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BIOMD0000000503 - Messiha2013 - combined glycolysis and pentose phosphate pathway model

 

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Reference Publication
Publication ID: 10.7287/peerj.prepri...
Messiha HL, Kent E, Malys N, Carroll KM, Mendes P, Smallbone K.
Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast
PeerJ PrePrints
School of Life Sciences, The University of Manchester, Manchester, United Kingdom 2 Manchester Center for Integrative Systems Biology, The University of Manchester, Manchester, United Kingdom  [more]
Model
Original Model: BIOMD0000000503.origin
Submitter: Kieran Smallbone
Submission ID: MODEL1311290001
Submission Date: 29 Nov 2013 10:53:43 UTC
Last Modification Date: 08 Apr 2016 17:38:15 UTC
Creation Date: 09 Nov 2008 00:00:00 UTC
Encoders:  Vijayalakshmi Chelliah
   Kieran Smallbone
set #1
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #2
bqbiol:hasPart Gene Ontology glycolytic process
Gene Ontology pentose-phosphate shunt
bqmodel:isDerivedFrom BioModels Database Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 18
BioModels Database Messiha2013 - Pentose phosphate pathway model
set #3
bqbiol:hasTaxon Taxonomy Saccharomyces cerevisiae
Notes
Messiha2013 - combined glycolysis and pentose phosphate pathway model

BIOMD0000000502 and MODEL1303260018 are combined to examine the response to oxidative stress.

This model is described in the article:

Hanan L. Messiha, Edward Kent, Naglis Malys, Kathleen M. Carroll, Pedro Mendes, Kieran Smallbone
PeerJ PrePrints 1:e146v2

Abstract:

We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows for the predicting changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis one to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardized enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network models by merging smaller pathway models.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Model
Publication ID: 10.7287/peerj.prepri... Submission Date: 29 Nov 2013 10:53:43 UTC Last Modification Date: 08 Apr 2016 17:38:15 UTC Creation Date: 09 Nov 2008 00:00:00 UTC
Mathematical expressions
Reactions
ADH AK ATPase ENO
FBA GPD GPM GPP
HXK PDC PFK PGI
PGK PGM PYK TDH
TPI TPP TPS UGP
acetate_branch udp_to_utp HXT GND
RKI RPE SOL TAL
TKL (E4P:F6P) TKL (R5P:S7P) ZWF NADPH oxidase
E4P sink R5P sink    
Rules
Assignment Rule (variable: AMP) Assignment Rule (variable: NADH) Assignment Rule (variable: UDG) Assignment Rule (variable: NADP)
Physical entities
Compartments Species
cell ADP ATP AcAld
BPG DHAP F16bP
F6P G1P G3P
G6P GAP GLC
NAD P2G P3G
PEP PYR T6P
UDP UTP AMP
NADH UDG ACE
EtOH F26bP GLY
SUC TRH ADH1
CDC19 ENO1 ENO2
FBA1 GLK1 GPD1
GPD2 GPM1 HOR2
HXK1 HXK2 PDC1
PDC5 PDC6 PFK1
PFK2 PGI1 PGK1
PGM1 PGM2 RHR2
TDH1 TDH3 TPI1
TPS1 TPS2 UGP1
E4P G6L NADPH
P6G R5P Ru5P
S7P X5P NADP
GND1 GND2 NQM1
RKI1 RPE1 SOL3
TAL1 TKL1 ZWF1
extracellular GLCx    
Global parameters
sum_AxP sum_NAD sum_UxP sum_NADP
Kx5p_TAL Ke4p_TAL Kr5p_TAL Kgap_TAL
Kf6p_TAL Ks7p_TAL    
Reactions (34)
 
