MODEL1204280034
type: SBMLModel
name: 1
event: COPASI19
parameter: COPASI18
function def: COPASI38
function def: COPASI39
curated: false
species: 235649
reaction: COPASI24
name: 9
name: 3
name: 2
name: 5
species: 235673
species: COPASI5
function def: COPASI32
species: 235697
function def: COPASI33
substance units: 235601
units def: 235577
parameter: COPASI12
parameter: COPASI17
parameter: COPASI9
species: COPASI6
length unit: length
function def: COPASI37
volume units: 235577
name: 7
name: 6
species: COPASI2
parameter: COPASI10
notes: Sarma2012 - Interaction topologies of MAPK cascade (M2_K2_QSS_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 [ MODEL1204…
species: 235637
function def: COPASI30
function def: COPASI31
reaction: COPASI29
reaction: COPASI27
reaction: COPASI21
reaction: COPASI23
name: 4
function def: COPASI36
parameter: COPASI16
parameter: COPASI8
parameter: COPASI14
compartment: 235625
time units: 291235
parameter: COPASI15
parameter: COPASI11
reaction: COPASI25
is described by: http://identifiers.org/pubmed/22748295
name: 8
species: COPASI4
species: COPASI3
species: 235685
name: Sarma2012 - Interaction topologies of MAPK cascade (M2_K2_QSS_USEQ)
units def: 235601
name: 10
reaction: COPASI28
species: 235661
reaction: COPASI26
function def: COPASI35
function def: COPASI34
parameter: COPASI7
reaction: COPASI20
parameter: COPASI13
area units: 061696
reaction: COPASI22

COPASI19
type: Event
event assignment: 237436
trigger: 237270
use values from trigger time: true
name: event_1

235697
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 20.0
initial amount: NaN
in compartment: 235625
name: Sig

235625
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment

237270
type: Trigger
persistant: true
initial value: true

COPASI18
type: Parameter
constant: true
value: 3.0E51
name: Kse2

235649
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: 235625
name: MKK

COPASI24
type: Reaction
product: 236448
reactant: 236436
modifier: 236496
modifier: 022096
fast: false
modifier: 022132
modifier: 022120
modifier: 236472
modifier: 236460
name: 5
modifier: 022108
modifier: 236484
kinetic law: 236520
modifier: 022156
modifier: 022144
modifier: 236508
reversible: false

236448
type: SpeciesReference
stoichiometry: 1.0
species: 235661

235661
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 235625
name: MKK_P

236436
type: SpeciesReference
stoichiometry: 1.0
species: 235673

235673
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 235625
name: MKK_PP

COPASI5
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
initial amount: NaN
in compartment: 235625
name: P1

235637
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 235625
name: MKKK_P

236532
type: LocalParameter
value: 0.092
name: k5

COPASI2
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 299.999985553313
initial amount: NaN
in compartment: 235625
name: MKKK

235601
type: SBMLUnitsDef
unit: 235613
name: substance

235613
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

235577
type: SBMLUnitsDef
unit: 235589
name: volume

235589
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE

COPASI12
type: Parameter
constant: true
value: 108.6
name: K6

COPASI17
type: Parameter
constant: true
value: 3.0E51
name: Kse1

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

COPASI6
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
in compartment: 235625
name: P3

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

COPASI29
type: Reaction
modifier: 237222
modifier: 022396
modifier: 022372
fast: false
reversible: false
modifier: 022360
name: 10
modifier: 237210
product: 237198
modifier: 237234
modifier: 022384
reactant: 237186
kinetic law: 237246

COPASI3
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1199.99994221325
initial amount: NaN
in compartment: 235625
name: MK

235685
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 235625
name: MK_PP

COPASI4
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 235625
name: MK_P

237198
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

237186
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

237258
type: LocalParameter
value: 0.086
name: k10

COPASI27
type: Reaction
fast: false
modifier: 022300
reactant: 236878
modifier: 236902
kinetic law: 237077
name: 8
modifier: 022288
product: 236890
reversible: false
modifier: 236914
modifier: 022276

236878
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

237090
type: LocalParameter
value: 15.0
name: k7

236890
type: SpeciesReference
stoichiometry: 1.0
species: 235685

COPASI21
type: Reaction
modifier: 021976
modifier: 236080
modifier: 236104
fast: false
modifier: 236068
modifier: 021964
reversible: false
modifier: 236056
modifier: 021988
reactant: 236032
modifier: 022012
modifier: 236092
name: 2
modifier: 021952
product: 236044
modifier: 022000
kinetic law: 236116

236032
type: SpeciesReference
stoichiometry: 1.0
species: 235637

236044
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

236128
type: LocalParameter
value: 0.086
name: k2

COPASI23
type: Reaction
reactant: 236212
product: 236224
kinetic law: 236412
reversible: false
name: 4
modifier: 236387
modifier: 022060
modifier: 022084
modifier: 022072
fast: false
modifier: 236400

236212
type: SpeciesReference
stoichiometry: 1.0
species: 235661

236224
type: SpeciesReference
stoichiometry: 1.0
species: 235673

236424
type: LocalParameter
value: 15.0
name: k4

COPASI16
type: Parameter
constant: true
value: 108.6
name: K10

COPASI8
type: Parameter
constant: true
value: 54.3
name: K2

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

COPASI15
type: Parameter
constant: true
value: 24.6
name: K9

COPASI11
type: Parameter
constant: true
value: 26.6
name: K5

COPASI25
type: Reaction
reactant: 236544
name: 6
reversible: false
product: 236556
modifier: 236580
modifier: 236568
kinetic law: 236782
modifier: 236770
modifier: 236758
modifier: 022168
fast: false
modifier: 022192
modifier: 022180
modifier: 236745
modifier: 022204
modifier: 022228
modifier: 022216

236544
type: SpeciesReference
stoichiometry: 1.0
species: 235661

236556
type: SpeciesReference
stoichiometry: 1.0
species: 235649

236794
type: LocalParameter
value: 0.086
name: k6

COPASI28
type: Reaction
name: 9
modifier: 022324
product: 237114
modifier: 237126
modifier: 022312
modifier: 237150
modifier: 022348
kinetic law: 237162
reactant: 237102
modifier: 237138
fast: false
reversible: false
modifier: 022336

237114
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

237174
type: LocalParameter
value: 0.092
name: k9

237102
type: SpeciesReference
stoichiometry: 1.0
species: 235685

COPASI26
type: Reaction
modifier: 022252
reactant: 236806
modifier: 236830
name: 7
product: 236818
modifier: 022264
modifier: 022240
reversible: false
kinetic law: 236854
fast: false
modifier: 236842

236806
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

236818
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

236866
type: LocalParameter
value: 0.01
name: k7

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

COPASI20
type: Reaction
fast: false
name: 1
reversible: false
product: 235721
reactant: 235709
kinetic law: 235745
modifier: 021928
modifier: 235733
modifier: 021940

235721
type: SpeciesReference
stoichiometry: 1.0
species: 235637

235709
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

236020
type: LocalParameter
value: 1.0
name: k1

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

COPASI22
type: Reaction
modifier: 022048
modifier: 236164
fast: false
name: 3
modifier: 236176
kinetic law: 236188
modifier: 022024
product: 236152
reactant: 236140
modifier: 022036
reversible: false

236200
type: LocalParameter
value: 0.01
name: k3

236152
type: SpeciesReference
stoichiometry: 1.0
species: 235661

236140
type: SpeciesReference
stoichiometry: 1.0
species: 235649