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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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049981
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

metaid_0000097
type: Reaction
kinetic law: 050408
product: 050396
reactant: 050384
reactant: 050371
fast: false
reversible: false
name: v26

050396
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

050384
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

050371
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

metaid_0000030
type: Species
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-eIF5

metaid_0000039
type: Parameter
constant: true
units: metaid_0000108
value: 8730000.0
name: K_M_ATP

metaid_0000060
type: Parameter
constant: true
units: metaid_0000110
value: 1.0
name: k20

metaid_0000043
type: Parameter
constant: true
units: metaid_0000110
value: 4.92
name: k5

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

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

050543
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

050531
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

050519
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

metaid_0000098
type: Reaction
kinetic law: 050458
product: 050445
reactant: 050433
reactant: 050421
fast: false
reversible: false
name: v27

050445
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000028

050433
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

050421
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

metaid_0000061
type: Parameter
constant: true
units: metaid_0000111
value: 5.38E-5
name: k21

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

049534
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

049522
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

ORG:
  orgname: School of Natural and Computing Sciences, University of Aberdeen, Computing Science Department, Aberdeen, AB24 3UE, UK
n:
  given: George
  family: Coghill

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

metaid_0000084
type: Reaction
kinetic law: 049787
product: 049775
product: 049763
reactant: 049751
fast: false
reversible: false
name: v13

049775
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

049763
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

049751
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000070
type: Parameter
constant: true
units: metaid_0000111
value: 1.14
name: k30

metaid_00000118
type: Reaction
kinetic law: 049218
product: 049206
fast: false
reversible: false
name: v1

049206
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

metaid_0000074
type: Reaction
kinetic law: 049302
product: 049290
reactant: 049278
reactant: 049266
fast: false
reversible: false
name: v3

049290
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

049278
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

049266
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

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

metaid_0000051
type: Parameter
constant: true
units: metaid_0000110
value: 1.41
name: k11

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

050200
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

050188
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

050176
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

metaid_0000101
type: Reaction
kinetic law: 050603
product: 050591
product: 050579
reactant: 050567
fast: false
reversible: false
name: v30

050591
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

050579
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

050567
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

metaid_0000091
type: Reaction
kinetic law: 050114
product: 050102
product: 050090
reactant: 050078
fast: false
reversible: false
name: v20

050102
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

050090
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

050078
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

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

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

050249
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

050236
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

050224
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

metaid_0000056
type: Parameter
constant: true
units: metaid_0000110
value: 1.0
name: k16

metaid_0000102
type: Reaction
kinetic law: 050653
product: 050641
reactant: 050629
reactant: 050616
fast: false
reversible: false
name: v31

050641
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000032

050629
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

050616
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

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

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

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

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

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

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

ORG:
  orgname: School of Natural and Computing Sciences, University of Aberdeen, Computing Science Department, Aberdeen, AB24 3UE, UK
n:
  given: George
  family: Coghill

ORG:
  orgname: School of Natural and Computing Sciences, University of Aberdeen, Computing Science Department, Aberdeen, AB24 3UE, UK
n:
  given: George
  family: Coghill

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

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

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