 ADH [AcAld] + [NADH] ↔ [EtOH] + [NAD];   {ADH1} , {ADH1} , {AcAld} , {NADH} , {EtOH} , {NAD}
 
 AK 2.0 × [ADP] ↔ [ATP] + [AMP];   {ADP} , {AMP} , {ATP}
 
 ATPase [ATP] → [ADP];   {ATP}
 
 ENO [P2G] ↔ [PEP];   {ENO1} , {ENO2} , {ENO1} , {P2G} , {PEP} , {ENO2}
 
 FBA [F16bP] ↔ [DHAP] + [GAP];   {FBA1} , {FBA1} , {F16bP} , {DHAP} , {GAP}
 
 GPD [DHAP] + [NADH] ↔ [G3P] + [NAD];   {ADP} , {ATP} , {F16bP} , {GPD1} , {GPD2} , {DHAP} , {NADH} , {G3P} , {NAD} , {F16bP} , {ATP} , {ADP}
 
 GPM [P3G] ↔ [P2G];   {GPM1} , {GPM1} , {P3G} , {P2G}
 
 GPP [G3P] → [GLY];   {HOR2} , {RHR2} , {G3P}
 
 HXK [GLC] + [ATP] ↔ [G6P] + [ADP];   {HXK1} , {T6P} , {HXK2} , {GLK1} , {HXK1} , {GLC} , {ATP} , {G6P} , {ADP} , {T6P} , {HXK2} , {GLK1}
 
 PDC [PYR] → [AcAld];   {PDC1} , {PDC5} , {PDC6} , {PDC1} , {PYR} , {PDC5} , {PDC6}
 
 PFK [ATP] + [F6P] → [ADP] + [F16bP];   {AMP} , {F26bP} , {PFK1} , {PFK2} , {PFK2} , {F6P} , {ATP} , {F16bP} , {ADP} , {AMP} , {F26bP}
 
 PGI [G6P] ↔ [F6P];   {PGI1} , {PGI1} , {G6P} , {F6P}
 
 PGK [ADP] + [BPG] ↔ [ATP] + [P3G];   {PGK1} , {PGK1} , {ADP} , {BPG} , {P3G} , {ATP}
 
 PGM [G6P] ↔ [G1P];   {PGM1} , {PGM2} , {G6P} , {G1P}
 
 PYK [ADP] + [PEP] ↔ [ATP] + [PYR];   {CDC19} , {F16bP} , {CDC19} , {PEP} , {ADP} , {PYR} , {ATP} , {F16bP}
 
 TDH [GAP] + [NAD] ↔ [BPG] + [NADH];   {TDH1} , {TDH3} , {TDH1} , {GAP} , {NAD} , {BPG} , {NADH} , {TDH3}
 
 TPI [DHAP] ↔ [GAP];   {TPI1} , {TPI1} , {DHAP} , {GAP}
 
 TPP [T6P] → [TRH];   {TPS1} , {TPS2} , {T6P}
 
 TPS [G6P] + [UDG] → [T6P] + [UDP];   {TPS1} , {TPS2} , {G6P} , {UDG}
 
 UGP [G1P] + [UTP] → [UDG];   {UGP1} , {UTP} , {G1P} , {UDG}
 
 acetate_branch [AcAld] + [NAD] → [ACE] + [NADH];   {AcAld} , {NAD}
 
 udp_to_utp [UDP] + [ATP] → [UTP] + [ADP];   {UDP} , {ATP}
 
 HXT [GLCx] ↔ [GLC];   {GLCx} , {GLC}
 
 GND [P6G] + [NADP] → [Ru5P] + [NADPH];   {GND1} , {GND2} , {GND1} , {P6G} , {NADP} , {Ru5P} , {NADPH} , {GND2}
 
 RKI [Ru5P] ↔ [R5P];   {RKI1} , {RKI1} , {Ru5P} , {R5P}
 
 RPE [Ru5P] ↔ [X5P];   {RPE1} , {RPE1} , {Ru5P} , {X5P}
 
 SOL [G6L] → [P6G];   {SOL3} , {SOL3} , {G6L} , {P6G}
 
 TAL [GAP] + [S7P] ↔ [F6P] + [E4P];   {TAL1} , {NQM1} , {TAL1} , {GAP} , {S7P} , {F6P} , {E4P} , {NQM1}
 
 TKL (E4P:F6P) [X5P] + [E4P] ↔ [GAP] + [F6P];   {TKL1} , {R5P} , {S7P} , {TKL1} , {X5P} , {E4P} , {GAP} , {F6P} , {R5P} , {S7P}
 
