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BIOMD0000000239 - Jiang2007 - GSIS system, Pancreatic Beta Cells

 

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Reference Publication
Publication ID: 17514510
Jiang N, Cox RD, Hancock JM.
A kinetic core model of the glucose-stimulated insulin secretion network of pancreatic beta cells.
Mamm. Genome 2007 Jul; 18(6-7): 508-520
Bioinformatics Group, MRC Mammalian Genetics Unit, Harwell, Oxfordshire, OX11 0RD, UK.  [more]
Model
Original Model: BIOMD0000000239.origin
Submitter: Kieran Smallbone
Submission ID: MODEL1469251725
Submission Date: 28 Aug 2009 15:20:55 UTC
Last Modification Date: 08 Apr 2016 16:06:10 UTC
Creation Date: 29 Nov 2011 12:14:22 UTC
Encoders:  Vijayalakshmi Chelliah
   Kieran Smallbone
set #1
bqbiol:hasTaxon Taxonomy Mammalia
set #2
bqbiol:hasProperty Human Disease Ontology diabetes mellitus
set #3
bqbiol:isVersionOf Gene Ontology regulation of insulin secretion involved in cellular response to glucose stimulus
Notes
Jiang2007 - GSIS system, Pancreatic Beta Cells
Description of a core kinetic model of the glucose-stimulated insulin secretion system (GSIS) in pancreatic beta cells.

This model is described in the article:

Jiang N, Cox RD, Hancock JM.
Mamm Genome 2007 Jul; 18(6-7):508-20.

Abstract:

The construction and characterization of a core kinetic model of the glucose-stimulated insulin secretion system (GSIS) in pancreatic beta cells is described. The model consists of 44 enzymatic reactions, 59 metabolic state variables, and 272 parameters. It integrates five subsystems: glycolysis, the TCA cycle, the respiratory chain, NADH shuttles, and the pyruvate cycle. It also takes into account compartmentalization of the reactions in the cytoplasm and mitochondrial matrix. The model shows expected behavior in its outputs, including the response of ATP production to starting glucose concentration and the induction of oscillations of metabolite concentrations in the glycolytic pathway and in ATP and ADP concentrations. Identification of choke points and parameter sensitivity analysis indicate that the glycolytic pathway, and to a lesser extent the TCA cycle, are critical to the proper behavior of the system, while parameters in other components such as the respiratory chain are less critical. Notably, however, sensitivity analysis identifies the first reactions of nonglycolytic pathways as being important for the behavior of the system. The model is robust to deletion of malic enzyme activity, which is absent in mouse pancreatic beta cells. The model represents a step toward the construction of a model with species-specific parameters that can be used to understand mouse models of diabetes and the relationship of these mouse models to the human disease state.

The model reproduces Figure 2 of the paper, and is built using files 'ModelNNT11.xml' and 'changed.m' available from http://www.har.mrc.ac.uk/research/bioinformatics/research_areas/systems_biology.html .

A couple of small errors in the model (in the original SBML file 'ModelNNT11.xml') have been corrected. The errors are:

  • v44 now produces Pyr rather than PYR
  • the kinetic law of v27 is now dependent on cytoplasmic (rather than mitochondrial) acetyl CoA and OXA

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: 17514510 Submission Date: 28 Aug 2009 15:20:55 UTC Last Modification Date: 08 Apr 2016 16:06:10 UTC Creation Date: 29 Nov 2011 12:14:22 UTC
Mathematical expressions
Reactions
GLCflow LACflow GAPflow glucokinase
6-phosphofructokinase fructose-bisphosphate aldolase glyceraldehyde 3-phosphate dehydrogenase bisphosphoglycerate phosphotase (1/2)
pyruvate kinase lactate dehydrogenase hidden_1 pyruvate carrier
pyruvate dehydrogenase complex citrate synthase aconitase isocitrate dehydrogenase (NAD+) (alpha/beta/gamma)
oxoglutarate dehydrogenase complex succinyl-CoA synthetase succinate dehydrogenase fumarase
malate dehydrogenase (mitochondrion) alanine transaminase aspartate transaminase aspartate/glutamate carrier
NADH:ubiquinone oxidoreductase ubiquinol:cytochrome c oxidoreductase cytochrome c oxidase citrate synthase
ATPase complex aconitase oxoglutarate carrier malate dehydrogenase (cytosol)
aspartate transaminase citrate carrier ETF:Q oxidoreductase glutathione reductase
pyruvate decarboxylase glycerol-3-phosphate dehydrogenase (FAD dependent) glycerol-3-phosphate dehydrogenase (NAD+ dependent) ATP/ADP carrier
cytosolic isocitrate dehydrogenase citrate carrier ATP/ADP carrier malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)      
Physical entities
Compartments Species
cytoplasm glucose fructose-6-phosphate fructose-1,6-bisphosphate
glyceraldehyde 3-phosphate 1,2-bisphospho-D-glycerate phosphoenolpyruvate
pyruvate adenine monophosphate lactate
glycerol-3-phosphate dihydrohxyacetone-phosphate oxaloacetate
aspartate glutamate oxoglutarate
malate acetyl CoA coenzyme A
isocitrate citrate adenine triphosphate
adenine diphosphate NAD NADH
NADP NADPH  
mitochondrial intermembrane space ubiquinone ubiquinol ferrocytochrome c
ferricytochrome c    
mitochondrial inner membrane      
mitochondrial matrix pyruvate carbon dioxide coenzyme A
acetyl CoA phosphate fumarate
succinyl-CoA succinate guanosine triphosphate
guanosine diphosphate slanine aspartate
glutamate water electron transfer flavoprotein (reduced form)
electron transfer flavoprotein (oxidised form) FADH2 FAD
oxoglutarate malate oxaloacetate
citrate isocitrate adenine triphosphate
adenine diphosphate NADP+ NADPH
NAD+ NADH  
Global parameters
flow      
Reactions (45)
 
 GLCflow  ↔ [glucose];  
 
 LACflow [lactate] → ;  
 
 GAPflow [glyceraldehyde 3-phosphate] → ;  
 
 glucokinase [glucose] + [adenine triphosphate] → [fructose-6-phosphate] + [adenine diphosphate];  
 
 6-phosphofructokinase [fructose-6-phosphate] + [adenine triphosphate] → [fructose-1,6-bisphosphate] + [adenine diphosphate];   {adenine monophosphate}
 
 fructose-bisphosphate aldolase [fructose-1,6-bisphosphate] ↔ 2.0 × [glyceraldehyde 3-phosphate];  
 
 glyceraldehyde 3-phosphate dehydrogenase [glyceraldehyde 3-phosphate] + [NAD] → [1,2-bisphospho-D-glycerate] + [NADH];  
 
 bisphosphoglycerate phosphotase (1/2) [1,2-bisphospho-D-glycerate] + [adenine diphosphate] ↔ [phosphoenolpyruvate] + [adenine triphosphate];  
 
 pyruvate kinase [phosphoenolpyruvate] + [adenine diphosphate] → [pyruvate] + [adenine triphosphate];  
 
 lactate dehydrogenase [pyruvate] + [NADH] ↔ [lactate] + [NAD];  
 
 hidden_1 [adenine monophosphate] + [adenine triphosphate] ↔ 2.0 × [adenine diphosphate];  
 
 pyruvate carrier [pyruvate] ↔ [pyruvate];  
 
 pyruvate dehydrogenase complex [pyruvate] + [coenzyme A] + [NAD+] → [carbon dioxide] + [acetyl CoA] + [NADH];  
 
 citrate synthase [oxaloacetate] + [acetyl CoA] ