MODEL1204280012
type: SBMLModel
is described by: http://identifiers.org/pubmed/22748295
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reaction: COPASI24
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length unit: length
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parameter: COPASI20
parameter: COPASI9
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reaction: COPASI31
area units: 061696
function def: 365164
function def: 365212
name: Sarma2012 - Interaction topologies of MAPK cascade (M4_K1_USEQ_short_duration_signal)
reaction: COPASI27
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parameter: COPASI16
reaction: COPASI23
parameter: COPASI10
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name: function_4_7_1
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parameter: COPASI19
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event: COPASI21
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reaction: COPASI30
parameter: COPASI14
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volume units: 365284
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reaction: COPASI26
units def: 365284
reaction: COPASI22
reaction: COPASI29
name: function_4_4_1
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function def: 365248
name: function_4_2_1
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notes: Sarma2012 - Interaction topologies of MAPK cascade (M4_K1_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…
species: COPASI6
name: function_4_8_1
compartment: COPASI3
name: function_4_1_1
curated: false
function def: 365272
function def: 365260
name: function_4_5_1
units def: 365308
time units: 291235
species: 365392
parameter: COPASI17
name: function_4_10_1
parameter: COPASI13
reaction: COPASI28
species: 365416

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COPASI9
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COPASI10
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COPASI7
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COPASI12
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constant: true
value: 30.0
name: K6a

COPASI19
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constant: true
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COPASI21
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use values from trigger time: true
name: event_1

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COPASI3
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spatial dimensions: 3.0
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COPASI17
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COPASI13
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COPASI28
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