

178638
type: LocalParameter
units: 310918
value: 7.20009E-16

311521
type: SpeciesReference
stoichiometry: 1.0
species: 698733

698733
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698533

311509
type: SpeciesReference
stoichiometry: 1.0
species: 698792

698792
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0185185185185185
initial amount: NaN
in compartment: 698533

311497
type: SpeciesReference
stoichiometry: 1.0
species: 698712

698813
type: Reaction
kinetic law: 311074
product: 311062
product: 311050
reactant: 311038
fast: false
reversible: true

311074
type: KineticLaw
local parameters: 178619
local parameters: 178618
notes: kf*Membrane_slash_MR-kb*Anchor*Internal_slash_IR

178619
type: LocalParameter
units: 310918
value: 0.0

178618
type: LocalParameter
units: 310882
value: 8.0E-21

311062
type: SpeciesReference
stoichiometry: 1.0
species: 698712

311050
type: SpeciesReference
stoichiometry: 1.0
species: 698773

698773
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 27.3333333333333
initial amount: NaN
in compartment: 698553

311038
type: SpeciesReference
stoichiometry: 1.0
species: 698653

699013
type: Reaction
kinetic law: 311776
product: 311764
product: 311752
reactant: 311740
fast: false
reversible: false

311776
type: KineticLaw
local parameters: 178649
notes: k3*PKA_minus_active_slash_internal_minus_PKA_minus_act_sbo_1_sbc__slash_internal_minus_PKA_minus_act_sbo_1_sbc__cplx

178649
type: LocalParameter
units: 310882
value: 5.4E-16

311764
type: SpeciesReference
stoichiometry: 1.0
species: 698792

311752
type: SpeciesReference
stoichiometry: 1.0
species: 698693

698693
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698533

311740
type: SpeciesReference
stoichiometry: 1.0
species: 698772

698772
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698533

698932
type: Reaction
kinetic law: 311484
product: 311471
product: 311459
reactant: 311447
fast: false
reversible: false

311484
type: KineticLaw
local parameters: 178637
notes: k3*PKA_minus_active_slash_memb_minus_PKA_minus_act_slash_memb_minus_PKA_minus_act_cplx

178637
type: LocalParameter
units: 310882
value: 5.4E-16

311471
type: SpeciesReference
stoichiometry: 1.0
species: 698792

311459
type: SpeciesReference
stoichiometry: 1.0
species: 698633

698633
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698553

311447
type: SpeciesReference
stoichiometry: 1.0
species: 698732

698852
type: Reaction
kinetic law: 311185
product: 311173
reactant: 311161
fast: false
reversible: true

311185
type: KineticLaw
local parameters: 178625
local parameters: 178624
notes: kf*Internal_slash_IR_star_-kb*Bulk_AMPAR

178625
type: LocalParameter
units: 310882
value: 0.0

178624
type: LocalParameter
units: 310882
value: 1.8E-21

311173
type: SpeciesReference
stoichiometry: 1.0
species: 698793

698793
type: Species
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.003
initial amount: NaN
in compartment: 698513

698513
type: Compartment
constant: true
size: 5.0E-15
spatial dimensions: 3.0

311161
type: SpeciesReference
stoichiometry: 1.0
species: 698713

698713
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698533

698833
type: Reaction
kinetic law: 311149
product: 311137
reactant: 311124
fast: false
reversible: true

311149
type: KineticLaw
local parameters: 178623
local parameters: 178622
notes: kf*Internal_slash_IR_star__star_-kb*Bulk_AMPAR

178623
type: LocalParameter
units: 310882
value: 0.0

178622
type: LocalParameter
units: 310882
value: 1.8E-21

311137
type: SpeciesReference
stoichiometry: 1.0
species: 698793

311124
type: SpeciesReference
stoichiometry: 1.0
species: 698693

698872
type: Reaction
kinetic law: 311283
product: 311271
product: 311259
reactant: 311247
fast: false
reversible: false

311283
type: KineticLaw
local parameters: 178628
notes: k3*Membrane_slash_PP1_minus_active_slash_PP1_slash_PP1_cplx

178628
type: LocalParameter
units: 310882
value: 3.5E-18

311271
type: SpeciesReference
stoichiometry: 1.0
species: 698573

311259
type: SpeciesReference
stoichiometry: 1.0
species: 698653

311247
type: SpeciesReference
stoichiometry: 1.0
species: 698593

698593
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698553

698952
type: Reaction
kinetic law: 311581
product: 311569
product: 311557
reactant: 311545
fast: false
reversible: false

311581
type: KineticLaw
local parameters: 178640
notes: k3*PKA_minus_active_slash_internal_minus_PKA_minus_act_slash_internal_minus_PKA_minus_act_cplx

178640
type: LocalParameter
units: 310882
value: 5.4E-16

311569
type: SpeciesReference
stoichiometry: 1.0
species: 698792

311557
type: SpeciesReference
stoichiometry: 1.0
species: 698713

311545
type: SpeciesReference
stoichiometry: 1.0
species: 698733

310978
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

699012
type: Reaction
kinetic law: 311728
product: 311716
reactant: 311703
reactant: 311691
notes: Note that Km is halved from the detailed model, as the reaction represents enzyme activity on 2 subunits.
fast: false
reversible: true

311728
type: KineticLaw
local parameters: 178648
local parameters: 178647
notes: k1*Internal_slash_IR_star_*PKA_minus_active-k2*PKA_minus_active_slash_internal_minus_PKA_minus_act_sbo_1_sbc__slash_internal_minus_PKA_minus_act_sbo_1_sbc__cplx

