175119
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COPASI23
reactant: 175107
modifier: 091363
reversible: true
modifier: 091375
fast: false
type: Reaction
name: 16
kinetic law: 175131
product: 175119
is version of: GO:0051169

175239
stoichiometry: 1.0
species: 173809
type: SpeciesReference

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value: 0.1
name: k2
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174818
value: 20.0
name: K10
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species: 173821
type: SpeciesReference

175515
value: 0.31
name: k22
type: LocalParameter

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species: 173881
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175311
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species: 173917
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species: 173785
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in compartment: COPASI2
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173929
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type: SpeciesReference

COPASI24
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modifier: 091387
reactant: 175167
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name: 17
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174662
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COPASI25
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COPASI9
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COPASI26
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kinetic law: 175263
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174253
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174854
stoichiometry: 1.0
species: COPASI4
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174758
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species: 173809
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175299
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species: 173821
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BIOMD0000000444
reaction: COPASI11
species: 173809
reaction: COPASI14
type: SBMLModel
function def: 173698
species: 173821
name: function_4_5_1
function def: 173673
function def: 173621
species: 173905
parameter: COPASI7
area units: area
reaction: COPASI16
name: Sarma2012 - Oscillations in MAPK cascade (S2n)
name: function_4_9_1
name: function_4_3_1
reaction: COPASI28
species: 173857
function def: COPASI34
species: 173845
reaction: COPASI19
reaction: COPASI22
name: function_4_2_1
name: function_4_4_1
notes: Sarma2012 - Oscillations in MAPK cascade (S2n) Two plausible designs (S1 and S2) of coupled positive and negative feedback loops of MAPK cascade has been described in this paper. Further these models were extended to S1n and S2n, to incorporate the nuclear-cytoplasmic translocation of the MK layer components of the cascade. This model corresponds to model S2n that comprises negative feedback from MK-PP to MKK-PP layer coupled to positive feedback from MK-PP to MKKK-PP layer, with the inclusion of nuclear-cytoplasmic translocation. This model is described in the article: Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops. Sarma U, Ghosh I. BMC Res Notes. 2012 Jun 13;5:287. Abstract: BACKGROUND: Feedback loops, both positive and negative are embedded in the Mitogen Activated Protein Kinase (MAPK) cascade. In the three layer MAPK cascade, both feedback loops originate from the terminal layer and their sites of action are either of the two upstream layers. Recent studies have shown that the cascade uses coupled positive and negative feedback loops in generating oscillations. Two plausible designs of coupled positive and negative feedback loops can be elucidated from the literature; in one design the positive feedback precedes the negative feedback in the direction of signal flow and vice-versa in another. But it remains unexplored how the two designs contribute towards triggering oscillations in MAPK cascade. Thus it is also not known how amplitude, frequency, robustness or nature (analogous/digital) of the oscillations would be shaped by these two designs. RESULTS: We built two models of MAPK cascade that exhibited oscillations as function of two underlying designs of coupled positive and negative feedback loops. Frequency, amplitude and nature (digital/analogous) of oscillations were found to be differentially determined by each design. It was observed that the positive feedback emerging from an oscillating M…
reaction: COPASI12
species: 173785
function def: 173609
reaction: COPASI9
species: 173773
curated: true
reaction: COPASI25
function def: 173634
species: 173917
species: COPASI6
compartment: COPASI2
is: MODEL1112190007
function def: 173660
species: COPASI5
function def: COPASI31
is: GO:0000165
species: 173893
species: 173881
units def: 173711
reaction: COPASI20
reaction: COPASI17
reaction: COPASI8
species: 173797
length unit: length
reaction: COPASI10
reaction: COPASI29
function def: COPASI30
name: function_4_6_1
name: function_4_10_1
reaction: COPASI23
reaction: COPASI26
function def: COPASI35
reaction: COPASI13
volume units: 173711
species: 173869
function def: 173686
name: 22
units def: 173737
name: function_4_8_1
name: function_4_7_1
is: http://identifiers.org/taxonomy/131567
name: function_4_1_1
name: 11
name: 12
function def: COPASI32
is described by: http://identifiers.org/pubmed/22694947
function def: 173596
species: 173761
reaction: COPASI15
reaction: COPASI18
function def: COPASI33
name: 15
species: COPASI4
time units: time
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174241
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COPASI20
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reversible: false
name: 13
type: Reaction

173773
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name: M_n

173893
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COPASI21
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174337
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COPASI22
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fast: false
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name: MKK_P
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174145
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173917
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name: M_P_n
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174121
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174541
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175443
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name: K21i
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174397
value: 0.1
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174830
value: 0.02
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type: LocalParameter

COPASI4
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has only substance units: false
occurs in: GO:0005634
name: M_PP_n
constant: false
boundary condition: false
type: Species
initial amount: NaN

