MODEL1204280001
type: SBMLModel
reaction: COPASI19
function def: COPASI33
parameter: COPASI16
function def: COPASI37
reaction: COPASI28
parameter: COPASI11
species: 629975
name: 2
reaction: COPASI23
species: COPASI3
parameter: COPASI7
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
name: 5
species: 630013
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

COPASI19
type: Reaction
kinetic law: 630074
product: 630050
fast: false
reactant: 630038
reversible: false
modifier: 630062
modifier: 843546
name: 1
modifier: 843534

630086
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value: 0.2
name: k1

630050
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species: 629951

629951
type: Species
constant: false
boundary condition: false
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initial concentration: 0.0
initial amount: NaN
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name: MKKK_P

629927
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size: 1.0
spatial dimensions: 3.0
name: compartment

630038
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629939
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initial amount: NaN
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name: MKKK

630025
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boundary condition: false
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initial amount: NaN
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name: Sig

COPASI16
type: Parameter
constant: true
value: 30.0
name: K8

COPASI28
type: Reaction
modifier: 843920
reversible: false
modifier: 630791
modifier: 630804
fast: false
name: 3
product: 630778
kinetic law: 630817
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629975
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630778
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species: 629975

630830
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630765
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629963
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initial amount: NaN
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name: MKK

COPASI11
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constant: true
value: 30.0
name: K3

COPASI23
type: Reaction
modifier: 843691
modifier: 630388
modifier: 843715
kinetic law: 630401
fast: false
reactant: 630337
reversible: false
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modifier: 630363
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629987
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name: MKK_PP

COPASI5
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initial amount: NaN
in compartment: 629927
name: P2

630414
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value: 0.1
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630337
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630350
type: SpeciesReference
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COPASI3
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
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name: MK_P

COPASI7
type: Parameter
constant: true
value: 30.0
name: K2

630013
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COPASI4
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initial concentration: 99.9999951844376
initial amount: NaN
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name: P1

COPASI14
type: Parameter
constant: true
value: 30.0
name: K6

COPASI20
type: Reaction
product: 630112
modifier: 630136
modifier: 843570
kinetic law: 630148
reversible: false
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reactant: 630099
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fast: false
name: 2
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630112
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species: 629939

630160
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value: 0.01
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630099
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species: 629951

COPASI22
type: Reaction
fast: false
reversible: false
kinetic law: 630311
modifier: 630274
product: 630261
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modifier: 630298
name: 5
modifier: 843643
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reactant: 630248
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630324
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value: 0.1
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630261
type: SpeciesReference
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species: 629975

630248
type: SpeciesReference
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species: 629987

COPASI15
type: Parameter
constant: true
value: 30.0
name: K7

COPASI27
type: Reaction
kinetic law: 630739
modifier: 843872
modifier: 630726
reversible: false
name: 10
reactant: 630674
product: 630687
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fast: false
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630752
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value: 0.1
name: k10

COPASI2
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.9998844265
initial amount: NaN
in compartment: 629927
name: MK

630674
type: SpeciesReference
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630687
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species: COPASI2

630000
type: Species
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initial concentration: 0.0
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name: MK_PP

629903
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629915
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exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

COPASI18
type: Parameter
constant: true
value: 30.0
name: K10

COPASI13
type: Parameter
constant: true
value: 30.0
name: K5

629879
type: SBMLUnitsDef
unit: 629891
name: volume

629891
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exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE

COPASI25
type: Reaction
modifier: 843788
kinetic law: 630557
fast: false
product: 630518
modifier: 630544
modifier: 630531
name: 8
modifier: 843764
reversible: false
modifier: 843776
reactant: 630505

630570
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value: 0.1
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630518
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stoichiometry: 1.0
species: 630000

630505
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

COPASI9
type: Parameter
constant: true
value: 3.0E51
name: Kse2

COPASI17
type: Parameter
constant: true
value: 30.0
name: K9

COPASI12
type: Parameter
constant: true
value: 30.0
name: K4

COPASI24
type: Reaction
modifier: 843752
modifier: 630453
modifier: 843727
modifier: 843739
reactant: 630427
product: 630440
reversible: false
name: 7
kinetic law: 630479
modifier: 630466
fast: false

630427
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

630440
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

630492
type: LocalParameter
value: 0.1
name: k7

COPASI26
type: Reaction
kinetic law: 630648
modifier: 843812
reversible: false
modifier: 630635
modifier: 843836
modifier: 630622
product: 630596
modifier: 843800
modifier: 630609
fast: false
name: 9
modifier: 843824
reactant: 630583

630661
type: LocalParameter
value: 0.1
name: k9

630596
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

630583
type: SpeciesReference
stoichiometry: 1.0
species: 630000

COPASI8
type: Parameter
constant: true
value: 3.0E51
name: Kse1

COPASI6
type: Parameter
constant: true
value: 30.0
name: K1

COPASI21
type: Reaction
modifier: 630198
kinetic law: 630223
modifier: 630210
modifier: 843607
reactant: 630173
product: 630185
modifier: 843594
reversible: false
name: 4
modifier: 843619
fast: false

630235
type: LocalParameter
value: 0.1
name: k4

630173
type: SpeciesReference
stoichiometry: 1.0
species: 629975

630185
type: SpeciesReference
stoichiometry: 1.0
species: 629987

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