BIOMD0000000433
type: SBMLModel
name: 8
reaction: COPASI21
is: MODEL1204280040
parameter: COPASI17
reaction: COPASI30
volume units: 584495
parameter: COPASI10
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species: 584591
reaction: COPASI25
area units: 844749
species: 584579
function def: COPASI35
species: 584615
units def: 584495
species: 584543
function def: COPASI31
substance units: 584519
compartment: COPASI3
name: 7
parameter: COPASI14
name: 6
species: COPASI5
parameter: COPASI8
occurs in: http://identifiers.org/taxonomy/131567
name: 10
function def: COPASI40
function def: COPASI36
is described by: http://identifiers.org/pubmed/22748295
species: COPASI6
function def: COPASI32
function def: COPASI37
reaction: COPASI22
function def: COPASI39
parameter: COPASI11
function def: COPASI33
parameter: COPASI18
creator:
  ORG:
    orgname: National Centre for Cell Science
  n:
    given: Uddipan
    family: Sarma
species: 584567
species: 584627
species: 584555
reaction: COPASI28
name: 5
curated: true
parameter: COPASI7
name: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_QSS_PSEQ)
reaction: COPASI26
created:
  W3 CDTF: Fri Nov 23 16:21:55 GMT 2012
name: 4
parameter: COPASI20
parameter: COPASI15
parameter: COPASI9
time units: 844725
is version of: GO:0000165
species: COPASI4
units def: 584519
reaction: COPASI23
name: 9
species: 584603
parameter: COPASI16
parameter: COPASI19
function def: COPASI38
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
function def: COPASI34
reaction: COPASI29
parameter: COPASI12
name: 3
reaction: COPASI24
reaction: COPASI27
name: 2
parameter: COPASI13
notes: Sarma2012 - Interaction topologies of MAPK cascade (M4_K2_QSS_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-MODEL1204280040). 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_USE…
compartment: COPASI2
modified:
  W3 CDTF: Fri Dec 14 14:16:31 GMT 2012
length unit: 844677

COPASI21
type: Reaction
modifier: 584663
is version of: GO:0016310
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reactant: 584639
reversible: false
modifier: 712593
product: 584651
kinetic law: 584675
name: 1
fast: false

584627
type: Species
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constant: false
boundary condition: false
has only substance units: false
initial concentration: 20.0
initial amount: NaN
in compartment: COPASI2
name: Sig

COPASI2
type: Compartment
is version of: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment

584543
type: Species
is version of: P04049
constant: false
boundary condition: false
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initial concentration: 300.0
initial amount: NaN
in compartment: COPASI2
name: MKKK

584639
type: SpeciesReference
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species: 584543

584651
type: SpeciesReference
stoichiometry: 1.0
species: 584555

584555
type: Species
boundary condition: false
initial amount: NaN
initial concentration: 0.0
is version of: P04049
is version of: C00562
has only substance units: false
name: MKKK_P
constant: false
in compartment: COPASI2

584687
type: LocalParameter
value: 1.0
name: k1

COPASI17
type: Parameter
constant: true
value: 0.06
name: Kse1

COPASI30
type: Reaction
modifier: 585623
modifier: 585587
reversible: false
modifier: 713205
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fast: false
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reactant: 585551
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name: 10

COPASI4
type: Species
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constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: COPASI2
name: MK

584579
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constant: false
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name: MKK_P
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initial amount: NaN
in compartment: COPASI2
boundary condition: false
has only substance units: false

584591
type: Species
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boundary condition: false
initial amount: NaN
constant: false
is version of: Q02750
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is version of: C00562
name: MKK_PP
initial concentration: 0.0

584567
type: Species
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boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: COPASI2
name: MKK

585551
type: SpeciesReference
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584603
type: Species
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initial amount: NaN
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constant: false
in compartment: COPASI2
initial concentration: 0.0

584615
type: Species
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name: MK_PP
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is version of: P27361
initial concentration: 0.0
constant: false
in compartment: COPASI2
has only substance units: false

585563
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

COPASI6
type: Species
is version of: P51452
constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
in compartment: COPASI2
name: P2

585659
type: LocalParameter
value: 0.086
name: k10b

584495
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unit: 584507
name: volume

