MODEL1204280003
type: SBMLModel
parameter: COPASI3
name: 1
function def: COPASI34
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species: 856277
parameter: COPASI10
reaction: COPASI20
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function def: COPASI26
species: 856337
is described by: http://identifiers.org/pubmed/22748295
parameter: COPASI5
name: 10
function def: COPASI25
curated: false
function def: COPASI29
species: 856253
compartment: 856217
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area units: 061696
length unit: length
name: 4
parameter: COPASI12
function def: COPASI30
parameter: COPASI14
reaction: COPASI24
reaction: COPASI16
parameter: COPASI9
reaction: COPASI18
function def: COPASI32
notes: Sarma2012 - Interaction topologies of MAPK cascade (M3_K1_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…
function def: COPASI28
name: 8
function def: COPASI33
function def: COPASI27
reaction: COPASI22
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parameter: COPASI7
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parameter: COPASI11
parameter: COPASI13
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reaction: COPASI15
reaction: COPASI17
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function def: COPASI31
name: Sarma2012 - Interaction topologies of MAPK cascade (M3_K1_USEQ)
reaction: COPASI21
species: COPASI2
substance units: 856193
parameter: COPASI6
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parameter: COPASI8
reaction: COPASI19
parameter: COPASI4
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species: 856265
time units: 291235
reaction: COPASI23
volume units: 856169
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COPASI10
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COPASI20
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COPASI2
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COPASI12
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COPASI14
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COPASI24
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COPASI16
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COPASI9
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COPASI18
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856613
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COPASI22
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856997
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COPASI7
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COPASI11
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COPASI13
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COPASI15
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COPASI6
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COPASI8
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constant: true
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COPASI19
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856637
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COPASI4
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