174746
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species: 173821
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175143
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name: k1
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COPASI19
is version of: GO:0009299
kinetic law: 174926
modifier: 091315
product: 174902
fast: false
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reversible: false
name: 12
modifier: 174914

COPASI3
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constant: false
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has only substance units: false
initial concentration: 3999.9998073775
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name: MKK
type: Species

175251
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174133
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175455
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COPASI10
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kinetic law: 174193
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type: Reaction
fast: false
reversible: false
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modifier: 091011
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name: 4
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initial concentration: 999.999903688753
initial amount: NaN
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name: MKKK
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value: 0.02
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174037
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species: 173785
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174385
value: 20.0
name: K8
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COPASI2
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constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

174109
value: 9.0
name: KI
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175359
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species: COPASI4
type: SpeciesReference

173809
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initial concentration: 999.999903688753
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name: M
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174890
value: 2.86
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exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

175155
value: 15.4
name: k2
type: LocalParameter

174565
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species: 173785
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174722
value: 20.0
name: K9
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COPASI8
modifier: 173953
name: 1
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kinetic law: 173965
modifier: 090939
reversible: false
product: 173941
reactant: 173929
is version of: GO:0016310
fast: false
type: Reaction

174638
value: 0.02
name: k6
type: LocalParameter

174938
value: 29.24
name: V12
type: LocalParameter

173711
unit: 173724
name: volume
type: SBMLUnitsDef

COPASI16
modifier: 091242
modifier: 174674
reversible: false
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type: Reaction
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fast: false
name: 9
modifier: 174686
is version of: GO:0016311
kinetic law: 174710
product: 174662
reactant: 174650
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175371
stoichiometry: 1.0
species: 173917
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175287
value: 2.86
name: k2
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COPASI12
modifier: 174349
reactant: 174325
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fast: false
type: Reaction
name: 8
reversible: false
kinetic law: 174373
modifier: 174361
product: 174337
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modifier: 091108
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174025
stoichiometry: 1.0
species: COPASI3
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173977
value: 100.0
name: A
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174950
value: 3.97
name: n12
type: LocalParameter

174217
value: 9.0
name: KI
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175347
value: 2.86
name: k2
type: LocalParameter

174577
stoichiometry: 1.0
species: COPASI3
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COPASI7
constant: true
value: 0.022
name: k13
type: Parameter

174650
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species: 173833
type: SpeciesReference

COPASI15
fast: false
modifier: 091206
product: 174577
type: Reaction
modifier: 091194
modifier: 174601
reactant: 174565
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kinetic law: 174614
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name: 6
reversible: false
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COPASI29
modifier: 175491
modifier: 175479
modifier: 091509
fast: false
modifier: 091521
reactant: 175455
name: 22
reversible: false
type: Reaction
is version of: GO:0016311
kinetic law: 175503
product: 175467
modifier: 091497

COPASI11
fast: false
is version of: GO:0016310
reversible: false
product: 174253
reactant: 174241
type: Reaction
kinetic law: 174289
name: 7
modifier: 091071
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modifier: 091059
modifier: 174277

173869
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constant: false
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initial concentration: 499.999975922188
initial amount: NaN
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name: P3
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COPASI6
boundary condition: false
name: P3_n
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type: Species
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constant: false
initial amount: NaN
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is version of: P51452

175431
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174553
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COPASI14
reversible: false
reactant: 174481
type: Reaction
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name: 5
kinetic law: 174529
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175275
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COPASI18
type: Reaction
reversible: true
modifier: 091291
kinetic law: 174866
modifier: 091303
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fast: false
reactant: 174842
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174013
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175058
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species: COPASI5
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174626
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COPASI28
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fast: false
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reversible: false
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kinetic law: 175407
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174205
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174481
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175419
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173989
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174962
value: 169.0
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COPASI5
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COPASI17
modifier: 091266
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type: Reaction
fast: false
product: 174758
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reversible: false
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name: 10
kinetic law: 174806

COPASI13
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kinetic law: 174445
modifier: 091120
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type: Reaction
reactant: 174409
fast: false
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product: 174421
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is version of: GO:0016311

173724
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

175335
value: 10.34
name: k1
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175107
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

COPASI27
fast: false
reactant: 175299
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kinetic law: 175323
modifier: 091436
name: 20
type: Reaction
reversible: true
is version of: GO:0051169
modifier: 091448

orgname: National Centre for Cell Science

W3 CDTF: Mon Mar 18 14:07:51 GMT 2013

n:
  given: Uddipan
  family: Sarma

given: Nick
family: Juty

ORG:
  orgname: EMBL-EBI

ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah

W3 CDTF: Wed May 22 14:50:32 BST 2013