584507
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE

COPASI10
type: Parameter
constant: true
value: 500.0
name: K4

COPASI25
type: Reaction
modifier: 712773
modifier: 712845
modifier: 585059
modifier: 584987
product: 584963
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fast: false
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kinetic law: 585083
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name: 5
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reactant: 584951
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reversible: false

584963
type: SpeciesReference
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species: 584579

585107
type: LocalParameter
value: 0.092
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585095
type: LocalParameter
value: 0.092
name: k5a

COPASI5
type: Species
is version of: P51452
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
initial amount: NaN
in compartment: COPASI2
name: P1

584951
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584519
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584531
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

COPASI3
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: No Name

COPASI14
type: Parameter
constant: true
value: 500.0
name: K8

COPASI8
type: Parameter
constant: true
value: 54.3
name: K2a

COPASI22
type: Reaction
modifier: 584735
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modifier: 584771
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modifier: 712617
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reversible: false
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name: 2
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584699
type: SpeciesReference
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584795
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value: 0.086
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584711
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species: 584543

COPASI11
type: Parameter
constant: true
value: 24.3
name: K5a

COPASI18
type: Parameter
constant: true
value: 0.06
name: Kse2

COPASI28
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product: 585371
name: 8
modifier: 585395
fast: false
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is version of: GO:0016310
kinetic law: 585407
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reversible: false
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585371
type: SpeciesReference
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species: 584615

585419
type: LocalParameter
value: 15.0
name: k7

585359
type: SpeciesReference
stoichiometry: 1.0
species: 584603

COPASI7
type: Parameter
constant: true
value: 100.0
name: K1

COPASI26
type: Reaction
modifier: 712929
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fast: false
modifier: 712893
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is version of: GO:0016311
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name: 6
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kinetic law: 585251
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product: 585131
reactant: 585119
reversible: false
modifier: 585203

585275
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value: 0.086
name: k6b

585263
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value: 0.086
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585131
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585119
type: SpeciesReference
stoichiometry: 1.0
species: 584579

COPASI20
type: Parameter
constant: true
value: 108.6
name: K6b

COPASI15
type: Parameter
constant: true
value: 24.3
name: K9b

COPASI9
type: Parameter
constant: true
value: 50.5
name: K3

COPASI23
type: Reaction
product: 584819
kinetic law: 584855
is version of: GO:0016310
reactant: 584807
modifier: 584831
modifier: 712677
reversible: false
modifier: 712689
modifier: 712701
name: 3
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fast: false

584819
type: SpeciesReference
stoichiometry: 1.0
species: 584579

584867
type: LocalParameter
value: 0.01
name: k3

584807
type: SpeciesReference
stoichiometry: 1.0
species: 584567

COPASI16
type: Parameter
constant: true
value: 108.6
name: K10b

COPASI19
type: Parameter
constant: true
value: 24.3
name: K5b

COPASI29
type: Reaction
reversible: false
name: 9
modifier: 585503
modifier: 713085
modifier: 585455
modifier: 713109
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reactant: 585431
modifier: 585467
modifier: 713061
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kinetic law: 585527
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585431
type: SpeciesReference
stoichiometry: 1.0
species: 584615

585539
type: LocalParameter
value: 0.092
name: k9b

585443
type: SpeciesReference
stoichiometry: 1.0
species: 584603

COPASI12
type: Parameter
constant: true
value: 108.6
name: K6a

COPASI24
type: Reaction
reactant: 584879
kinetic law: 584927
fast: false
modifier: 584915
product: 584891
is version of: GO:0016310
modifier: 584903
modifier: 712737
name: 4
modifier: 712713
reversible: false
modifier: 712725

584879
type: SpeciesReference
stoichiometry: 1.0
species: 584579

584939
type: LocalParameter
value: 15.0
name: k4

584891
type: SpeciesReference
stoichiometry: 1.0
species: 584591

COPASI27
type: Reaction
modifier: 713013
reversible: false
modifier: 585311
is version of: GO:0016310
fast: false
reactant: 585287
name: 7
modifier: 712989
kinetic law: 585335
modifier: 713001
product: 585299
modifier: 585323

585287
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

585347
type: LocalParameter
value: 0.01
name: k7

585299
type: SpeciesReference
stoichiometry: 1.0
species: 584603

COPASI13
type: Parameter
constant: true
value: 50.5
name: K7