MODEL1204280031
type: SBMLModel
area units: 061696
reaction: COPASI31
reaction: COPASI27
reaction: COPASI45
time units: 291235
units def: 145191
reaction: COPASI43
name: Sarma2012 - Interaction topologies of MAPK cascade (M3_K2_PSEQ_short_duration_signal)
parameter: COPASI25
species: COPASI19
compartment: 145215
species: COPASI13
species: COPASI22
species: COPASI10
reaction: COPASI39
species: COPASI16
is described by: http://identifiers.org/pubmed/22748295
reaction: COPASI37
species: COPASI14
units def: 144939
species: 145228
species: COPASI8
reaction: COPASI34
species: COPASI2
species: COPASI3
reaction: COPASI32
reaction: COPASI28
length unit: length
reaction: COPASI46
reaction: COPASI44
species: COPASI24
species: COPASI18
species: COPASI12
substance units: 145191
species: COPASI6
species: COPASI7
species: COPASI4
reaction: COPASI41
reaction: COPASI35
reaction: COPASI33
reaction: COPASI29
reaction: COPASI49
reaction: COPASI47
reaction: COPASI30
event: COPASI26
reaction: COPASI42
volume units: 144939
reaction: COPASI40
species: COPASI20
species: COPASI21
species: COPASI23
curated: false
notes: Sarma2012 - Interaction topologies of MAPK cascade (M3_K2_PSEQ_short_duration_signal) The paper presents the various interaction topologies between the kinases and phosphatases of MAPK cascade. They are represented as M1, M2, M3 and M4. The kinases of the cascades are MKKK, MKK and MK, and Phos1, Phos2 and Phos3 are phosphatases of the system. All three kinases in a M1 type network have specific phosphatases Phos1, Phos2 and Phos3 for the dephosphorylation process. In a M2 type system, kinases MKKK and MKK are dephosphorylated by Phos1 and MK is dephosphorylated by Phos2. The architecture of system like M3 is such that MKKK gets dephosphorylated by Phos1, whereas Phos2 dephosphorylates both MKK and MK. Finally, the MAPK cascade exhibiting more complex design of interaction such as M4 is such that MKKK and MKK are dephosphorylated by Phos1 whereas MKK and MK are dephosphorylated by Phos2. In addition, as it is plausible that the kinases can sequester their respective phosphatases by binding to them, this is considered in the design of the systems (PSEQ-sequestrated system; USEQ-Unsequestrated system). The robustness of different interaction designs of the systems is checked, considering both MichaelisMenten type kinetics (K1) and elementary mass action kinetics (K2). In the living systems, the MAPK cascade transmit both short and long duration signals where short duration signals trigger proliferation and long duration signals trigger cell differentiation. These signal variants are considered to interpret the systems behaviour. It is also tested how the robustness and signal response behaviour of K2 models are affected when K2 assumes quasi steady state (QSS). The combinations of the above variants resulted in 40 models (MODEL1204280001-40). All these 40 models are available from BioModels Database . Models that correspond to type M4 with mass-action kinetics K2, in four condition 1) USEQ [ MODEL1204280020 - M4_K2_USEQ], 2) PSEQ [ MODEL1204280024 - M4_K2_PSEQ], 3) QS…
species: COPASI5
reaction: COPASI38
reaction: COPASI36
species: COPASI9
species: COPASI11
species: COPASI17
reaction: COPASI48
species: COPASI15

COPASI31
type: Reaction
reactant: 145732
modifier: 006028
kinetic law: 145756
reactant: 145720
modifier: 006040
fast: false
reversible: true
modifier: 006016
product: 145744
name: 19

145732
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI14
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
in compartment: 145215
name: P2

145215
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment

145780
type: LocalParameter
value: 1.0
name: k2

145768
type: LocalParameter
value: 0.045
name: k1

145720
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

COPASI7
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MK-PP

COPASI22
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MK-PP_P2

145744
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

COPASI27
type: Reaction
modifier: 005931
reactant: 145252
kinetic law: 145276
reactant: 145240
product: 145264
modifier: 005919
name: 15
reversible: true
fast: false
modifier: 005944

COPASI3
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MKK-PP

145252
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

145300
type: LocalParameter
value: 1.0
name: k2

145288
type: LocalParameter
value: 0.02
name: k1

145240
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

COPASI2
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1200.0
initial amount: NaN
in compartment: 145215
name: MK

