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notes: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_USEQ_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…
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name: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_USEQ_short_duration_signal)
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is described by: http://identifiers.org/pubmed/22748295
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041688
type: LocalParameter
value: 0.045
name: k1

041640
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

041653
type: SpeciesReference
stoichiometry: 1.0
species: COPASI21

041664
type: SpeciesReference
stoichiometry: 1.0
species: COPASI25

COPASI35
type: Reaction
kinetic law: 039708
modifier: 988983
product: 039696
product: 039684
reactant: 039671
fast: false
reversible: false
name: 20

039720
type: LocalParameter
value: 0.092
name: k1

039696
type: SpeciesReference
stoichiometry: 1.0
species: COPASI14

039684
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

039671
type: SpeciesReference
stoichiometry: 1.0
species: COPASI22