COPASI21
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COPASI15
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630752
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629915
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629975
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630414
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COPASI22
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630112
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630596
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630661
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COPASI9
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COPASI16
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630248
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COPASI8
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630492
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COPASI17
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COPASI27
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630687
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COPASI20
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COPASI7
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629891
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MODEL1204280001
reaction: COPASI19
function def: COPASI33
parameter: COPASI16
function def: COPASI37
reaction: COPASI28
type: SBMLModel
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notes: Sarma2012 - Interaction topologies of MAPK cascade (M1_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…
name: 3
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species: COPASI4
parameter: COPASI14
species: 629951
reaction: COPASI20
function def: COPASI30
reaction: COPASI22
curated: false
function def: COPASI31
parameter: COPASI15
function def: COPASI35
name: 6
length unit: length
reaction: COPASI27
name: 1
species: 629963
name: 7
name: 9
units def: 629903
parameter: COPASI18
name: 10
parameter: COPASI13
name: 4
volume units: 629879
units def: 629879
species: 630000
reaction: COPASI25
species: COPASI5
parameter: COPASI9
compartment: 629927
time units: 291235
function def: COPASI34
species: 629939
species: 630025
function def: COPASI38
parameter: COPASI17
is described by: http://identifiers.org/pubmed/22748295
name: 8
function def: COPASI29
substance units: 629903
species: COPASI2
parameter: COPASI12
species: 629987
area units: 061696
reaction: COPASI24
reaction: COPASI26
name: Sarma2012 - Interaction topologies of MAPK cascade (M1_K1_USEQ)
parameter: COPASI8
parameter: COPASI6
reaction: COPASI21
function def: COPASI32
function def: COPASI36
parameter: COPASI10

COPASI10
constant: true
value: 3.0E51
name: Kse3
type: Parameter

630185
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630518
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630099
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630337
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COPASI18
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COPASI28
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630765
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629939
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629951
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630505
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COPASI4
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630440
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630830
value: 0.1
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630013
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COPASI11
constant: true
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COPASI25
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629879
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630261
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COPASI19
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COPASI5
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COPASI6
constant: true
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630324
value: 0.1
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COPASI12
constant: true
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COPASI26
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630778
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629927
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630350
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630235
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COPASI2
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630173
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COPASI13
constant: true
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COPASI23
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630427
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630086
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COPASI3
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COPASI14
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630570
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COPASI24
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630000
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name: MK_PP
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