BIOMD0000000002
type: SBMLModel
reaction: 986503
parameter: metaid_0000041
parameter: metaid_0000039
reaction: 986722
parameter: metaid_0000037
reaction: 986462
parameter: metaid_0000053
reaction: 986423
parameter: metaid_0000044
parameter: metaid_0000050
parameter: metaid_0000065
reaction: 986643
parameter: metaid_0000056
area units: area
name: Edelstein1996 - EPSP ACh species
parameter: metaid_0000062
parameter: metaid_0000068
substance units: substance
reaction: 986542
length unit: length
parameter: metaid_0000047
reaction: 986563
species: 986142
modified:
  W3 CDTF: Tue Dec 11 15:25:56 GMT 2012
parameter: metaid_0000059
species: 986302
species: 986242
volume units: volume
reaction: 986522
parameter: metaid_0000060
reaction: 986702
species: 986262
species: 986222
parameter: metaid_0000045
reaction: 986623
curated: true
parameter: metaid_0000051
parameter: metaid_0000042
parameter: metaid_0000057
parameter: metaid_0000048
time units: time
species: 986182
parameter: metaid_0000063
parameter: metaid_0000054
parameter: metaid_0000069
is described by: http://identifiers.org/pubmed/8983160
species: 986202
parameter: metaid_0000066
reaction: 986602
species: 986162
species: 986362
reaction: 986683
parameter: metaid_0000040
parameter: metaid_0000038
occurs in: http://identifiers.org/taxonomy/7787
parameter: metaid_0000036
parameter: metaid_0000061
parameter: metaid_0000052
parameter: metaid_0000064
species: 986342
compartment: 986127
is version of: GO:0007274
reaction: 986485
species: 986382
is: MODEL6614086398
parameter: metaid_0000043
reaction: 986583
is version of: GO:0007166
parameter: metaid_0000049
parameter: metaid_0000055
parameter: metaid_0000046
species: 986322
notes: Edelstein1996 - EPSP ACh species Model of a nicotinic Excitatory Post-Synaptic Potential in a Torpedo electric organ. Acetylcholine is represented explicitely as a molecular species. This model has initially been encoded using StochSim. This model is described in the article: A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions. Edelstein SJ, Schaad O, Henry E, Bertrand D, Changeux JP. Biol. Cybern. 1996 Nov; 75(5):361-79 Abstract: Nicotinic acetylcholine receptors are transmembrane oligomeric proteins that mediate interconversions between open and closed channel states under the control of neurotransmitters. Fast in vitro chemical kinetics and in vivo electrophysiological recordings are consistent with the following multi-step scheme. Upon binding of agonists, receptor molecules in the closed but activatable resting state (the Basal state, B) undergo rapid transitions to states of higher affinities with either open channels (the Active state, A) or closed channels (the initial Inactivatable and fully Desensitized states, I and D). In order to represent the functional properties of such receptors, we have developed a kinetic model that links conformational interconversion rates to agonist binding and extends the general principles of the Monod-Wyman-Changeux model of allosteric transitions. The crucial assumption is that the linkage is controlled by the position of the interconversion transition states on a hypothetical linear reaction coordinate. Application of the model to the peripheral nicotine acetylcholine receptor (nAChR) accounts for the main properties of ligand-gating, including single-channel events, and several new relationships are predicted. Kinetic simulations reveal errors inherent in using the dose-response analysis, but justify its application under defined conditions. The model predicts that (in order to overcome the intrinsic stability of the B state and to produce the appropriate cooperativity) chann…
parameter: metaid_0000067
parameter: metaid_0000058
reaction: 986443
reaction: 986402
reaction: 986663
species: 986282

986503
type: Reaction
kinetic law: 349000
product: 348988
reactant: 348976
notes: opening of unliganded
is: GO:0004889
fast: false
reversible: true
name: React5

349000
type: KineticLaw
notes: kf_5 * B - kr_5 * A

348988
type: SpeciesReference
stoichiometry: 1.0
species: 986202

986202
type: Species
name: Active
notes: unkiganded active state
is version of: GO:0005892
boundary condition: false
initial amount: 0.0
in compartment: 986127
constant: false
initial concentration: NaN
has only substance units: false

986127
type: Compartment
is: GO:0031594
constant: true
size: 1.0E-16
spatial dimensions: 3.0
name: compartment1

