MODEL1204280035
type: SBMLModel
parameter: COPASI6
species: 275046
curated: false
parameter: COPASI3
length unit: length
function def: COPASI30
name: 7
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name: 9
area units: 061696
event: COPASI15
reaction: COPASI17
function def: COPASI35
parameter: COPASI11
parameter: COPASI13
species: 275131
reaction: COPASI20
name: 4
reaction: COPASI22
reaction: COPASI24
species: 275107
function def: COPASI28
function def: COPASI29
species: 275083
reaction: COPASI19
parameter: COPASI5
parameter: COPASI8
function def: COPASI33
name: 8
function def: COPASI34
species: COPASI2
compartment: 274897
reaction: COPASI16
species: 275059
substance units: 274873
reaction: COPASI23
parameter: COPASI10
parameter: COPASI4
parameter: COPASI12
species: 275119
function def: COPASI26
function def: COPASI27
species: 274909
species: 275071
name: 1
name: Sarma2012 - Interaction topologies of MAPK cascade (M3_K2_QSS_USEQ)
volume units: 274849
reaction: COPASI18
units def: 274849
parameter: COPASI7
function def: COPASI31
function def: COPASI32
parameter: COPASI14
name: 10
species: 275143
name: 3
name: 2
name: 5
time units: 291235
units def: 274873
reaction: COPASI21
species: 275095
reaction: COPASI25
parameter: COPASI9
notes: Sarma2012 - Interaction topologies of MAPK cascade (M3_K2_QSS_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 [ MODEL1204…
is described by: http://identifiers.org/pubmed/22748295

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value: 500.0
name: K4

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274897
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spatial dimensions: 3.0
name: compartment

COPASI3
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value: 100.0
name: K1

COPASI15
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event assignment: 276705
trigger: 276693
use values from trigger time: true
name: event_1

275143
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COPASI17
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274909
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COPASI11
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value: 24.6
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COPASI13
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constant: true
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275131
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COPASI20
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COPASI22
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276255
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COPASI24
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276573
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COPASI19
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275687
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COPASI5
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COPASI8
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constant: true
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name: K6

COPASI16
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COPASI4
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COPASI18
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275457
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275505
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COPASI7
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COPASI14
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constant: true
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COPASI21
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276056
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COPASI25
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276681
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COPASI9
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