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BIOMD0000000071 - Bakker2001_Glycolysis

 

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Reference Publication
Publication ID: 11415442
Helfert S, Estévez AM, Bakker B, Michels P, Clayton C.
Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei.
Biochem. J. 2001 Jul; 357(Pt 1): 117-125
Zentrum für Molekularbiologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany.  [more]
Model
Original Model: JWS logo
Submitter: Nicolas Le Novère
Submission ID: MODEL6624099213
Submission Date: 25 Sep 2006 20:12:09 UTC
Last Modification Date: 08 Apr 2016 15:30:15 UTC
Creation Date: 09 Oct 2008 19:54:12 UTC
Encoders:  Jacky L Snoep
   Harish Dharuri
   Lukas Endler
set #1
bqmodel:isDerivedFrom BioModels Database Bakker1997_Glycolysis
PubMed 10468568
set #2
bqbiol:isHomologTo Reactome REACT_1383
bqbiol:isVersionOf Gene Ontology glycolytic process
bqbiol:is KEGG Pathway Glycolysis / Gluconeogenesis - Trypanosoma brucei
bqbiol:hasTaxon Taxonomy Trypanosoma brucei
Notes

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SBML level 2 code generated for the JWS Online project by Jacky Snoep using PySCeS
Run this model online at http://jjj.biochem.sun.ac.za
To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based modelling using JWS Online , Bioinformatics, 20:2143-2144

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Biomodels Curation: The paper refers to the model equations present in Bakker et al's " Glycolysis in bloodstream from Trypanosoma brucei can be understood in terms of the kinetics of glycolytic enzymes" (Pubmed ID: 9013556), also, the authors claim that some of the modifications in these equations were made based on the experimental results from the paper "Contribution of glucose transport in the control of glycolytic flux in Trypanosoma brucei" (Pubmed ID: 10468568). The model reproduces the various flux values in Fig 3 for 100% TPI activity. It also matches with the values provided in Table 2 of the paper. The model was successfully tested with Copasi and SBML ODE Solver.
The volumes are set to the values containing 1 mg of total protein per microlitre total cell volume. To change the protein concentration use Vt , the total cell volume in micro litre per mg protein.
To change the TPI activity use the global parameter TPIact .


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: 11415442 Submission Date: 25 Sep 2006 20:12:09 UTC Last Modification Date: 08 Apr 2016 15:30:15 UTC Creation Date: 09 Oct 2008 19:54:12 UTC
Mathematical expressions
Reactions
Glucose transport Hexokinase Glucose-phosphate isomerase Phosphofructokinase
Aldolase Triosephosphate isomerase Glyceraldehyde 3-phosphate dehydrogenase Glycerol 3-phosphate dehydrogenase
Glycerol 3-phosphate oxidase Pyruvate transport Phosphoglycerate kinase Pyruvate kinase
ATPase Glycerol kinase    
Rules
Assignment Rule (variable: Vc) Assignment Rule (variable: Vg) Assignment Rule (variable: ATP gly.) Assignment Rule (variable: ADP gly.)
Assignment Rule (variable: ATP cyt.) Assignment Rule (variable: ADP cyt.) Assignment Rule (variable: DHAP cyt.) Assignment Rule (variable: DHAP gly.)
Assignment Rule (variable: Gy3P c.) Assignment Rule (variable: Gy3P g.) Assignment Rule (variable: Glycerol 3-phosphate) Assignment Rule (variable: 3-PGA g.)
Assignment Rule (variable: PEP c.)      
Physical entities
Compartments Species
total cell Glucose Dihydroxyacetone phosphate 3-PGA 2-PGA PEP
Glycerol 3-phosphate    
glycosome Phosphates in Glycosome Glucose 6-phosphate Fructose 6-phosphate
Fructose 1,6-bisphosphate Glyceraldehyde 3-phosphate NAD
1,3-bisphosphoglycerate NADH Glycerol
ATP gly. ADP gly. DHAP gly.
Gy3P g. 3-PGA g.  
cytosol Pyruvate Phosphates cytosol ATP cyt.
ADP cyt. DHAP cyt. Gy3P c.
PEP c.    
extracellular Pyruvate external Glucose external  
Global parameters
tot volume per mg protein Vc Vg TPIact
sumAc sumAg KeqAK Keq_anti
sumc4 sumc5 Keq_PGM Keq_ENO
Reactions (14)
 
 Glucose transport [Glucose external] ↔ [Glucose];  
 
 Hexokinase [Phosphates in Glycosome] + [Glucose] → [Glucose 6-phosphate];   {ATP gly.} , {ADP gly.}
 
 Glucose-phosphate isomerase [Glucose 6-phosphate] ↔ [Fructose 6-phosphate];  
 
 Phosphofructokinase [Phosphates in Glycosome] + [Fructose 6-phosphate] → [Fructose 1,6-bisphosphate];   {ATP gly.}
 
 Aldolase [Fructose 1,6-bisphosphate] ↔ [Glyceraldehyde 3-phosphate] + [Dihydroxyacetone phosphate];   {DHAP gly.} , {ATP gly.} , {ADP gly.}
 
 Triosephosphate isomerase [Dihydroxyacetone phosphate] ↔ [Glyceraldehyde 3-phosphate];   {DHAP gly.}
 
 Glyceraldehyde 3-phosphate dehydrogenase [Glyceraldehyde 3-phosphate] + [NAD] ↔ [NADH] + [1,3-bisphosphoglycerate];  
 
 Glycerol 3-phosphate dehydrogenase [Dihydroxyacetone phosphate] + [NADH] ↔ [NAD] + [Glycerol 3-phosphate];   {DHAP gly.} , {Gy3P g.}
 
 Glycerol 3-phosphate oxidase [Glycerol 3-phosphate] → [Dihydroxyacetone phosphate];   {Gy3P c.}
 
 Pyruvate transport [Pyruvate] → [Pyruvate external];  
 
 Phosphoglycerate kinase [1,3-bisphosphoglycerate] ↔ [3-PGA 2-PGA PEP] + [Phosphates in Glycosome];   {ADP gly.} , {ATP gly.} , {3-PGA g.}
 
 Pyruvate kinase [3-PGA 2-PGA PEP] → [Phosphates cytosol] + [Pyruvate];   {PEP c.} , {ADP cyt.} , {ATP cyt.}
 
 ATPase [Phosphates cytosol] → ;   {ATP cyt.} , {ADP cyt.}
 
 Glycerol kinase [Glycerol 3-phosphate] ↔ [Phosphates in Glycosome] + [Glycerol];   {ADP gly.} , {Gy3P g.} , {ATP gly.}
 
Rules (13)
 
 Assignment Rule (name: Vc) Vc = cytosol*Vt/tot_cell
 
 Assignment Rule (name: Vg) Vg = glycosome*Vt/tot_cell
 
 Assignment Rule (name: ATPg) ATP gly. = (Pg*(1-4*KeqAK)-sumAg+((sumAg-(1-4*KeqAK)*Pg)^2+4*(1-4*KeqAK)*KeqAK*Pg^2)^0.5)/(2*(1-4*KeqAK))
 
 Assignment Rule (name: ADPg) ADP gly. = Pg-2*ATPg
 
 Assignment Rule (name: ATPc) ATP cyt. = (Pc*(1-4*KeqAK)-sumAc+((sumAc-(1-4*KeqAK)*Pc)^2+4*(1-4*KeqAK)*KeqAK*Pc^2)^0.5)/(2*(1-4*KeqAK))
 
 Assignment Rule (name: ADPc) ADP cyt. = Pc-2*ATPc
 
 Assignment Rule (name: DHAPc) DHAP cyt. = sumc5*(1+Vc/Vg)*DHAP/(sumc4+sumc5*Vc/Vg-(BPGA13+2*Fru16BP+Fru6P+GAP+Glc6P+Pg))
 
 Assignment Rule (name: DHAPg) DHAP gly. = (DHAP*Vt-DHAPc*Vc)/Vg
 
 Assignment Rule (name: Gly3Pc) Gy3P c. = sumc5-DHAPc
 
 Assignment Rule (name: Gly3Pg) Gy3P g. = Gly3Pc*DHAPg/(Keq_anti*DHAPc)
 
 Assignment Rule (name: Gly3P) Glycerol 3-phosphate = (Gly3Pc*cytosol+Gly3Pg*glycosome)/tot_cell
 
 Assignment Rule (name: PGAg) 3-PGA g. = Nb*(1+Vc/Vg)/(1+(1+Keq_PGM+Keq_PGM*Keq_ENO)*Vc/Vg)
 
 Assignment Rule (name: PEPc) PEP c. = Keq_ENO*Keq_PGM*PGAg
 
   total cell Spatial dimensions: 3.0  Compartment size: 5.7
 
 Glucose
Compartment: total cell
Initial concentration: 0.0340009
 
 Dihydroxyacetone phosphate
Compartment: total cell
Initial concentration: 3.89921
 
 3-PGA 2-PGA PEP
Compartment: total cell
Initial concentration: 1.59603
 
  Glycerol 3-phosphate
Compartment: total cell
Initial concentration: 0.0
 
 glycosome Spatial dimensions: 3.0  Compartment size: 0.2446
 
 Phosphates in Glycosome
Compartment: glycosome
Initial concentration: 7.63936
 
 Glucose 6-phosphate
Compartment: glycosome
Initial concentration: 2.07199
 
 Fructose 6-phosphate
Compartment: glycosome
Initial concentration: 0.511773
 
 Fructose 1,6-bisphosphate
Compartment: glycosome
Initial concentration: 16.5371
 
 Glyceraldehyde 3-phosphate
Compartment: glycosome
Initial concentration: 0.0399329
 
 NAD
Compartment: glycosome
Initial concentration: 3.95514
 
 1,3-bisphosphoglycerate
Compartment: glycosome
Initial concentration: 0.0326745
 
 NADH
Compartment: glycosome
Initial concentration: 0.0448639
 
 Glycerol
Compartment: glycosome
Initial concentration: 0.0
 
  ATP gly.
Compartment: glycosome
 
  ADP gly.
Compartment: glycosome
 
  DHAP gly.
Compartment: glycosome
 
  Gy3P g.
Compartment: glycosome
 
  3-PGA g.
Compartment: glycosome
 
 cytosol Spatial dimensions: 3.0  Compartment size: 5.4554
 
 Pyruvate
Compartment: cytosol
Initial concentration: 4.77413
 
 Phosphates cytosol
Compartment: cytosol
Initial concentration: 6.51839
 
  ATP cyt.
Compartment: cytosol
 
  ADP cyt.
Compartment: cytosol
 
  DHAP cyt.
Compartment: cytosol
 
  Gy3P c.
Compartment: cytosol
 
  PEP c.
Compartment: cytosol
 
 extracellular Spatial dimensions: 3.0  Compartment size: 1.0
 
 Pyruvate external
Compartment: extracellular
Initial concentration: 0.0
 
 Glucose external
Compartment: extracellular
Initial concentration: 5.0
 
Global Parameters (12)
 
   tot volume per mg protein
Value: 5.7   (Units: microlitre_per_mg)
Constant
 
   Vc
Value: NaN   (Units: microlitre_per_mg)
 
   Vg
Value: NaN   (Units: microlitre_per_mg)
 
   TPIact
Value: 1.0   (Units: dimensionless)
Constant
 
   sumAc
Value: 3.9   (Units: mM)
Constant
 
   sumAg
Value: 6.0   (Units: mM)
Constant
 
   KeqAK
Value: 0.442   (Units: dimensionless)
Constant
 
   Keq_anti
Value: 1.0   (Units: dimensionless)
Constant
 
   sumc4
Value: 45.0   (Units: mM)
Constant
 
   sumc5
Value: 5.0   (Units: mM)
Constant
 
   Keq_PGM
Value: 0.187   (Units: dimensionless)
Constant
 
   Keq_ENO
Value: 6.7   (Units: dimensionless)
Constant
 
Glucose transport (3)
 
   Vm1
Value: 106.2   (Units: nanomole_per_min_per_mg)
Constant
 
   K1Glc
Value: 2.0   (Units: mM)
Constant
 
   afac
Value: 0.75   (Units: dimensionless)
Constant
 
Hexokinase (5)
 
   Vm2
Value: 625.0   (Units: nanomole_per_min_per_mg)
Constant
 
   K2ATPg
Value: 0.116   (Units: mM)
Constant
 
   K2GlcI
Value: 0.1   (Units: mM)
Constant
 
   K2Glc6P
Value: 12.0   (Units: mM)
Constant
 
   K2ADPg
Value: 0.126   (Units: mM)
Constant
 
Glucose-phosphate isomerase (3)
 
   Vm3
Value: 848.0   (Units: nanomole_per_min_per_mg)
Constant
 
   K3Glc6P
Value: 0.4   (Units: mM)
Constant
 
   K3Fru6P
Value: 0.12   (Units: mM)
Constant
 
Phosphofructokinase (5)
 
   K4i1Fru16BP
Value: 15.8   (Units: mM)
Constant
 
   Vm4
Value: 780.0   (Units: nanomole_per_min_per_mg)
Constant
 
   K4ATPg
Value: 0.026   (Units: mM)
Constant
 
   K4Fru6P
Value: 0.82   (Units: mM)
Constant
 
   K4i2Fru16BP
Value: 10.7   (Units: mM)
Constant
 
Aldolase (5)
 
   Vm5r
Value: 219.555   (Units: nanomole_per_min_per_mg)
Constant
 
   K5DHAP
Value: 0.015   (Units: mM)
Constant
 
   K5GAP
Value: 0.067   (Units: mM)
Constant
 
   Vm5f
Value: 184.5   (Units: nanomole_per_min_per_mg)
Constant
 
   K5GAPi
Value: 0.098   (Units: mM)
Constant
 
Triosephosphate isomerase (3)
 
   Vm6
Value: 842.0   (Units: nanomole_per_min_per_mg)
Constant
 
   K6GAP
Value: 0.25   (Units: mM)
Constant
 
   K6DHAPg
Value: 1.2   (Units: mM)
Constant
 
Glyceraldehyde 3-phosphate dehydrogenase (7)
 
   Vm7
Value: 1.0   (Units: dimensionless)
Constant
 
   Vm7f
Value: 1470.0   (Units: nanomole_per_min_per_mg)
Constant
 
   K7GAP
Value: 0.15   (Units: mM)
Constant
 
   K7NAD
Value: 0.45   (Units: mM)
Constant
 
   Vm7r
Value: 984.9   (Units: nanomole_per_min_per_mg)
Constant
 
   K7BPGA13
Value: 0.1   (Units: mM)
Constant
 
   K7NADH
Value: 0.02   (Units: mM)
Constant
 
Glycerol 3-phosphate dehydrogenase (7)
 
   Vm8
Value: 1.0   (Units: dimensionless)
Constant
 
   Vm8f
Value: 533.0   (Units: nanomole_per_min_per_mg)
Constant
 
   K8DHAPg
Value: 0.1   (Units: mM)
Constant
 
   K8NADH
Value: 0.01   (Units: mM)
Constant
 
   Vm8r
Value: 149.24   (Units: nanomole_per_min_per_mg)
Constant
 
   K8Gly3Pg
Value: 2.0   (Units: mM)
Constant
 
   K8NAD
Value: 0.4   (Units: mM)
Constant
 
Glycerol 3-phosphate oxidase (2)
 
   Vm9
Value: 368.0   (Units: nanomole_per_min_per_mg)
Constant
 
   K9Gly3Pc
Value: 1.7   (Units: mM)
Constant
 
Pyruvate transport (2)
 
   Vm10
Value: 200.0   (Units: nanomole_per_min_per_mg)
Constant
 
   K10Pyr
Value: 1.96   (Units: mM)
Constant
 
Phosphoglycerate kinase (7)
 
   Vm11
Value: 1.0   (Units: dimensionless)
Constant
 
   Vm11f
Value: 640.0   (Units: nanomole_per_min_per_mg)
Constant
 
   Vm11r
Value: 18.56   (Units: nanomole_per_min_per_mg)
Constant
 
   K11ATPg
Value: 0.29   (Units: mM)
Constant
 
   K11PGA3
Value: 1.62   (Units: mM)
Constant
 
   K11ADPg
Value: 0.1   (Units: dimensionless)
Constant
 
   K11BPGA13
Value: 0.05   (Units: dimensionless)
Constant
 
Pyruvate kinase (3)
 
   n12
Value: 2.5   (Units: dimensionless)
Constant
 
   Vm12
Value: 2600.0   (Units: nanomole_per_min_per_mg)
Constant
 
   K12ADP
Value: 0.114   (Units: mM)
Constant
 
ATPase (1)
 
   K13
Value: 50.0   (Units: nanomole_per_min_per_mg)
Constant
 
Glycerol kinase (7)
 
   Vm14
Value: 1.0   (Units: dimensionless)
Constant
 
   Vm14r
Value: 33400.0   (Units: nanomole_per_min_per_mg)
Constant
 
   K14ATPg
Value: 0.19   (Units: mM)
Constant
 
   K14Gly
Value: 0.12   (Units: mM)
Constant
 
   Vm14f
Value: 200.0   (Units: nanomole_per_min_per_mg)
Constant
 
   K14ADPg
Value: 0.12   (Units: mM)
Constant
 
   K14Gly3Pg
Value: 5.1   (Units: mM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000071

Curator's comment: (updated: 30 Oct 2008 17:11:15 GMT)

reproduction of some of the values from fig 3A,B and table 2 from the original publication.
Calculations were performed using Copasi 4.4.27

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