MODEL1204280033
type: SBMLModel
function def: COPASI30
species: 208355
parameter: COPASI6
name: Sarma2012 - Interaction topologies of MAPK cascade (M1_K2_QSS_USEQ)
name: 7
units def: 208133
volume units: 208109
reaction: COPASI25
parameter: COPASI15
name: 6
parameter: COPASI11
name: 9
species: 208169
function def: COPASI35
name: 4
function def: COPASI36
species: COPASI3
length unit: length
parameter: COPASI7
species: 208379
reaction: COPASI26
substance units: 208133
units def: 208109
function def: COPASI31
parameter: COPASI18
reaction: COPASI24
function def: COPASI32
area units: 061696
name: 3
species: 208330
species: 208318
event: COPASI19
reaction: COPASI21
parameter: COPASI16
name: 2
parameter: COPASI12
time units: 291235
name: 10
parameter: COPASI8
name: 5
species: 208305
function def: COPASI37
is described by: http://identifiers.org/pubmed/22748295
reaction: COPASI27
function def: COPASI38
curated: false
reaction: COPASI29
reaction: COPASI22
notes: Sarma2012 - Interaction topologies of MAPK cascade (M1_K2_QSS_USEQ) 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) QSS_USEQ [ MODEL1204…
compartment: 208157
function def: COPASI33
parameter: COPASI14
parameter: COPASI17
reaction: COPASI20
name: 8
parameter: COPASI10
parameter: COPASI13
function def: COPASI34
species: 208343
species: COPASI2
species: COPASI5
parameter: COPASI9
name: 1
function def: COPASI39
species: COPASI4
reaction: COPASI28
species: 208367
reaction: COPASI23

208355
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 208157
name: MK_PP

208157
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment

COPASI6
type: Parameter
constant: true
value: 100.0
name: K1

208133
type: SBMLUnitsDef
unit: 208145
name: substance

208145
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

208109
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unit: 208121
name: volume

208121
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE

COPASI25
type: Reaction
fast: false
modifier: 017104
reactant: 209005
modifier: 209029
modifier: 209041
reversible: false
kinetic law: 209053
modifier: 017116
name: 7
product: 209017
modifier: 017092

COPASI2
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: 208157
name: MK

209005
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

208343
type: Species
constant: false
boundary condition: false
has only substance units: false
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initial amount: NaN
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name: MKK_PP

COPASI3
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 208157
name: MK_P

209065
type: LocalParameter
value: 0.01
name: k7

209017
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

COPASI15
type: Parameter
constant: true
value: 50.5
name: K7

COPASI11
type: Parameter
constant: true
value: 50.5
name: K3

208169
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 299.999985553313
initial amount: NaN
in compartment: 208157
name: MKKK

COPASI7
type: Parameter
constant: true
value: 54.3
name: K2

208379
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 20.0
initial amount: NaN
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name: Sig

COPASI26
type: Reaction
modifier: 209236
reversible: false
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fast: false
kinetic law: 209248
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reactant: 209077
name: 8
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209260
type: LocalParameter
value: 15.0
name: k7

209077
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

209212
type: SpeciesReference
stoichiometry: 1.0
species: 208355

COPASI18
type: Parameter
constant: true
value: 108.6
name: K10

COPASI24
type: Reaction
modifier: 017080
fast: false
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product: 208933
reversible: false
modifier: 208969
modifier: 017068
name: 6
modifier: 017056
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kinetic law: 208981
reactant: 208921
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COPASI5
type: Species
constant: false
boundary condition: false
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initial concentration: 100.0
initial amount: NaN
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name: P2

208933
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species: 208318

208318
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initial amount: NaN
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name: MKK

208330
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
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name: MKK_P

208993
type: LocalParameter
value: 0.086
name: k6

208921
type: SpeciesReference
stoichiometry: 1.0
species: 208330

COPASI19
type: Event
event assignment: 209649
trigger: 209637
use values from trigger time: true
name: event_1

209637
type: Trigger
persistant: true
initial value: true

COPASI21
type: Reaction
reversible: false
name: 2
modifier: 016935
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kinetic law: 208622
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product: 208464
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fast: false

COPASI4
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
initial amount: NaN
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name: P1

208635
type: LocalParameter
value: 0.086
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208464
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208305
type: Species
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has only substance units: false
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initial amount: NaN
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name: MKKK_P

208452
type: SpeciesReference
stoichiometry: 1.0
species: 208305

COPASI16
type: Parameter
constant: true
value: 500.0
name: K8

COPASI12
type: Parameter
constant: true
value: 500.0
name: K4

COPASI8
type: Parameter
constant: true
value: 3.0E51
name: Kse1

COPASI27
type: Reaction
modifier: 209321
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product: 209285
kinetic law: 209333
reactant: 209272
fast: false
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name: 9
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reversible: false

208367
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initial amount: NaN
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name: P3

209285
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

209345
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value: 0.092
name: k9

209272
type: SpeciesReference
stoichiometry: 1.0
species: 208355

COPASI29
type: Reaction
product: 209577
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reversible: false
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fast: false
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value: 0.01
name: k3

COPASI22
type: Reaction
reversible: false
name: 4
fast: false
kinetic law: 208695
modifier: 016971
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208707
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value: 15.0
name: k4

208659
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208647
type: SpeciesReference
stoichiometry: 1.0
species: 208330

COPASI14
type: Parameter
constant: true
value: 108.6
name: K6

COPASI17
type: Parameter
constant: true
value: 24.3
name: K9

COPASI20
type: Reaction
modifier: 016899
name: 1
kinetic law: 208428
reversible: false
product: 208404
modifier: 208416
reactant: 208392
modifier: 016911
fast: false

208440
type: LocalParameter
value: 1.0
name: k1

208404
type: SpeciesReference
stoichiometry: 1.0
species: 208305

208392
type: SpeciesReference
stoichiometry: 1.0
species: 208169

COPASI10
type: Parameter
constant: true
value: 3.0E51
name: Kse3

COPASI13
type: Parameter
constant: true
value: 24.3
name: K5

COPASI9
type: Parameter
constant: true
value: 3.0E51
name: Kse2

COPASI28
type: Reaction
modifier: 209516
modifier: 209529
modifier: 017212
reversible: false
reactant: 209357
product: 209369
modifier: 209381
modifier: 017236
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fast: false
name: 10
kinetic law: 209541
modifier: 017249

209357
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

209369
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

209553
type: LocalParameter
value: 0.086
name: k10

COPASI23
type: Reaction
modifier: 017007
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kinetic law: 208779
name: 5
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product: 208731
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reactant: 208719
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modifier: 017031
fast: false
reversible: false

208791
type: LocalParameter
value: 0.092
name: k5

208731
type: SpeciesReference
stoichiometry: 1.0
species: 208330

208719
type: SpeciesReference
stoichiometry: 1.0
species: 208343