MODEL1204280013
type: SBMLModel
time units: 291235
reaction: COPASI22
function def: COPASI37
compartment: 368149
substance units: 368125
name: Sarma2012 - Interaction topologies of MAPK cascade (M1_K1_PSEQ_short_duration_signal)
parameter: COPASI10
species: 368185
is described by: http://identifiers.org/pubmed/22748295
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parameter: COPASI18
function def: COPASI38
function def: COPASI31
species: 368161
reaction: COPASI28
parameter: COPASI13
function def: COPASI32
area units: 061696
species: COPASI5
reaction: COPASI21
reaction: COPASI23
reaction: COPASI26
parameter: COPASI8
units def: 368125
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notes: Sarma2012 - Interaction topologies of MAPK cascade (M1_K1_PSEQ_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…
parameter: COPASI17
function def: COPASI36
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function def: COPASI30
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function def: COPASI35
species: COPASI3
parameter: COPASI15
reaction: COPASI20
name: 10
units def: 368101
reaction: COPASI25
parameter: COPASI7
reaction: COPASI27
parameter: COPASI9
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parameter: COPASI16
length unit: length
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function def: COPASI39
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parameter: COPASI11
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parameter: COPASI6
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function def: COPASI33
reaction: COPASI29
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parameter: COPASI14
volume units: 368101
function def: COPASI34
species: COPASI4
reaction: COPASI24
event: COPASI19

COPASI22
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COPASI10
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COPASI18
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COPASI28
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COPASI3
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COPASI13
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COPASI5
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COPASI21
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COPASI4
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368329
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COPASI23
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COPASI26
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369012
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COPASI8
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COPASI17
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COPASI12
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COPASI15
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COPASI20
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COPASI7
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COPASI27
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COPASI16
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COPASI11
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COPASI6
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