 TKL (R5P:S7P) [X5P] + [R5P] ↔ [GAP] + [S7P];   {TKL1} , {E4P} , {F6P} , {TKL1} , {X5P} , {R5P} , {GAP} , {S7P} , {E4P} , {F6P}
 
 ZWF [G6P] + [NADP] → [G6L] + [NADPH];   {ZWF1} , {ZWF1} , {G6P} , {NADP} , {G6L} , {NADPH}
 
 NADPH oxidase [NADPH] → [NADP];   {NADPH}
 
 E4P sink [E4P] → ;   {E4P}
 
 R5P sink [R5P] → ;   {R5P}
 
Rules (4)
 
 Assignment Rule (name: AMP) AMP = (sum_AxP-ATP)-ADP
 
 Assignment Rule (name: NADH) NADH = sum_NAD-NAD
 
 Assignment Rule (name: UDG) UDG = (sum_UxP-UTP)-UDP
 
 Assignment Rule (name: NADP) NADP = sum_NADP-NADPH
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 ADP
Compartment: cell
Initial concentration: 1.29
 
 ATP
Compartment: cell
Initial concentration: 4.29
 
 AcAld
Compartment: cell
Initial concentration: 0.178140579850657
 
 BPG
Compartment: cell
Initial concentration: 7.36873499865602E-4
 
 DHAP
Compartment: cell
Initial concentration: 1.1613768527467
 
 F16bP
Compartment: cell
Initial concentration: 4.58321859006931
 
 F6P
Compartment: cell
Initial concentration: 0.235441221891221
 
 G1P
Compartment: cell
Initial concentration: 0.539248506344921
 
 G3P
Compartment: cell
Initial concentration: 0.274002929191284
 
 G6P
Compartment: cell
Initial concentration: 0.772483203645216
 
 GAP
Compartment: cell
Initial concentration: 0.315891028770503
 
 GLC
Compartment: cell
Initial concentration: 6.28000179338242
 
 NAD
Compartment: cell
Initial concentration: 1.50329030201531
 
 P2G
Compartment: cell
Initial concentration: 0.0677379081099344
 
 P3G
Compartment: cell
Initial concentration: 0.469825011134444
 
 PEP
Compartment: cell
Initial concentration: 0.610005413358042
 
 PYR
Compartment: cell
Initial concentration: 2.10847140717419
 
 T6P
Compartment: cell
Initial concentration: 0.02
 
 UDP
Compartment: cell
Initial concentration: 0.2815
 
 UTP
Compartment: cell
Initial concentration: 0.6491
 
  AMP
Compartment: cell
Initial concentration: 0.44
 
  NADH
Compartment: cell
Initial concentration: 0.0867096979846952
 
  UDG
Compartment: cell
Initial concentration: 0.467246194874247
 
 ACE
Compartment: cell
Initial concentration: 223.000253398294
Constant
 
 EtOH
Compartment: cell
Initial concentration: 221.890311417536
Constant
 
 F26bP
Compartment: cell
Initial concentration: 0.003
Constant
 
 GLY
Compartment: cell
Initial concentration: 0.15
Constant
 
 SUC
Compartment: cell
Initial concentration: 0.0
Constant
 
 TRH
Compartment: cell
Initial concentration: 0.0153878853696526
Constant
 
 ADH1
Compartment: cell
Initial concentration: 0.163908510928009
Constant
 
 CDC19
Compartment: cell
Initial concentration: 2.0483901071712
Constant
 
 ENO1
Compartment: cell
Initial concentration: 0.686371954155832
Constant
 
 ENO2
Compartment: cell
Initial concentration: 1.97444629317817
Constant
 
 FBA1
Compartment: cell
Initial concentration: 1.33839465704882
Constant
 
 GLK1
Compartment: cell
Initial concentration: 0.0450869624419226
Constant
 
 GPD1
Compartment: cell
Initial concentration: 0.00683511177089872
Constant
 
 GPD2
Compartment: cell
Initial concentration: 7.93405666424228E-4
Constant
 
 GPM1
Compartment: cell
Initial concentration: 0.73000029889707
Constant
 
 HOR2
Compartment: cell
Initial concentration: 0.0054734695639756
Constant
 
 HXK1
Compartment: cell
Initial concentration: 0.0167807457149784
Constant
 
 HXK2
Compartment: cell
Initial concentration: 0.0613313539705155
Constant
 
 PDC1
Compartment: cell
Initial concentration: 1.06781077822834
Constant
 
 PDC5
Compartment: cell
Initial concentration: 0.0123547443267676
Constant
 
 PDC6
Compartment: cell
Initial concentration: 0.00654086421106118
Constant
 
 PFK1
Compartment: cell
Initial concentration: 0.0467850299063124
Constant
 
 PFK2
Compartment: cell
Initial concentration: 0.0390366215332091
Constant
 
 PGI1
Compartment: cell
Initial concentration: 0.1382907072901
Constant
 
 PGK1
Compartment: cell
Initial concentration: 0.257656912658955
Constant
 
 PGM1
Compartment: cell
Initial concentration: 0.00326229546307459
Constant
 
 PGM2
Compartment: cell
Initial concentration: 0.00125868877176552
Constant
 
 RHR2
Compartment: cell
Initial concentration: 0.0511804773718313
Constant
 
 TDH1
Compartment: cell
Initial concentration: 0.350864642801396
Constant
 
 TDH3
Compartment: cell
Initial concentration: 4.20440474648547
Constant
 
 TPI1
Compartment: cell
Initial concentration: 0.294357819645508
Constant
 
 TPS1
Compartment: cell
Initial concentration: 0.00339248174237065
Constant
 
 TPS2
Compartment: cell
Initial concentration: 0.00265985181347494
Constant
 
 UGP1
Compartment: cell
Initial concentration: 0.00620211419860714
Constant
 
 E4P
Compartment: cell
Initial concentration: 0.029
 
 G6L
Compartment: cell
Initial concentration: 0.1
 
 NADPH
Compartment: cell
Initial concentration: 0.16
 
 P6G
Compartment: cell
Initial concentration: 0.25
 
 R5P
Compartment: cell
Initial concentration: 0.118
 
 Ru5P
Compartment: cell
Initial concentration: 0.033
 
 S7P
Compartment: cell
Initial concentration: 0.082
 
 X5P
Compartment: cell
Initial concentration: 0.041
 
  NADP
Compartment: cell
Initial concentration: 0.17
 
 GND1
Compartment: cell
Initial concentration: 0.013
Constant
 
 GND2
Compartment: cell
Initial concentration: 0.003
Constant
 
 NQM1
Compartment: cell
Initial concentration: 0.02
Constant
 
 RKI1
Compartment: cell
Initial concentration: 0.05
Constant
 
 RPE1
Compartment: cell
Initial concentration: 0.03
Constant
 
 SOL3
Compartment: cell
Initial concentration: 0.0296
Constant
 
 TAL1
Compartment: cell
Initial concentration: 0.144
Constant
 
 TKL1
Compartment: cell
Initial concentration: 0.455
Constant
 
 ZWF1
Compartment: cell
Initial concentration: 0.02
Constant
 
 extracellular Spatial dimensions: 3.0  Compartment size: 1.0
 
 GLCx
Compartment: extracellular
Initial concentration: 74.0
Constant
 
Global Parameters (10)
 
   sum_AxP
Value: 6.02   (Units: mM)
Constant
 
   sum_NAD
Value: 1.59   (Units: mM)
Constant
 
   sum_UxP
Value: 1.39784619487425   (Units: mM)
Constant
 
   sum_NADP
Value: 0.33   (Units: mM)
Constant
 
   Kx5p_TAL
Value: 0.67   (Units: mM)
Constant
 
   Ke4p_TAL
Value: 0.946   (Units: mM)
Constant
 
   Kr5p_TAL
Value: 0.235   (Units: mM)
Constant
 
   Kgap_TAL
Value: 0.1   (Units: mM)
Constant
 
   Kf6p_TAL
Value: 1.1   (Units: mM)
Constant
 
   Ks7p_TAL
Value: 0.15   (Units: mM)
Constant
 
ADH (10)
 
