BIOMD0000000430
type: SBMLModel
modified:
  W3 CDTF: Fri Dec 14 14:23:41 GMT 2012
name: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_USEQ)
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creator:
  ORG:
    orgname: National Centre for Cell Science
  n:
    given: Uddipan
    family: Sarma
reaction: COPASI34
notes: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_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 [ MODEL12042800…
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creator:
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    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
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created:
  W3 CDTF: Fri Nov 23 15:47:02 GMT 2012
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is described by: http://identifiers.org/pubmed/22748295
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type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

384875
type: LocalParameter
value: 0.01
name: k1

COPASI35
type: Reaction
is version of: GO:0006461
fast: false
modifier: 618873
kinetic law: 385187
modifier: 618849
reversible: true
reactant: 385163
product: 385175
name: 21
modifier: 618861
reactant: 385151

385211
type: LocalParameter
value: 1.0
name: k2

385199
type: LocalParameter
value: 0.01
name: k1

385163
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

385175
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

385151
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

COPASI36
type: Reaction
modifier: 618885
reversible: false
product: 385235
reactant: 385223
is version of: GO:0016311
fast: false
kinetic law: 385259
is version of: GO:0043241
name: 22
product: 385247

385235
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

385223
type: SpeciesReference
stoichiometry: 1.0
species: COPASI23

385271
type: LocalParameter
value: 0.086
name: k1

385247
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

COPASI53
type: Reaction
modifier: 619305
modifier: 619329
modifier: 619317
fast: false
is version of: GO:0006461
reversible: true
reactant: 386380
name: 12_P1
kinetic law: 386416
product: 386404
reactant: 386392

386380
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

386440
type: LocalParameter
value: 1.0
name: k2

386428
type: LocalParameter
value: 0.01
name: k1

386404
type: SpeciesReference
stoichiometry: 1.0
species: COPASI26

386392
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

COPASI45
type: Reaction
product: 385849
name: 13_P2
modifier: 619113
is version of: GO:0016311
reactant: 385824
product: 385837
is version of: GO:0043241
reversible: false
kinetic law: 385862
fast: false

385849
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

385824
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

385837
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

385875
type: LocalParameter
value: 0.086
name: k1

COPASI54
type: Reaction
modifier: 619341
name: 13_P1
reversible: false
is version of: GO:0016311
fast: false
product: 386466
is version of: GO:0043241
kinetic law: 386491
product: 386479
reactant: 386453

386466
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

386503
type: LocalParameter
value: 0.086
name: k1

386479
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

386453
type: SpeciesReference
stoichiometry: 1.0
species: COPASI26

COPASI44
type: Reaction
reactant: 385751
modifier: 619089
name: 12_P2
fast: false
kinetic law: 385787
product: 385775
modifier: 619101
modifier: 619077
is version of: GO:0006461
reversible: true
reactant: 385763

385751
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

385811
type: LocalParameter
value: 1.0
name: k2

385799
type: LocalParameter
value: 0.01
name: k1

385775
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

385763
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14