MODEL1204280037
species: 307756
parameter: COPASI14
substance units: 307434
parameter: COPASI7
type: SBMLModel
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species: COPASI3
name: 8
parameter: COPASI17
parameter: COPASI11
function def: COPASI47
species: 307719
function def: COPASI46
time units: 291235
units def: 307434
parameter: COPASI18
function def: COPASI42
reaction: COPASI26
reaction: COPASI22
is described by: http://identifiers.org/pubmed/22748295
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notes: Sarma2012 - Interaction topologies of MAPK cascade (M1_K2_QSS_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 (MODEL1204280001-40). 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…
function def: COPASI44
species: COPASI5
function def: COPASI41
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compartment: 307694
parameter: COPASI13
function def: COPASI40
parameter: COPASI6
name: 3
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event: COPASI19
reaction: COPASI28
reaction: COPASI24
name: 6
species: 307780
species: COPASI2
parameter: COPASI15
species: 307743
name: Sarma2012 - Interaction topologies of MAPK cascade (M1_K2_QSS_PSEQ)
function def: COPASI43
reaction: COPASI21
parameter: COPASI8
name: 7
name: 9
parameter: COPASI12
function def: COPASI49
species: 307706
units def: 307410
function def: COPASI48
curated: false
volume units: 307410
length unit: length
name: 4
reaction: COPASI27
reaction: COPASI23
reaction: COPASI29
reaction: COPASI25
species: 307791

COPASI19
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use values from trigger time: true
name: event_1
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COPASI24
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COPASI6
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COPASI18
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COPASI25
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COPASI11
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name: K3
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COPASI4
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COPASI12
constant: true
value: 500.0
name: K4
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COPASI2
constant: false
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initial concentration: 1199.99994221325
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COPASI23
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COPASI3
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initial concentration: 0.0
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COPASI13
constant: true
value: 24.3
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309132
persistant: true
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COPASI29
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reversible: false
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COPASI15
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exponent: 1.0
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COPASI9
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COPASI8
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COPASI17
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COPASI27
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COPASI16
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COPASI26
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