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name: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_PSEQ)
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notes: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_PSEQ) 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-MODEL1204280040). 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 [ …
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958413
value: 15.0
name: k1
type: LocalParameter

958629
stoichiometry: 1.0
species: COPASI23
type: SpeciesReference

COPASI29
modifier: 085893
kinetic law: 958197
reactant: 958161
reactant: 958173
reversible: true
name: 15
fast: false
modifier: 085905
modifier: 085881
type: Reaction
product: 958185
is version of: GO:0006461

959943
stoichiometry: 1.0
species: COPASI17
type: SpeciesReference

958557
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

958641
stoichiometry: 1.0
species: COPASI24
type: SpeciesReference

959229
stoichiometry: 1.0
species: COPASI16
type: SpeciesReference

COPASI49
modifier: 086409
kinetic law: 959506
is version of: GO:0006461
fast: false
reactant: 959470
type: Reaction
reactant: 959482
name: 3
reversible: true
modifier: 086385
modifier: 086397
product: 959494

959313
value: 0.086
name: k1
type: LocalParameter

COPASI8
is version of: Q02750
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1200.0
initial amount: NaN
in compartment: 958136
name: MKK
type: Species

959385
value: 0.02
name: k1
type: LocalParameter

COPASI19
is version of: P61225
constant: false
boundary condition: false
has only substance units: false
initial concentration: 10.0
initial amount: NaN
in compartment: 958136
name: Sig
type: Species

959675
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

COPASI39
kinetic law: 958857
type: Reaction
product: 958845
is version of: GO:0043241
fast: false
reversible: false
modifier: 086145
product: 958833
reactant: 958821
name: 7
is version of: GO:0016310

959097
stoichiometry: 1.0
species: COPASI11
type: SpeciesReference

959157
stoichiometry: 1.0
species: COPASI14
type: SpeciesReference

COPASI18
type: Species
initial amount: NaN
has part: P04049
in compartment: 958136
constant: false
initial concentration: 0.0
has part: P61225
name: MKKK_Sig
boundary condition: false
has only substance units: false

COPASI28
constant: true
value: 0.0
name: quantity_1
type: Parameter

COPASI48
product: 959421
fast: false
is version of: GO:0016310
name: 2
product: 959433
is version of: GO:0043241
kinetic law: 959445
type: Reaction
modifier: 086373
reversible: false
reactant: 959409

958365
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

958965
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

COPASI9
initial concentration: 0.0
initial amount: NaN
is version of: C00562
has only substance units: false
is version of: P04049
in compartment: 958136
name: MKKK-P
constant: false
boundary condition: false
type: Species

959013
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

COPASI38
modifier: 086133
type: Reaction
modifier: 086109
name: 6
product: 958773
reactant: 958749
reactant: 958761
kinetic law: 958785
is version of: GO:0006461
reversible: true
fast: false
modifier: 086121

959470
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference