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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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type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

958389
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

958413
type: LocalParameter
value: 15.0
name: k1

958377
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

COPASI7
type: Species
is version of: C00562
has only substance units: false
initial amount: NaN
in compartment: 958136
name: MK-PP
is version of: P27361
boundary condition: false
constant: false
initial concentration: 0.0

COPASI33
type: Reaction
fast: false
modifier: 086001
modifier: 085989
product: 958449
reversible: true
name: 19
modifier: 085977
reactant: 958437
kinetic law: 958461
reactant: 958425
is version of: GO:0006461

958449
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22

958437
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

958485
type: LocalParameter
value: 1.0
name: k2

958473
type: LocalParameter
value: 0.045
name: k1

958425
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

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

958773
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

958749
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

958761
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

958809
type: LocalParameter
value: 1.0
name: k2

958797
type: LocalParameter
value: 0.02
name: k1

COPASI50
type: Reaction
kinetic law: 959566
modifier: 086421
product: 959554
reactant: 959542
is version of: GO:0016311
fast: false
reversible: false
name: 4

959578
type: LocalParameter
value: 0.5
name: k1

959554
type: SpeciesReference
stoichiometry: 1.0
species: 958149

959542
type: SpeciesReference
stoichiometry: 1.0
species: COPASI20

COPASI45
type: Reaction
reversible: false
kinetic law: 959241
is version of: GO:0016311
product: 959229
name: 13_P2
reactant: 959217
modifier: 086289
is version of: GO:0043241
fast: false

959253
type: LocalParameter
value: 0.5
name: k1

959229
type: SpeciesReference
stoichiometry: 1.0
species: COPASI16

959217
type: SpeciesReference
stoichiometry: 1.0
species: COPASI15

COPASI53
type: Reaction
is version of: GO:0006461
reactant: 959737
reactant: 959724
fast: false
modifier: 086481
reversible: true
kinetic law: 959761
name: 12_P1
product: 959749
modifier: 086505
modifier: 086493

959737
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

959724
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

959787
type: LocalParameter
value: 1.0
name: k2

959774
type: LocalParameter
value: 0.01
name: k1

959749
type: SpeciesReference
stoichiometry: 1.0
species: COPASI26