348976
type: SpeciesReference
stoichiometry: 1.0
species: 986242

986242
type: Species
notes: unliganded basal state
is version of: GO:0005892
initial amount: 1.0E-22
name: Basal
boundary condition: false
has only substance units: false
is version of: IPR002394
constant: false
initial concentration: NaN
in compartment: 986127

metaid_0000041
type: Parameter
constant: true
value: 700.0

metaid_0000039
type: Parameter
constant: true
value: 16000.0

986722
type: Reaction
kinetic law: 349447
product: 349435
reactant: 349423
notes: bilig interm <=> bilig desen
fast: false
reversible: true
name: React16

349447
type: KineticLaw
notes: kf_16 * ILL - kr_16 * DLL

349435
type: SpeciesReference
stoichiometry: 1.0
species: 986262

986262
type: Species
has only substance units: false
boundary condition: false
name: DesensitisedACh2
initial concentration: NaN
constant: false
in compartment: 986127
notes: biliganded desensitised state
is version of: GO:0005892
initial amount: 0.0

349423
type: SpeciesReference
stoichiometry: 1.0
species: 986302

986302
type: Species
initial concentration: NaN
is version of: GO:0005892
constant: false
in compartment: 986127
name: IntermediateACh2
is version of: IPR002394
notes: biliganded intermediate
initial amount: 0.0
has only substance units: false
boundary condition: false

metaid_0000037
type: Parameter
constant: true
value: 8000.0

986462
type: Reaction
product: 348904
notes: first ligand on active
reactant: 348892
is: GO:0042166
fast: false
reversible: true
kinetic law: 348916
reactant: 348880
name: React3

348904
type: SpeciesReference
stoichiometry: 1.0
species: 986182

986182
type: Species
constant: false
is version of: IPR002394
boundary condition: false
initial concentration: NaN
in compartment: 986127
notes: monoliganded active state
name: ActiveACh
is version of: GO:0005892
has only substance units: false
initial amount: 0.0

348892
type: SpeciesReference
stoichiometry: 1.0
species: 986382

986382
type: Species
is: C01996
initial concentration: NaN
is: CHEBI:15355
in compartment: 986127
boundary condition: false
constant: false
notes: ligand
has only substance units: false
name: ACh
initial amount: 1.0E-21

348916
type: KineticLaw
notes: kf_3 * A * L - kr_3 * AL

348880
type: SpeciesReference
stoichiometry: 1.0
species: 986202

metaid_0000053
type: Parameter
constant: true
value: 8.0

986423
type: Reaction
reversible: true
notes: second ligand on basal
fast: false
kinetic law: 348832
reactant: 348808
is: GO:0042166
product: 348820
name: React1
reactant: 348796

348832
type: KineticLaw
notes: kf_1 * BL * L - kr_1 * BLL

348808
type: SpeciesReference
stoichiometry: 1.0
species: 986382

348820
type: SpeciesReference
stoichiometry: 1.0
species: 986142

986142
type: Species
initial concentration: NaN
is version of: IPR002394
in compartment: 986127
name: BasalACh2
has only substance units: false
constant: false
initial amount: 0.0
boundary condition: false
notes: biliganded basal state
is version of: GO:0005892

348796
type: SpeciesReference
stoichiometry: 1.0
species: 986222

986222
type: Species
is version of: GO:0005892
initial concentration: NaN
is version of: IPR002394
in compartment: 986127
initial amount: 0.0
has only substance units: false
name: BasalACh
notes: monoliganded basal state
boundary condition: false
constant: false

metaid_0000044
type: Parameter
constant: true
value: 1.5E8

metaid_0000050
type: Parameter
constant: true
value: 3.0E8

metaid_0000065
type: Parameter
constant: true
value: 0.0012

986643
type: Reaction
name: React12
is: GO:0042166
reactant: 349255
fast: false
product: 349279
reactant: 349267
notes: first ligand on desensitised
reversible: true
kinetic law: 349291

349255
type: SpeciesReference
stoichiometry: 1.0
species: 986282

986282
type: Species
notes: fully desensitised state
constant: false
is version of: IPR002394
is version of: GO:0005892
boundary condition: false
initial amount: 0.0
has only substance units: false
initial concentration: NaN
in compartment: 986127
name: Desensitised

349279
type: SpeciesReference
stoichiometry: 1.0
species: 986322

986322
type: Species
is version of: IPR002394
notes: monoliganded desensitised state
initial concentration: NaN
boundary condition: false
has only substance units: false
in compartment: 986127
is version of: GO:0005892
initial amount: 0.0
name: DesensitisedACh
constant: false

349267
type: SpeciesReference
stoichiometry: 1.0
species: 986382

349291
type: KineticLaw
notes: kf_12 * D * L - kr_12 * DL

metaid_0000056
type: Parameter
constant: true
value: 19.85

metaid_0000062
type: Parameter
constant: true
value: 1.5E8

metaid_0000068
type: Parameter
constant: true
value: 0.05

986542
type: Reaction
notes: first ligand on intermediate
product: 349072
kinetic law: 349085
reactant: 349060
reactant: 349048
is: GO:0042166
reversible: true
fast: false
name: React7

349072
type: SpeciesReference
stoichiometry: 1.0
species: 986162

986162
type: Species
boundary condition: false
name: IntermediateACh
in compartment: 986127
is version of: GO:0005892
is version of: IPR002394
initial concentration: NaN
constant: false
has only substance units: false
notes: monoliganded intermediate
initial amount: 0.0

349085
type: KineticLaw
notes: kf_7 * I * L - kr_7 * IL

349060
type: SpeciesReference
stoichiometry: 1.0
species: 986382

349048
type: SpeciesReference
stoichiometry: 1.0
species: 986342

986342
type: Species
boundary condition: false
is version of: IPR002394
in compartment: 986127
is version of: GO:0005892
has only substance units: false
notes: unliganted intermediate
initial amount: 0.0
name: Intermediate
initial concentration: NaN
constant: false

metaid_0000047
type: Parameter
constant: true
value: 10800.0

986563
type: Reaction
reversible: true
fast: false
reactant: 349109
product: 349121
kinetic law: 349134
is: GO:0042166
notes: second ligand on intermediate
reactant: 349097
name: React8

349109
type: SpeciesReference
stoichiometry: 1.0
species: 986382

349121
type: SpeciesReference
stoichiometry: 1.0
species: 986302

349134
type: KineticLaw
notes: kf_8 * IL * L - kr_8 * ILL

349097
type: SpeciesReference
stoichiometry: 1.0
species: 986162

metaid_0000059
type: Parameter
constant: true
value: 0.81

986522
type: Reaction
kinetic law: 349036
product: 349024
reactant: 349012
notes: opening of monoliganded
is: GO:0004889
fast: false
reversible: true
name: React6

349036
type: KineticLaw
notes: kf_6 * BL - kr_6 * AL

349024
type: SpeciesReference
stoichiometry: 1.0
species: 986182

349012
type: SpeciesReference
stoichiometry: 1.0
species: 986222

metaid_0000060
type: Parameter
constant: true
value: 3.0E8

986702
type: Reaction
kinetic law: 349411
product: 349399
reactant: 349387
notes: monolig interm <=> monolig desen
fast: false
reversible: true
name: React15

349411
type: KineticLaw
notes: kf_15 * IL - kr_15 * DL

349399
type: SpeciesReference
stoichiometry: 1.0
species: 986322

349387
type: SpeciesReference
stoichiometry: 1.0
species: 986162

metaid_0000045
type: Parameter
constant: true
value: 17.28

986623
type: Reaction
kinetic law: 349243
product: 349231
reactant: 349219
notes: bilig act <=> bilig interm
is: GO:0004889
fast: false
reversible: true
name: React11

349243
type: KineticLaw
notes: kf_11 * ALL - kr_11 * ILL

349231
type: SpeciesReference
stoichiometry: 1.0
species: 986302

349219
type: SpeciesReference
stoichiometry: 1.0
species: 986362

986362
type: Species
initial amount: 0.0
notes: biliganted active state
has only substance units: false
is version of: IPR002394
initial concentration: NaN
is version of: GO:0005892
boundary condition: false
constant: false
name: ActiveACh2
in compartment: 986127

metaid_0000051
type: Parameter
constant: true
value: 4.0

metaid_0000042
type: Parameter
constant: true
value: 3.0E8

metaid_0000057
type: Parameter
constant: true
value: 1.74

metaid_0000048
type: Parameter
constant: true
value: 130.0

metaid_0000063
type: Parameter
constant: true
value: 8.0

metaid_0000054
type: Parameter
constant: true
value: 19.7

metaid_0000069
type: Parameter
constant: true
value: 0.0012

metaid_0000066
type: Parameter
constant: true
value: 0.05

986602
type: Reaction
kinetic law: 349207
product: 349194
reactant: 349182
notes: monolig act <=> monolig interm
is: GO:0004889
fast: false
reversible: true
name: React10

