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notes: This the model from the article: A quantitative model for mRNA translation in Saccharomyces cerevisiae. You T, Coghill GM, Brown AJ. Yeast. 2010 Mar 19. epub ahead of print, PMID: 20306461 , doi: 10.1002/yea.1770 Abstract: Messenger RNA (mRNA) translation is an essential step in eukaryotic gene expression that contributes to the regulation of this process. We describe a deterministic model based on ordinary differential equations that describe mRNA translation in Saccharomyces cerevisiae. This model, which was parameterized using published data, was developed to examine the kinetic behaviour of translation initiation factors in response to amino acid availability. The model predicts that the abundance of the eIF1-eIF3-eIF5 complex increases under amino acid starvation conditions, suggesting a possible auxiliary role for these factors in modulating translation initiation in addition to the known mechanisms involving eIF2. Our analyses of the robustness of the mRNA translation model suggest that individual cells within a randomly generated population are sensitive to external perturbations (such as changes in amino acid availability) through Gcn2 signalling. However, the model predicts that individual cells exhibit robustness against internal perturbations (such as changes in the abundance of translation initiation factors and kinetic parameters). Gcn2 appears to enhance this robustness within the system. These findings suggest a trade-off between the robustness and performance of this biological network. The model also predicts that individual cells exhibit considerable heterogeneity with respect to their absolute translation rates, due to random internal perturbations. Therefore, averaging the kinetic behaviour of cell populations probably obscures the dynamic robustness of individual cells. This highlights the importance of single-cell measurements for evaluating network properties. Copyright (c) 2010 John Wiley and Sons, Ltd. This model originates from BioModels D…
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product: 050006
product: 049994
reactant: 049981
fast: false
reversible: false
name: v18
type: Reaction

metaid_0000103
kinetic law: 050751
fast: false
reactant: 050666
product: 050679
modifier: 050739
product: 050703
product: 050715
reversible: false
name: v32
product: 050691
product: 050727
type: Reaction

metaid_0000079
kinetic law: 049558
modifier: 049546
product: 049534
reactant: 049522
fast: false
reversible: false
name: v8
type: Reaction

049933
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

metaid_0000066
constant: true
units: metaid_0000111
value: 1.07E-4
name: k26
type: Parameter

050666
stoichiometry: 1.0
species: metaid_0000032
type: SpeciesReference

metaid_0000052
constant: true
units: metaid_0000111
value: 0.0157
name: k12
type: Parameter

049909
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

049667
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

050127
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

049145
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

metaid_0000012
constant: false
boundary condition: false
has only substance units: false
substance units: metaid_0000106
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000004
name: Gcn2(P)
type: Species

metaid_0000093
kinetic law: 050212
product: 050200
reactant: 050188
reactant: 050176
fast: false
reversible: false
name: v22
type: Reaction

049206
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

050042
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

050483
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

049485
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

metaid_0000067
constant: true
units: metaid_0000111
value: 0.00688
name: k27
type: Parameter

049945
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

metaid_0000053
constant: true
units: metaid_0000110
value: 1.41
name: k13
type: Parameter

049606
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000013
constant: false
boundary condition: false
has only substance units: false
substance units: metaid_0000106
initial concentration: NaN
initial amount: 63000.0
in compartment: metaid_0000004
name: eIF2-GDP
type: Species

metaid_0000092
kinetic law: 050164
product: 050152
reactant: 050139
reactant: 050127
fast: false
reversible: false
name: v21
type: Reaction

metaid_0000003
constant: true
units: metaid_0000107
size: 1.0
spatial dimensions: 3.0
name: vacuole
type: Compartment

049230
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

metaid_0000064
constant: true
units: metaid_0000111
value: 1.31E-6
name: k24
type: Parameter

049655
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000054
constant: true
units: metaid_0000110
value: 0.423
name: k14
type: Parameter

050090
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

050054
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

metaid_0000095
kinetic law: 050310
product: 050298
reactant: 050285
reactant: 050273
fast: false
reversible: false
name: v24
type: Reaction

049498
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000014
constant: false
boundary condition: false
has only substance units: false
substance units: metaid_0000106
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000004
name: eIF2(P)-GDP
type: Species

049315
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

050691
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

050763
stoichiometry: 1.0
species: metaid_0000033
type: SpeciesReference

050495
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

049133
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

metaid_0000029
constant: false
boundary condition: false
has only substance units: false
substance units: metaid_0000106
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000004
name: MFC
type: Species

metaid_0000100
kinetic law: 050555
product: 050543
reactant: 050531
reactant: 050519
fast: false
reversible: false
name: v29
type: Reaction

050679
stoichiometry: 1.0
species: metaid_0000033
type: SpeciesReference

049957
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

050445
stoichiometry: 1.0
species: metaid_0000028
type: SpeciesReference

metaid_0000065
constant: true
units: metaid_0000111
value: 0.0482
name: k25
type: Parameter

metaid_0000016
constant: false
boundary condition: false
has only substance units: false
substance units: metaid_0000106
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000004
name: eIF2B-eIF2-GDP
type: Species

metaid_0000055
constant: true
units: metaid_0000111
value: 5.04E-4
name: k15
type: Parameter

050200
stoichiometry: 1.0
species: metaid_0000026
type: SpeciesReference

metaid_0000094
kinetic law: 050261
product: 050249
product: 050236
reactant: 050224
fast: false
reversible: false
name: v23
type: Reaction

050102
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

metaid_0000015
constant: false
boundary condition: false
has only substance units: false
substance units: metaid_0000106
initial concentration: NaN
initial amount: 5000.0
in compartment: metaid_0000004
name: eIF2B
type: Species

metaid_00000119
kinetic law: 049254
product: 049242
reactant: 049230
fast: false
reversible: false
name: v2
type: Reaction

049109
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

049751
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

ORG:
  orgname: University of Aberdeen
n:
  given: Tao
  family: You

W3 CDTF: Tue Mar 23 23:49:09 GMT 2010

orgname: School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Aberdeen, AB25 3ZD, UK

W3 CDTF: Tue Mar 23 23:49:09 GMT 2010

given: Alistair
family: Brown

W3 CDTF: Fri Aug 08 18:30:55 BST 2008

given: Tao
family: You

W3 CDTF: Tue Mar 23 23:49:09 GMT 2010

ORG:
  orgname: University of Aberdeen

given: Alistair
family: Brown

orgname: School of Natural and Computing Sciences, University of Aberdeen, Computing Science Department, Aberdeen, AB24 3UE, UK

orgname: School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Aberdeen, AB25 3ZD, UK

ORG:
  orgname: School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Aberdeen, AB25 3ZD, UK
n:
  given: Alistair
  family: Brown

n:
  given: George
  family: Coghill

orgname: School of Natural and Computing Sciences, University of Aberdeen, Computing Science Department, Aberdeen, AB24 3UE, UK

n:
  given: George
  family: Coghill