   kcat
Value: 176.0   (Units: per s)
Constant
 
   Ketoh
Value: 17.0   (Units: mM)
Constant
 
   Kinad
Value: 0.92   (Units: mM)
Constant
 
   Knad
Value: 0.17   (Units: mM)
Constant
 
   Knadh
Value: 0.11   (Units: mM)
Constant
 
   Kinadh
Value: 0.031   (Units: mM)
Constant
 
   Kacald
Value: 0.4622   (Units: mM)
Constant
 
   Kiacald
Value: 1.1   (Units: mM)
Constant
 
   Kietoh
Value: 90.0   (Units: mM)
Constant
 
   Keq
Value: 14492.7536231884   (Units: dimensionless)
Constant
 
AK (2)
 
   k
Value: 0.75   (Units: per_mM_per_s)
Constant
 
   Keq
Value: 0.45   (Units: dimensionless)
Constant
 
ATPase (2)
 
   Vmax
Value: 6.16   (Units: mM per s)
Constant
 
   Katp
Value: 3.0   (Units: mM)
Constant
 
ENO (7)
 
   kcat_ENO1
Value: 7.6   (Units: per s)
Constant
 
   Kp2g_ENO1
Value: 0.043   (Units: mM)
Constant
 
   Kpep_ENO1
Value: 0.5   (Units: mM)
Constant
 
   kcat_ENO2
Value: 19.87   (Units: per s)
Constant
 
   Kp2g_ENO2
Value: 0.104   (Units: mM)
Constant
 
   Kpep_ENO2
Value: 0.5   (Units: mM)
Constant
 
   Keq
Value: 6.7   (Units: dimensionless)
Constant
 
FBA (6)
 
   kcat
Value: 4.139   (Units: per s)
Constant
 
   Kf16bp
Value: 0.4507   (Units: mM)
Constant
 
   Keq
Value: 0.069   (Units: mM)
Constant
 
   Kdhap
Value: 2.0   (Units: mM)
Constant
 
   Kgap
Value: 2.4   (Units: mM)
Constant
 
   Kigap
Value: 10.0   (Units: mM)
Constant
 
GPD (9)
 
   Vmax
Value: 0.783333333333333   (Units: mM per s)
Constant
 
   Knadh
Value: 0.023   (Units: mM)
Constant
 
   Kdhap
Value: 0.54   (Units: mM)
Constant
 
   Keq
Value: 10000.0   (Units: dimensionless)
Constant
 
   Kfbp
Value: 4.8   (Units: mM)
Constant
 
   Katp
Value: 0.73   (Units: mM)
Constant
 
   Kadp
Value: 2.0   (Units: mM)
Constant
 
   Knad
Value: 0.93   (Units: mM)
Constant
 
   Kg3p
Value: 1.2   (Units: mM)
Constant
 
GPM (4)
 
   kcat
Value: 400.0   (Units: per s)
Constant
 
   Kp3g
Value: 1.2   (Units: mM)
Constant
 
   Keq
Value: 0.19   (Units: dimensionless)
Constant
 
   Kp2g
Value: 1.41   (Units: mM)
Constant
 
GPP (2)
 
   Vmax
Value: 0.883333333333333   (Units: mM per s)
Constant
 
   Kg3p
Value: 3.5   (Units: mM)
Constant
 
HXK (18)
 
   kcat_HXK1
Value: 10.2   (Units: per s)
Constant
 
   Kglc_HXK1
Value: 0.15   (Units: mM)
Constant
 
   Katp_HXK1
Value: 0.293   (Units: mM)
Constant
 
   Kg6p_HXK1
Value: 30.0   (Units: mM)
Constant
 
   Kadp_HXK1
Value: 0.23   (Units: mM)
Constant
 
   Kit6p_HXK1
Value: 0.2   (Units: mM)
Constant
 
   kcat_HXK2
Value: 63.1   (Units: per s)
Constant
 
   Kglc_HXK2
Value: 0.2   (Units: mM)
Constant
 
   Katp_HXK2
Value: 0.195   (Units: mM)
Constant
 
   Kg6p_HXK2
Value: 30.0   (Units: mM)
Constant
 
   Kadp_HXK2
Value: 0.23   (Units: mM)
Constant
 
   Kit6p_HXK2
Value: 0.04   (Units: mM)
Constant
 
   kcat_GLK1
Value: 0.0721   (Units: per s)
Constant
 
   Kglc_GLK1
Value: 0.0106   (Units: mM)
Constant
 
   Katp_GLK1
Value: 0.865   (Units: mM)
Constant
 
   Kg6p_GLK1
Value: 30.0   (Units: mM)
Constant
 
   Kadp_GLK1
Value: 0.23   (Units: mM)
Constant
 
   Keq
Value: 2000.0   (Units: dimensionless)
Constant
 
PDC (6)
 
   kcat_PDC1
Value: 12.14   (Units: per s)
Constant
 
   Kpyr_PDC1
Value: 8.5   (Units: mM)
Constant
 
   kcat_PDC5
Value: 10.32   (Units: per s)
Constant
 
   Kpyr_PDC5
Value: 7.08   (Units: mM)
Constant
 
   kcat_PDC6
Value: 9.21   (Units: per s)
Constant
 
   Kpyr_PDC6
Value: 2.92   (Units: mM)
Constant
 
PFK (16)
 
   kcat
Value: 209.6   (Units: per s)
Constant
 
   gR
Value: 5.12   (Units: dimensionless)
Constant
 
   Kf6p
Value: 0.1   (Units: mM)
Constant
 
   Katp
Value: 0.71   (Units: mM)
Constant
 
   L0
Value: 0.66   (Units: dimensionless)
Constant
 
   Ciatp
Value: 100.0   (Units: dimensionless)
Constant
 
   Kiatp
Value: 0.65   (Units: mM)
Constant
 
   Camp
Value: 0.0845   (Units: dimensionless)
Constant
 
   Kamp
Value: 0.0995   (Units: mM)
Constant
 
   Cf26
Value: 0.0174   (Units: dimensionless)
Constant
 
   Kf26
Value: 6.82E-4   (Units: mM)
Constant
 
   Cf16
Value: 0.397   (Units: dimensionless)
Constant
 
   Kf16
Value: 0.111   (Units: mM)
Constant
 
   Catp
Value: 3.0   (Units: dimensionless)
Constant
 
   Kadp
Value: 1.0   (Units: mM)
Constant
 
   Keq
Value: 800.0   (Units: dimensionless)
Constant
 
PGI (4)
 
   kcat
Value: 487.36   (Units: per s)
Constant
 
   Kg6p
Value: 1.0257   (Units: mM)
Constant
 
   Keq
Value: 0.29   (Units: dimensionless)
Constant
 
   Kf6p
Value: 0.307   (Units: mM)
Constant
 
PGK (7)
 
   kcat
Value: 58.6   (Units: per s)
Constant
 
   Keq
Value: 3200.0   (Units: dimensionless)
Constant
 
   Kp3g
Value: 4.58   (Units: mM)
Constant
 
   Katp
Value: 1.99   (Units: mM)
Constant
 
   Kbpg
Value: 0.003   (Units: mM)
Constant
 
   Kadp
Value: 0.2   (Units: mM)
Constant
 
   nHadp
Value: 2.0   (Units: dimensionless)
Constant
 
PGM (4)
 
   Vmax
Value: 0.12762   (Units: mM per s)
Constant
 
   Kg6p
Value: 0.05   (Units: mM)
Constant
 
   Kg1p
Value: 0.023   (Units: mM)
Constant
 
   Keq
Value: 0.1667   (Units: dimensionless)
Constant
 
PYK (9)
 
   kcat
Value: 20.146   (Units: per s)
Constant
 
   Kpep
Value: 0.281   (Units: mM)
Constant
 
   Kadp
Value: 0.243   (Units: mM)
Constant
 
   Kpyr
Value: 21.0   (Units: mM)
Constant
 
   Katp
Value: 1.5   (Units: mM)
Constant
 
   Kiatp
Value: 9.3   (Units: mM)
Constant
 
   Kf16p
Value: 0.2   (Units: mM)
Constant
 
   L0
Value: 100.0   (Units: dimensionless)
Constant
 
   Keq
Value: 6500.0   (Units: dimensionless)
Constant
 
TDH (11)
 
   kcat_TDH1
Value: 19.12   (Units: per s)
Constant
 
   Kgap_TDH1
Value: 0.495   (Units: mM)
Constant
 
   Knad_TDH1
Value: 0.09   (Units: mM)
Constant
 
   Kbpg_TDH1
Value: 0.0098   (Units: mM)
Constant
 
   Knadh_TDH1
Value: 0.06   (Units: mM)
Constant
 
   kcat_TDH3
Value: 18.162   (Units: per s)
Constant
 
   Kgap_TDH3
Value: 0.423   (Units: mM)
Constant
 
   Knad_TDH3
Value: 0.09   (Units: mM)
Constant
 
   Kbpg_TDH3
Value: 0.909   (Units: mM)
Constant
 
   Knadh_TDH3
Value: 0.06   (Units: mM)
Constant
 
   Keq
Value: 0.00533412710224736   (Units: dimensionless)
Constant
 
TPI (5)
 
   kcat
Value: 564.38   (Units: per s)
Constant
 
   Kdhap
Value: 6.454   (Units: mM)
Constant
 
   Kgap
Value: 5.25   (Units: mM)
Constant
 
   Kigap
Value: 35.1   (Units: mM)
Constant
 
   Keq
Value: 0.045   (Units: dimensionless)
Constant
 
TPP (2)
 
   Vmax
Value: 2.33999999999999   (Units: mM per s)
Constant
 
   Kt6p
Value: 0.5   (Units: mM)
Constant
 
TPS (3)
 
   Vmax
Value: 0.49356   (Units: mM per s)
Constant
 
   Kg6p
Value: 3.8   (Units: mM)
Constant
 
   Kudg
Value: 0.886   (Units: mM)
Constant
 
UGP (5)
 
   Vmax
Value: 13.2552   (Units: mM per s)
Constant
 
   Kutp
Value: 0.11   (Units: mM)
Constant
 
   Kiutp
Value: 0.11   (Units: mM)
Constant
 
   Kg1p
Value: 0.32   (Units: mM)
Constant
 
   Kiudg
Value: 0.0035   (Units: mM)
Constant
 
acetate_branch (1)
 
   k
Value: 0.00554339592436782   (Units: per_mM_per_s)
Constant
 
udp_to_utp (1)
 
   k
Value: 0.0745258294103764   (Units: per_mM_per_s)
Constant
 
HXT (3)
 
   Vmax
Value: 3.35   (Units: mM per s)
Constant
 
   Kglc
Value: 0.9   (Units: mM)
Constant
 
   Ki
Value: 0.91   (Units: dimensionless)
Constant
 
GND (10)
 
   kcat_GND1
Value: 28.0   (Units: per s)
Constant
 
   Kp6g_GND1
Value: 0.062   (Units: mM)
Constant
 
   Knadp_GND1
Value: 0.094   (Units: mM)
Constant
 
   Kru5p_GND1
Value: 0.1   (Units: mM)
Constant
 
   Knadph_GND1
Value: 0.055   (Units: mM)
Constant
 
   kcat_GND2
Value: 27.3   (Units: per s)
Constant
 
   Kp6g_GND2
Value: 0.115   (Units: mM)
Constant
 
   Knadp_GND2
Value: 0.094   (Units: mM)
Constant
 
   Kru5p_GND2
Value: 0.1   (Units: mM)
Constant
 
   Knadph_GND2
Value: 0.055   (Units: mM)
Constant
 
RKI (5)
 
