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750524
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COPASI3
constant: false
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name: MK
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COPASI28
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COPASI11
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COPASI21
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COPASI17
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name: Kse1
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750572
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COPASI4
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COPASI12
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COPASI27
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750824
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COPASI5
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MODEL1204280002
name: 7
function def: COPASI35
reaction: COPASI27
substance units: 750536
parameter: COPASI17
parameter: COPASI13
reaction: COPASI20
name: 4
time units: 291235
name: Sarma2012 - Interaction topologies of MAPK cascade (M2_K1_USEQ)
reaction: COPASI25
parameter: COPASI7
function def: COPASI38
function def: COPASI34
parameter: COPASI9
species: COPASI6
function def: COPASI33
function def: COPASI29
species: 750572
units def: 750512
reaction: COPASI22
reaction: COPASI24
is described by: http://identifiers.org/pubmed/22748295
name: 8
volume units: 750512
species: COPASI2
units def: 750536
species: COPASI3
area units: 061696
parameter: COPASI15
parameter: COPASI11
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function def: COPASI32
species: 750632
parameter: COPASI16
function def: COPASI31
species: 750620
reaction: COPASI21
reaction: COPASI23
compartment: 750560
reaction: COPASI19
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reaction: COPASI28
name: 2
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parameter: COPASI18
notes: Sarma2012 - Interaction topologies of MAPK cascade (M2_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…
species: COPASI4
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parameter: COPASI10
name: 10
parameter: COPASI12
species: 750596
function def: COPASI30
species: COPASI5
reaction: COPASI26
parameter: COPASI8
function def: COPASI36
name: 6
length unit: length
species: 750608
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750896
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750884
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COPASI23
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name: 5
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reversible: false
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fast: false
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COPASI26
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reversible: false
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kinetic law: 751292
name: 8
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750560
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
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750548
exponent: 1.0
scale: -9
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kind: MOLE
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COPASI19
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750620
constant: false
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751232
value: 0.1
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751328
stoichiometry: 1.0
species: COPASI4
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COPASI2
constant: false
boundary condition: false
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initial concentration: 299.999971106626
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name: MKKK
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751472
value: 0.1
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COPASI10
constant: true
value: 30.0
name: K4
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750656
stoichiometry: 1.0
species: 750572
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COPASI25
fast: false
modifier: 849296
reversible: false
name: 7
product: 751184
kinetic law: 751220
reactant: 751172
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modifier: 849308
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COPASI24
modifier: 849236
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kinetic law: 751148
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reversible: false

COPASI14
constant: true
value: 30.0
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COPASI8
constant: true
value: 30.0
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750596
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name: MKK_P
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750800
value: 0.01
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COPASI13
constant: true
value: 30.0
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751064
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COPASI9
constant: true
value: 30.0
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750644
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751172
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species: COPASI3
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751316
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751388
value: 0.1
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751400
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750944
value: 0.1
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COPASI16
constant: true
value: 30.0
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COPASI6
constant: false
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initial concentration: 199.999990368875
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name: P3
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750512
unit: 750524
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750584
constant: false
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name: MKK
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751052
value: 0.1
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750608
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COPASI15
constant: true
value: 30.0
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750632
constant: false
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name: Sig
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COPASI7
constant: true
value: 30.0
name: K1
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750704
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750812
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COPASI20
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type: Reaction
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751184
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