145264
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

COPASI4
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MK_MKK-PP

COPASI45
type: Reaction
modifier: 006388
product: 147238
reactant: 147100
fast: false
kinetic law: 147251
reversible: true
name: 1
modifier: 006400
reactant: 147112
modifier: 006376

COPASI19
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 10.0
initial amount: NaN
in compartment: 145215
name: Sig

147238
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

COPASI18
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MKKK_Sig

147100
type: SpeciesReference
stoichiometry: 1.0
species: COPASI17

COPASI17
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 300.0
initial amount: NaN
in compartment: 145215
name: MKKK

147275
type: LocalParameter
value: 1.0
name: k2

147263
type: LocalParameter
value: 0.02
name: k1

147112
type: SpeciesReference
stoichiometry: 1.0
species: COPASI19

145191
type: SBMLUnitsDef
unit: 145203
name: substance

145203
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

COPASI43
type: Reaction
kinetic law: 147004
modifier: 006328
product: 146992
reactant: 146980
fast: false
reversible: false
name: 13

147016
type: LocalParameter
value: 0.5
name: k1

COPASI15
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MKK-P_P2

146992
type: SpeciesReference
stoichiometry: 1.0
species: COPASI16

COPASI16
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MKK_P2

146980
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

COPASI25
type: Parameter
constant: true
value: 0.0
name: quantity_1

COPASI13
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MKK-PP_P2

COPASI10
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MKK_MKKK-P

COPASI39
type: Reaction
kinetic law: 146517
modifier: 006232
product: 146505
product: 146493
reactant: 146481
fast: false
reversible: false
name: 9

146648
type: LocalParameter
value: 15.0
name: k1

COPASI12
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MKK-P_MKKK-P

146505
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

COPASI9
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MKKK-P

146493
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

146481
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

COPASI37
type: Reaction
kinetic law: 146385
modifier: 006184
product: 146373
product: 146361
reactant: 146349
fast: false
reversible: false
name: 7

146397
type: LocalParameter
value: 0.01
name: k1

146373
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

146361
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

COPASI11
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MKK-P

146349
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

144939
type: SBMLUnitsDef
unit: 144951
name: volume

144951
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE

145228
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MKKK_P1

COPASI8
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1200.0
initial amount: NaN
in compartment: 145215
name: MKK

COPASI34
type: Reaction
kinetic law: 146065
modifier: 006100
product: 146052
reactant: 146040
fast: false
reversible: false
name: 22

146077
type: LocalParameter
value: 0.5
name: k1

COPASI23
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MK-P_P2

146052
type: SpeciesReference
stoichiometry: 1.0
species: COPASI24

COPASI24
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MK_P2

146040
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

COPASI32
type: Reaction
kinetic law: 145828
modifier: 006052
product: 145816
product: 145804
reactant: 145792
fast: false
reversible: false
name: 20

145840
type: LocalParameter
value: 0.092
name: k1

145816
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

145804
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

COPASI5
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MK-P

145792
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

COPASI28
type: Reaction
kinetic law: 145348
modifier: 005956
product: 145336
product: 145324
reactant: 145312
fast: false
reversible: false
name: 16

145360
type: LocalParameter
value: 0.01
name: k1

145336
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

145324
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

145312
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

COPASI46
type: Reaction
kinetic law: 147323
modifier: 006412
product: 147311
product: 147299
reactant: 147287
fast: false
reversible: false
name: 2

147335
type: LocalParameter
value: 1.0
name: k1

147311
type: SpeciesReference
stoichiometry: 1.0
species: COPASI19

147299
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

147287
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

COPASI44
type: Reaction
product: 147040
product: 147052
reactant: 147028
modifier: 006364
name: 14
modifier: 006340
reversible: true
kinetic law: 147064
fast: false
modifier: 006352

147040
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

147052
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

147028
type: SpeciesReference
stoichiometry: 1.0
species: COPASI16

147088
type: LocalParameter
value: 0.005
name: k2

147076
type: LocalParameter
value: 0.086
name: k1

COPASI6
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MK-P_MKK-PP

COPASI41
type: Reaction
kinetic law: 146768
modifier: 006280
product: 146756
product: 146744
reactant: 146732
fast: false
reversible: false
name: 11

146780
type: LocalParameter
value: 0.092
name: k1

146756
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

146744
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

146732
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

COPASI35
type: Reaction
reversible: true
name: 23
reactant: 146089
product: 146113
modifier: 006136
fast: false
product: 146101
modifier: 006124
modifier: 006112
kinetic law: 146125