   kcat
Value: 335.0   (Units: per s)
Constant
 
   Kru5p
Value: 2.47   (Units: mM)
Constant
 
   Kr5p
Value: 5.7   (Units: mM)
Constant
 
   Kiru5p
Value: 9.88   (Units: mM)
Constant
 
   Keq
Value: 4.0   (Units: dimensionless)
Constant
 
RPE (4)
 
   kcat
Value: 4020.0   (Units: per s)
Constant
 
   Kru5p
Value: 5.97   (Units: mM)
Constant
 
   Kx5p
Value: 7.7   (Units: mM)
Constant
 
   Keq
Value: 1.4   (Units: dimensionless)
Constant
 
SOL (3)
 
   kcat
Value: 4.3   (Units: per s)
Constant
 
   Kg6l
Value: 0.8   (Units: mM)
Constant
 
   Kp6g
Value: 0.5   (Units: mM)
Constant
 
TAL (11)
 
   kcat_TAL1
Value: 0.694   (Units: per s)
Constant
 
   Kgap_TAL1
Value: 0.272   (Units: mM)
Constant
 
   Ks7p_TAL1
Value: 0.786   (Units: mM)
Constant
 
   Kf6p_TAL1
Value: 1.44   (Units: mM)
Constant
 
   Ke4p_TAL1
Value: 0.362   (Units: mM)
Constant
 
   kcat_NQM1
Value: 0.694   (Units: per s)
Constant
 
   Kgap_NQM1
Value: 0.272   (Units: mM)
Constant
 
   Ks7p_NQM1
Value: 0.786   (Units: mM)
Constant
 
   Kf6p_NQM1
Value: 1.04   (Units: mM)
Constant
 
   Ke4p_NQM1
Value: 0.305   (Units: mM)
Constant
 
   Keq
Value: 1.05   (Units: dimensionless)
Constant
 
TKL (E4P:F6P) (2)
 
   kcat
Value: 47.1   (Units: per s)
Constant
 
   Keq
Value: 10.0   (Units: dimensionless)
Constant
 
TKL (R5P:S7P) (2)
 
   kcat
Value: 40.5   (Units: per s)
Constant
 
   Keq
Value: 1.2   (Units: dimensionless)
Constant
 
ZWF (5)
 
   kcat
Value: 189.0   (Units: per s)
Constant
 
   Kg6p
Value: 0.042   (Units: mM)
Constant
 
   Knadp
Value: 0.045   (Units: mM)
Constant
 
   Kg6l
Value: 0.01   (Units: mM)
Constant
 
   Knadph
Value: 0.017   (Units: mM)
Constant
 
NADPH oxidase (1)
 
   k
Value: 1.0   (Units: per s)
Constant
 
E4P sink (1)
 
   k
Value: 1.0   (Units: per s)
Constant
 
R5P sink (1)
 
   k
Value: 1.0   (Units: per s)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000503

Curator's comment: (updated: 13 Jan 2014 11:40:26 GMT)

There are no figures in the paper that correspond to this model.
The only result that correspond to this model is Table 6, i.e the change in steady state values of the metabolites under normal and oxidative stress condition.
First, the steady state concentrations of the metabolites under normal (reference) was obtained. Secondly, the steady state concentrations of the metabolites at the oxidative stress condition was obtained. The following changes were made to the parameters below to simulate the stress condition:
[TDH1]: 0.351 (reference) -> 0.08775 (stress = 25% of reference);
[TDH3]: 4.20 (reference) -> 1.05 (stress = 25% of reference);
k (E4P sink) 1 (reference) -> 0.01 (stress);
k (R5P sink) 1 (reference) -> 0.01 (stress);
k (NADPH oxidase) 1 (reference) -> 100 (stress);

The changes in metabolite concentration under normal (reference) and stress conditions are presented as log10([stressed]/[reference]).

With the above settings, the last column of Table 6 of the reference publication was reproduced.

The steady state concentrations of the metabolite was obtained using Copasi v4.11 (Build 64).

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