178648
type: LocalParameter
units: 310882
value: 2.16E-15

178647
type: LocalParameter
units: 310918
value: 7.20009E-16

311716
type: SpeciesReference
stoichiometry: 1.0
species: 698772

311703
type: SpeciesReference
stoichiometry: 1.0
species: 698792

311691
type: SpeciesReference
stoichiometry: 1.0
species: 698713

698499
type: Compartment
constant: true
size: 1.0E-18
spatial dimensions: 3.0

698853
type: Reaction
kinetic law: 311234
product: 311222
reactant: 311209
reactant: 311197
notes: Note that Km is halved from 2 to 1, as compared to original detailed model. This is because each substrate represents two subunits of the original detailed model.
fast: false
reversible: true

311234
type: KineticLaw
local parameters: 178627
local parameters: 178626
notes: k1*Membrane_slash_MR_star_*Membrane_slash_PP1_minus_active-k2*Membrane_slash_PP1_minus_active_slash_PP1_slash_PP1_cplx

178627
type: LocalParameter
units: 310882
value: 1.4E-17

178626
type: LocalParameter
units: 310918
value: 1.75002E-17

311222
type: SpeciesReference
stoichiometry: 1.0
species: 698593

311209
type: SpeciesReference
stoichiometry: 1.0
species: 698573

311197
type: SpeciesReference
stoichiometry: 1.0
species: 698633

698832
type: Reaction
kinetic law: 311111
product: 311098
reactant: 311086
fast: false
reversible: true

311111
type: KineticLaw
local parameters: 178621
local parameters: 178620
notes: kf*Bulk_AMPAR-kb*Internal_slash_IR

178621
type: LocalParameter
units: 310882
value: 9.0E-17

178620
type: LocalParameter
units: 310882
value: 9.0E-17

311098
type: SpeciesReference
stoichiometry: 1.0
species: 698712

311086
type: SpeciesReference
stoichiometry: 1.0
species: 698793

698972
type: Reaction
kinetic law: 311630
product: 311617
reactant: 311605
reactant: 311593
notes: Note halving of Km. See notes for internal-PKA-act enzyme step.
fast: false
reversible: true

311630
type: KineticLaw
local parameters: 178644
local parameters: 178642
notes: k1*Membrane_slash_MR_star_*PKA_minus_active-k2*PKA_minus_active_slash_memb_minus_PKA_minus_act_sbo_1_sbc__slash_memb_minus_PKA_minus_act_sbo_1_sbc__cplx

178644
type: LocalParameter
units: 310882
value: 2.16E-15

178642
type: LocalParameter
units: 310918
value: 8.0001E-17

311617
type: SpeciesReference
stoichiometry: 1.0
species: 698753

698753
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 698533

311605
type: SpeciesReference
stoichiometry: 1.0
species: 698792

311593
type: SpeciesReference
stoichiometry: 1.0
species: 698633

698992
type: Reaction
kinetic law: 311679
product: 311667
product: 311654
reactant: 311642
fast: false
reversible: false

311679
type: KineticLaw
local parameters: 178646
notes: k3*PKA_minus_active_slash_memb_minus_PKA_minus_act_sbo_1_sbc__slash_memb_minus_PKA_minus_act_sbo_1_sbc__cplx

178646
type: LocalParameter
units: 310882
value: 5.4E-16

311667
type: SpeciesReference
stoichiometry: 1.0
species: 698792

311654
type: SpeciesReference
stoichiometry: 1.0
species: 698673

311642
type: SpeciesReference
stoichiometry: 1.0
species: 698753

698812
type: Reaction
kinetic law: 311026
product: 311014
reactant: 311002
reactant: 310990
fast: false
reversible: true

311026
type: KineticLaw
local parameters: 178617
local parameters: 178616
notes: kf*Anchor*Internal_slash_IR_star__star_-kb*Membrane_slash_MR_star__star_

178617
type: LocalParameter
units: 310882
value: 8.0E-20

178616
type: LocalParameter
units: 310918
value: 1.08E-19

311014
type: SpeciesReference
stoichiometry: 1.0
species: 698673

311002
type: SpeciesReference
stoichiometry: 1.0
species: 698693

310990
type: SpeciesReference
stoichiometry: 1.0
species: 698773

698892
type: Reaction
kinetic law: 311383
product: 311370
product: 311357
reactant: 311344
fast: false
reversible: false

311383
type: KineticLaw
local parameters: 178634
notes: k3*Membrane_slash_PP1_minus_active_slash_PP1_sbo_1_sbc__slash_PP1_sbo_1_sbc__cplx

178634
type: LocalParameter
units: 310882
value: 3.5E-18

311370
type: SpeciesReference
stoichiometry: 1.0
species: 698573

311357
type: SpeciesReference
stoichiometry: 1.0
species: 698633

311344
type: SpeciesReference
stoichiometry: 1.0
species: 698613

698912
type: Reaction
kinetic law: 311435
product: 311422
reactant: 311409
reactant: 311396
notes: Note halving of Km. See notes for internal-PKA-act enzymatic step.
fast: false
reversible: true

311435
type: KineticLaw
local parameters: 178636
local parameters: 178635
notes: k1*Membrane_slash_MR*PKA_minus_active-k2*PKA_minus_active_slash_memb_minus_PKA_minus_act_slash_memb_minus_PKA_minus_act_cplx

178636
type: LocalParameter
units: 310882
value: 2.16E-15

178635
type: LocalParameter
units: 310918
value: 8.0001E-17

311422
type: SpeciesReference
stoichiometry: 1.0
species: 698732

311409
type: SpeciesReference
stoichiometry: 1.0
species: 698792

311396
type: SpeciesReference
stoichiometry: 1.0
species: 698653