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created:
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notes: This a model described in the article: Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters. Curien G, Bastien O, Robert-Genthon M, Cornish-Bowden A, Cárdenas ML, Dumas R. Mol Syst Biol. 2009;5:271. Epub 2009 May 19. PMID: 19455135 , doi: 10.1038/msb.2009.29 Abstract: The aspartate-derived amino-acid pathway from plants is well suited for analysing the function of the allosteric network of interactions in branched pathways. For this purpose, a detailed kinetic model of the system in the plant model Arabidopsis was constructed on the basis of in vitro kinetic measurements. The data, assembled into a mathematical model, reproduce in vivo measurements and also provide non-intuitive predictions. A crucial result is the identification of allosteric interactions whose function is not to couple demand and supply but to maintain a high independence between fluxes in competing pathways. In addition, the model shows that enzyme isoforms are not functionally redundant, because they contribute unequally to the flux and its regulation. Another result is the identification of the threonine concentration as the most sensitive variable in the system, suggesting a regulatory role for threonine at a higher level of integration. The limiting rates for the tRNA synthetase reactions, V_Lys_RS, V_Thr_RS and V_Ile_RS, are all assigned a joined value, Vmax_AA_RS, to facilitate reproduction of the results in the publication. To alter these rates seperately these assignments have to be changed or removed. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team. For more information see the terms of use . To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, …
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initial amount: NaN
in compartment: metaid_0000010
is: SBO:0000245
constant: false

638856
type: LocalParameter
units: metaid_0000005
value: 100.0

metaid_0000043
type: Reaction
modifier: 693940
kinetic law: 693952
is: R00480
modifier: 693928
fast: false
product: 693916
reversible: true
is version of: GO:0004072
is: SBO:0000402
reactant: 693904
name: Aspartate kinase 2 react.
is: http://identifiers.org/ec-code/2.7.2.4

638783
type: LocalParameter
is: SBO:0000190
units: dimensionless
value: 1.1

638780
type: LocalParameter
is: SBO:0000363
units: metaid_0000005
value: 22.0

638779
type: LocalParameter
is: SBO:0000321
units: metaid_0000008
value: 0.86

638778
type: LocalParameter
is: SBO:0000320
units: metaid_0000003
value: 3.15

693916
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

693904
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000046
type: Reaction
is version of: GO:0004073
name: Aspartate semialdehyde dehydrogenase react.
reversible: true
modifier: 694110
product: 694098
is: http://identifiers.org/ec-code/1.2.1.11
reactant: 694086
fast: false
is: SBO:0000200
kinetic law: 694122
is: R02291

694098
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

694086
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

638797
type: LocalParameter
is: SBO:0000321
units: metaid_0000008
value: 0.23

638796
type: LocalParameter
is: SBO:0000320
units: metaid_0000008
value: 0.9

metaid_0000059
type: Reaction
reactant: 694796
is version of: GO:0004793
is: SBO:0000178
is: R00751
is: http://identifiers.org/ec-code/4.1.2.5
product: 694808
name: Thr aldolase react.
modifier: 694820
reversible: false
kinetic law: 694832
fast: false

694796
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

694808
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000041

638863
type: LocalParameter
units: metaid_0000005
value: 7100.0

638862
type: LocalParameter
units: metaid_0000003
value: 1.7

metaid_0000049
type: Reaction
kinetic law: 694302
modifier: 694290
reversible: true
product: 694266
is: SBO:0000200
name: homoserine dehydrogenase react. (AKI-HSDHI)
reactant: 694254
is: http://identifiers.org/ec-code/1.1.1.3
is version of: GO:0004412
fast: false
is: R01775
modifier: 694278

638814
type: LocalParameter
units: metaid_0000005
value: 400.0

638811
type: LocalParameter
units: dimensionless
value: 0.86

638808
type: LocalParameter
units: dimensionless
value: 0.14

638805
type: LocalParameter
units: metaid_0000008
value: 0.84

694266
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

694254
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

638853
type: Parameter
constant: false
units: metaid_0000006
value: 0.43

metaid_0000051
type: Reaction
fast: false
kinetic law: 694411
is: R01771
is: http://identifiers.org/ec-code/2.7.1.39
is: SBO:0000402
is version of: GO:0004413
product: 694387
name: homoserine kinase react.
reactant: 694375
modifier: 694399
reversible: false

638822
type: LocalParameter
units: metaid_0000005
value: 14.0

638821
type: LocalParameter
units: metaid_0000003
value: 2.8

694387
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

694375
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

metaid_0000054
type: Reaction
has version: http://identifiers.org/ec-code/2.6.1.42
fast: false
kinetic law: 694627
has version: http://identifiers.org/ec-code/2.2.1.6
modifier: 694615
is: SBO:0000205
is version of: GO:0009097
reversible: false
reactant: 694567
modifier: 694603
has version: http://identifiers.org/ec-code/4.3.1.19
product: 694579
has version: http://identifiers.org/ec-code/4.2.1.9
has version: http://identifiers.org/ec-code/1.1.1.86
name: Threonine deaminase react.
modifier: 694591

638852
type: LocalParameter
units: dimensionless
value: 3.0

638849
type: LocalParameter
units: metaid_0000005
value: 615.0

638848
type: LocalParameter
units: dimensionless
value: 73.0

638847
type: LocalParameter
units: dimensionless
value: 30.0

638846
type: LocalParameter
units: dimensionless
value: 0.0124

694567
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

694579
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000033

ORG:
  orgname: EMBL-EBI
n:
  given: Lukas
  family: Endler

ORG:
  orgname: Centre National de la Recherchce Scientifique (CNRS)
n:
  given: Gilles
  family: Curien

W3 CDTF: Mon Dec 13 09:51:40 GMT 2010