MODEL1204280005
type: SBMLModel
parameter: COPASI9
reaction: COPASI21
parameter: COPASI13
name: 10
parameter: COPASI12
species: 978922
species: COPASI4
name: 9
reaction: COPASI19
name: 2
parameter: COPASI15
function def: COPASI30
curated: false
reaction: COPASI25
name: 7
parameter: COPASI6
substance units: 978814
compartment: 978838
function def: COPASI38
reaction: COPASI28
reaction: COPASI27
units def: 978790
function def: COPASI35
species: 978910
volume units: 978790
parameter: COPASI14
units def: 978814
species: 978934
time units: 291235
function def: COPASI31
length unit: length
parameter: COPASI17
area units: 061696
name: 4
parameter: COPASI16
species: COPASI3
species: 978898
function def: COPASI29
function def: COPASI33
species: 978862
name: 6
species: 978886
species: 978850
reaction: COPASI22
function def: COPASI36
parameter: COPASI8
parameter: COPASI7
name: 5
parameter: COPASI10
reaction: COPASI20
parameter: COPASI11
parameter: COPASI18
notes: Sarma2012 - Interaction topologies of MAPK cascade (M1_K1_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 [ MODEL12042800…
function def: COPASI32
species: COPASI5
reaction: COPASI26
name: 3
species: COPASI2
name: 8
reaction: COPASI24
reaction: COPASI23
function def: COPASI34
name: 1
function def: COPASI37
is described by: http://identifiers.org/pubmed/22748295
name: Sarma2012 - Interaction topologies of MAPK cascade (M1_K1_PSEQ)
species: 978874

COPASI9
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constant: true
value: 30.0
name: Kse2

COPASI21
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name: 4
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name: MKK

978838
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spatial dimensions: 3.0
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978862
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978886
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979138
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979090
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978898
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979078
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COPASI13
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COPASI12
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978922
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COPASI4
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COPASI19
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reversible: false
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978994
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978958
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species: 978862

COPASI15
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constant: true
value: 30.0
name: K7

COPASI25
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COPASI2
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COPASI3
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name: MK_P

979390
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979450
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979402
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978910
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COPASI6
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constant: true
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978814
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978826
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COPASI28
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product: 979642
reversible: false
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979690
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979642
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979630
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COPASI27
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979546
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979558
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978790
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unit: 978802
name: volume

978802
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scale: -3
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kind: LITRE

COPASI14
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constant: true
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name: K6

COPASI17
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constant: true
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COPASI16
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COPASI22
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979150
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COPASI8
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COPASI7
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COPASI10
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COPASI20
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fast: false
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979006
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979018
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COPASI11
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constant: true
value: 30.0
name: K3

COPASI18
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constant: true
value: 30.0
name: K10

COPASI26
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reactant: 979462
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product: 979474
kinetic law: 979522
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979462
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979474
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979534
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COPASI24
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product: 979330
modifier: 867582
kinetic law: 979366
name: 7
fast: false
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979330
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979378
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979318
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COPASI23
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reversible: false
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979306
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979234
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979246
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