349207
type: KineticLaw
notes: kf_10 * AL - kr_10 * IL

349194
type: SpeciesReference
stoichiometry: 1.0
species: 986162

349182
type: SpeciesReference
stoichiometry: 1.0
species: 986182

986683
type: Reaction
kinetic law: 349375
product: 349363
reactant: 349351
notes: unlig interm <=> unlig desen
fast: false
reversible: true
name: React14

349375
type: KineticLaw
notes: kf_14 * I - kr_14 * D

349363
type: SpeciesReference
stoichiometry: 1.0
species: 986282

349351
type: SpeciesReference
stoichiometry: 1.0
species: 986342

metaid_0000040
type: Parameter
constant: true
value: 30000.0

metaid_0000038
type: Parameter
constant: true
value: 1.5E8

metaid_0000036
type: Parameter
constant: true
value: 3.0E8

metaid_0000061
type: Parameter
constant: true
value: 4.0

metaid_0000052
type: Parameter
constant: true
value: 1.5E8

metaid_0000064
type: Parameter
constant: true
value: 0.05

986485
type: Reaction
fast: false
reactant: 348928
name: React4
product: 348952
kinetic law: 348964
reversible: true
notes: second ligand on active
is: GO:0042166
reactant: 348940

348928
type: SpeciesReference
stoichiometry: 1.0
species: 986182

348952
type: SpeciesReference
stoichiometry: 1.0
species: 986362

348964
type: KineticLaw
notes: kf_4 * AL * L - kr_4 * ALL

348940
type: SpeciesReference
stoichiometry: 1.0
species: 986382

metaid_0000043
type: Parameter
constant: true
value: 8.64

986583
type: Reaction
kinetic law: 349170
product: 349158
reactant: 349146
notes: unlig act <=> unlig interm
is: GO:0004889
fast: false
reversible: true
name: React9

349170
type: KineticLaw
notes: kf_9 * A - kr_9 * I

349158
type: SpeciesReference
stoichiometry: 1.0
species: 986342

349146
type: SpeciesReference
stoichiometry: 1.0
species: 986202

metaid_0000049
type: Parameter
constant: true
value: 2740.0

metaid_0000055
type: Parameter
constant: true
value: 3.74

metaid_0000046
type: Parameter
constant: true
value: 0.54

metaid_0000067
type: Parameter
constant: true
value: 0.0012

metaid_0000058
type: Parameter
constant: true
value: 20.0

986443
type: Reaction
kinetic law: 348868
product: 348856
reactant: 348844
notes: opening of biliganded
is: GO:0004889
fast: false
reversible: true
name: React2

348868
type: KineticLaw
notes: kf_2 * BLL - kr_2 * ALL

348856
type: SpeciesReference
stoichiometry: 1.0
species: 986362

348844
type: SpeciesReference
stoichiometry: 1.0
species: 986142

986402
type: Reaction
reactant: 348746
kinetic law: 348784
fast: false
name: React0
reversible: true
product: 348772
reactant: 348760
notes: first ligand on basal
is: GO:0042166

348746
type: SpeciesReference
stoichiometry: 1.0
species: 986242

348784
type: KineticLaw
notes: kf_0 * B * L - kr_0 * BL

348772
type: SpeciesReference
stoichiometry: 1.0
species: 986222

348760
type: SpeciesReference
stoichiometry: 1.0
species: 986382

986663
type: Reaction
kinetic law: 349339
reactant: 349303
fast: false
notes: second ligand on desensitised
reversible: true
reactant: 349315
is: GO:0042166
name: React13
product: 349327

349339
type: KineticLaw
notes: kf_13 * DL * L - kr_13 * DLL

349303
type: SpeciesReference
stoichiometry: 1.0
species: 986322

349315
type: SpeciesReference
stoichiometry: 1.0
species: 986382

349327
type: SpeciesReference
stoichiometry: 1.0
species: 986262

ORG:
  orgname: EMBL-EBI
n:
  given: Nicolas
  family: Le Novère

W3 CDTF: Wed Feb 02 14:41:42 GMT 2005