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BIOMD0000000172 - Pritchard2002_glycolysis

 

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Reference Publication
Publication ID: 12180966
Pritchard L, Kell DB.
Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis.
Eur. J. Biochem. 2002 Aug; 269(16): 3894-3904
Institute of Biological Sciences, University of Wales, Aberystwyth, UK.  [more]
Model
Original Model: http://www.gepasi.org/Yeas...
Submitter: Nicolas Le Novère
Submission ID: MODEL8293171637
Submission Date: 20 May 2008 16:01:54 UTC
Last Modification Date: 27 May 2014 22:33:43 UTC
Creation Date: 14 Sep 2006 10:35:04 UTC
Encoders:  Lukas Endler
   Pedro Mendes
set #1
bqmodel:isDerivedFrom BioModels Database Teusink2000_Glycolysis
set #2
bqbiol:hasTaxon Taxonomy Saccharomyces cerevisiae
set #3
bqbiol:isPartOf KEGG Pathway sce00010
set #4
bqbiol:isVersionOf Gene Ontology glycolytic process
Notes

from:
Schemes of fluc control in a model of Saccharomyces cerevisiae glycolysis

Pritchard, L and Kell, DB Eur. J. Biochem. 269(2002), 3894-3904.
It represents a modified version of Teusink et al. Eur. J. Biochem. 267(2000), 5313-5329.
The model is a translation from the GEPASI file encoded by Leighton Pritchard.
This version uses the Vmaxes found by the best fit (R1) of Table 1 of the Pritchard and Kell paper and simulates a decrease of external glucose concentration from 100 to 2 mM.
To reproduce the values in table 2 of the publication, set GLCo to 50 mM and compute the steady state.


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.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 12180966 Submission Date: 20 May 2008 16:01:54 UTC Last Modification Date: 27 May 2014 22:33:43 UTC Creation Date: 14 Sep 2006 10:35:04 UTC
Mathematical expressions
Reactions
glucose transport hexokinase phosphoglucose isomerase phosphofructosekinase
fructosebisphosphate aldolase triosephosphate isomerase glyceraldehyde phosphate dehydrogenase 3-phosphoglycerate kinase
phosphoglyceromutase enolase pyruvate kinase pyruvate decarboxylase
alcohol dehydrogenase ATPase AK glycerol-3-phosphate dehydrogenase
Glycogen_Branch Trehalose_Branch Succinate_Branch  
Physical entities
Compartments Species
cytosol Glc(int) ATP Glu6P
ADP Fru6-P Fru1,6-P2
AMP Fru2,6-P2 glycerone phosphate
Gra3P NAD Gri2,3P2
NADH Gri3P Gri2P
phosphoenolpyruvate pyruvate acetaldehyde
CO2 ethanol glycerol
glycogen trehalose succinate
exterior Glc(ext)    
Reactions (19)
 
 glucose transport [Glc(ext)] ↔ [Glc(int)];  
 
 hexokinase [Glc(int)] + [ATP] ↔ [Glu6P] + [ADP];  
 
 phosphoglucose isomerase [Glu6P] ↔ [Fru6-P];  
 
 phosphofructosekinase [ATP] + [Fru6-P] → [ADP] + [Fru1,6-P2];   {AMP} , {Fru2,6-P2}
 
 fructosebisphosphate aldolase [Fru1,6-P2] ↔ [glycerone phosphate] + [Gra3P];  
 
 triosephosphate isomerase [glycerone phosphate] ↔ [Gra3P];  
 
 glyceraldehyde phosphate dehydrogenase [Gra3P] + [NAD] ↔ [Gri2,3P2] + [NADH];  
 
 3-phosphoglycerate kinase [ADP] + [Gri2,3P2] ↔ [ATP] + [Gri3P];  
 
 phosphoglyceromutase [Gri3P] ↔ [Gri2P];  
 
 enolase [Gri2P] ↔ [phosphoenolpyruvate];  
 
 pyruvate kinase [ADP] + [phosphoenolpyruvate] ↔ [ATP] + [pyruvate];  
 
 pyruvate decarboxylase [pyruvate] → [acetaldehyde] + [CO2];  
 
 alcohol dehydrogenase [NAD] + [ethanol] ↔ [NADH] + [acetaldehyde];  
 
 ATPase [ATP] → [ADP];  
 
 AK 2.0 × [ADP] ↔ [ATP] + [AMP];  
 
 glycerol-3-phosphate dehydrogenase [glycerone phosphate] + [NADH] → [NAD] + [glycerol];  
 
 Glycogen_Branch [ATP] + [Glu6P] → [ADP] + [glycogen];  
 
 Trehalose_Branch [ATP] + 2.0 × [Glu6P] → [ADP] + [trehalose];  
 
 Succinate_Branch 3.0 × [NAD] + 2.0 × [acetaldehyde] → 3.0 × [NADH] + [succinate];  
 
 cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 Glc(int)
Compartment: cytosol
Initial concentration: 0.097652231064563
 
 ATP
Compartment: cytosol
Initial concentration: 2.52512746499271
 
 Glu6P
Compartment: cytosol
Initial concentration: 2.67504014044787
 
 ADP
Compartment: cytosol
Initial concentration: 1.28198768168719
 
 Fru6-P
Compartment: cytosol
Initial concentration: 0.624976405532373
 
 Fru1,6-P2
Compartment: cytosol
Initial concentration: 6.22132076069411
 
 AMP
Compartment: cytosol
Initial concentration: 0.292884853320091
 
 Fru2,6-P2
Compartment: cytosol
Initial concentration: 0.02
 
 glycerone phosphate
Compartment: cytosol
Initial concentration: 1.00415254899644
 
 Gra3P
Compartment: cytosol
Initial concentration: 0.0451809175780963
 
 NAD
Compartment: cytosol
Initial concentration: 1.50329030201531
 
 Gri2,3P2
Compartment: cytosol
Initial concentration: 7.36873499865602E-4
 
 NADH
Compartment: cytosol
Initial concentration: 0.0867096979846952
 
 Gri3P
Compartment: cytosol
Initial concentration: 0.885688538360659
 
 Gri2P
Compartment: cytosol
Initial concentration: 0.127695817386632
 
 phosphoenolpyruvate
Compartment: cytosol
Initial concentration: 0.0632352144936527
 
 pyruvate
Compartment: cytosol
Initial concentration: 1.81531251192736
 
 acetaldehyde
Compartment: cytosol
Initial concentration: 0.178140579850657
 
 CO2
Compartment: cytosol
Initial concentration: 1.0
 
 ethanol
Compartment: cytosol
Initial concentration: 50.0
 
 glycerol
Compartment: cytosol
Initial concentration: 0.15
 
 glycogen
Compartment: cytosol
Initial concentration: 0.0
 
 trehalose
Compartment: cytosol
Initial concentration: 0.0
 
 succinate
Compartment: cytosol
Initial concentration: 0.0
 
 exterior Spatial dimensions: 3.0  Compartment size: 1.0
 
 Glc(ext)
Compartment: exterior
Initial concentration: 2.0
 
glucose transport (3)
 
   Vmax_1
Value: 97.24
Constant
 
   Kglc_1
Value: 1.1918
Constant
 
   Ki_1
Value: 0.91
Constant
 
hexokinase (6)
 
   Vmax_2
Value: 236.7
Constant
 
   Kglc_2
Value: 0.08
Constant
 
   Katp_2
Value: 0.15
Constant
 
   Keq_2
Value: 2000.0
Constant
 
   Kg6p_2
Value: 30.0
Constant
 
   Kadp_2
Value: 0.23
Constant
 
phosphoglucose isomerase (4)
 
   Vmax_3
Value: 1056.0
Constant
 
   Kg6p_3
Value: 1.4
Constant
 
   Keq_3
Value: 0.29
Constant
 
   Kf6p_3
Value: 0.3
Constant
 
phosphofructosekinase (14)
 
   Vmax_4
Value: 110.0
Constant
 
   gR_4
Value: 5.12
Constant
 
   Kf6p_4
Value: 0.1
Constant
 
   Katp_4
Value: 0.71
Constant
 
   L0_4
Value: 0.66
Constant
 
   Ciatp_4
Value: 100.0
Constant
 
   Kiatp_4
Value: 0.65
Constant
 
   Camp_4
Value: 0.0845
Constant
 
   Kamp_4
Value: 0.0995
Constant
 
   Cf26_4
Value: 0.0174
Constant
 
   Kf26_4
Value: 6.82E-4
Constant
 
   Cf16_4
Value: 0.397
Constant
 
   Kf16_4
Value: 0.111
Constant
 
   Catp_4
Value: 3.0
Constant
 
fructosebisphosphate aldolase (6)
 
   Vmax_5
Value: 94.69
Constant
 
   Kf16bp_5
Value: 0.3
Constant
 
   Keq_5
Value: 0.069
Constant
 
   Kdhap_5
Value: 2.0
Constant
 
   Kgap_5
Value: 2.4
Constant
 
   Kigap_5
Value: 10.0
Constant
 
triosephosphate isomerase (2)
 
   k1_6
Value: 450000.0
Constant
 
   k2_6
Value: 1.0E7
Constant
 
glyceraldehyde phosphate dehydrogenase (7)
 
   C_7
Value: 1.0
Constant
 
   Vmaxf_7
Value: 1152.0
Constant
 
   Kgap_7
Value: 0.21
Constant
 
   Knad_7
Value: 0.09
Constant
 
   Vmaxr_7
Value: 6719.0
Constant
 
   Kbpg_7
Value: 0.0098
Constant
 
   Knadh_7
Value: 0.06
Constant
 
3-phosphoglycerate kinase (6)
 
   Vmax_8
Value: 1288.0
Constant
 
   Keq_8
Value: 3200.0
Constant
 
   Kp3g_8
Value: 0.53
Constant
 
   Katp_8
Value: 0.3
Constant
 
   Kbpg_8
Value: 0.0030
Constant
 
   Kadp_8
Value: 0.2
Constant
 
phosphoglyceromutase (4)
 
   Vmax_9
Value: 2585.0
Constant
 
   Kp3g_9
Value: 1.2
Constant
 
   Keq_9
Value: 0.19
Constant
 
   Kp2g_9
Value: 0.08
Constant
 
enolase (4)
 
   Vmax_10
Value: 201.6
Constant
 
   Kp2g_10
Value: 0.04
Constant
 
   Keq_10
Value: 6.7
Constant
 
   Kpep_10
Value: 0.5
Constant
 
pyruvate kinase (6)
 
   Vmax_11
Value: 1000.0
Constant
 
   Kpep_11
Value: 0.14
Constant
 
   Kadp_11
Value: 0.53
Constant
 
   Keq_11
Value: 6500.0
Constant
 
   Kpyr_11
Value: 21.0
Constant
 
   Katp_11
Value: 1.5
Constant
 
pyruvate decarboxylase (3)
 
   Vmax_12
Value: 857.8
Constant
 
   Kpyr_12
Value: 4.33
Constant
 
   nH_12
Value: 1.9
Constant
 
alcohol dehydrogenase (10)
 
   Vmax_13
Value: 209.5
Constant
 
   Ketoh_13
Value: 17.0
Constant
 
   Kinad_13
Value: 0.92
Constant
 
   Keq_13
Value: 6.9E-5
Constant
 
   Knad_13
Value: 0.17
Constant
 
   Knadh_13
Value: 0.11
Constant
 
   Kinadh_13
Value: 0.031
Constant
 
   Kacald_13
Value: 1.11
Constant
 
   Kiacald_13
Value: 1.1
Constant
 
   Kietoh_13
Value: 90.0
Constant
 
ATPase (1)
 
   Katpase_14
Value: 39.5
Constant
 
AK (2)
 
   k1_15
Value: 45.0
Constant
 
   k2_15
Value: 100.0
Constant
 
glycerol-3-phosphate dehydrogenase (6)
 
   Vmax_16
Value: 47.11
Constant
 
   Kdhap_16
Value: 0.4
Constant
 
   Knadh_16
Value: 0.023
Constant
 
   Keq_16
Value: 4300.0
Constant
 
   Kglycerol_16
Value: 1.0
Constant
 
   Knad_16
Value: 0.93
Constant
 
Glycogen_Branch (1)
 
   KGLYCOGEN_17
Value: 6.0
Constant
 
Trehalose_Branch (1)
 
   Ktrehalose_18
Value: 2.4
Constant
 
Succinate_Branch (1)
 
   k_19
Value: 21.4
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000172

Curator's comment: (updated: 16 May 2008 14:24:36 BST)

These are the results for the steady state at an external glucose concentration of 50mM.
The results fit the R1 column of table 2 in the publication.
They were obtained using copasi 4.4(b.26)
Lukas

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