146089
type: SpeciesReference
stoichiometry: 1.0
species: COPASI24

146113
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

146101
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

146149
type: LocalParameter
value: 0.005
name: k2

146137
type: LocalParameter
value: 0.086
name: k1

COPASI33
type: Reaction
modifier: 006064
fast: false
modifier: 006076
reversible: true
name: 21
kinetic law: 146004
modifier: 006088
reactant: 145864
product: 145992
reactant: 145852

146028
type: LocalParameter
value: 1.0
name: k2

146016
type: LocalParameter
value: 0.01
name: k1

145864
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

145992
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

145852
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

COPASI29
type: Reaction
product: 145396
kinetic law: 145408
reactant: 145384
reactant: 145372
modifier: 005980
modifier: 005968
fast: false
name: 17
reversible: true
modifier: 005992

145396
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

145432
type: LocalParameter
value: 1.0
name: k2

145420
type: LocalParameter
value: 0.032
name: k1

145384
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

145372
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

COPASI49
type: Reaction
name: 5
modifier: 006484
modifier: 006496
reversible: true
reactant: 147584
kinetic law: 147620
fast: false
modifier: 006472
product: 147608
product: 147596

COPASI21
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
initial amount: NaN
in compartment: 145215
name: P1

147584
type: SpeciesReference
stoichiometry: 1.0
species: 145228

147644
type: LocalParameter
value: 0.005
name: k2

147632
type: LocalParameter
value: 0.086
name: k1

147608
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

147596
type: SpeciesReference
stoichiometry: 1.0
species: COPASI17

COPASI47
type: Reaction
name: 3
fast: false
kinetic law: 147383
reactant: 147359
modifier: 006448
reversible: true
modifier: 006436
modifier: 006424
product: 147371
reactant: 147347

147407
type: LocalParameter
value: 1.0
name: k2

147395
type: LocalParameter
value: 0.02
name: k1

147359
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

COPASI20
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 145215
name: MKKK-P_P1

147371
type: SpeciesReference
stoichiometry: 1.0
species: COPASI20

147347
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

COPASI30
type: Reaction
kinetic law: 145696
modifier: 006004
product: 145683
product: 145456
reactant: 145444
fast: false
reversible: false
name: 18

145708
type: LocalParameter
value: 15.0
name: k1

145683
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

145456
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

145444
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

COPASI26
type: Event
event assignment: 147680
event assignment: 147668
trigger: 147656
use values from trigger time: true
name: 1

147656
type: Trigger
persistant: true
initial value: true

COPASI42
type: Reaction
modifier: 006304
reactant: 146804
product: 146816
modifier: 006316
name: 12
reversible: true
kinetic law: 146944
modifier: 006292
reactant: 146792
fast: false

146804
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

146816
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

146968
type: LocalParameter
value: 1.0
name: k2

146956
type: LocalParameter
value: 0.01
name: k1

146792
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

COPASI40
type: Reaction
reversible: true
modifier: 006268
reactant: 146660
modifier: 006256
modifier: 006244
reactant: 146672
name: 10
kinetic law: 146696
fast: false
product: 146684

146660
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

146672
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

146720
type: LocalParameter
value: 1.0
name: k2

146708
type: LocalParameter
value: 0.045
name: k1

146684
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

COPASI38
type: Reaction
reversible: true
modifier: 006208
kinetic law: 146445
reactant: 146409
name: 8
modifier: 006220
modifier: 006196
fast: false
reactant: 146421
product: 146433

146469
type: LocalParameter
value: 1.0
name: k2

146457
type: LocalParameter
value: 0.032
name: k1

146409
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

146421
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

146433
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

COPASI36
type: Reaction
modifier: 006172
product: 146301
name: 6
modifier: 006160
reversible: true
fast: false
reactant: 146161
reactant: 146289
modifier: 006148
kinetic law: 146313

146301
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

146161
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

146289
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

146337
type: LocalParameter
value: 1.0
name: k2

146325
type: LocalParameter
value: 0.02
name: k1

COPASI48
type: Reaction
kinetic law: 147560
modifier: 006460
product: 147548
reactant: 147535
fast: false
reversible: false
name: 4

147572
type: LocalParameter
value: 0.5
name: k1

147548
type: SpeciesReference
stoichiometry: 1.0
species: 145228

147535
type: SpeciesReference
stoichiometry: 1.0
species: COPASI20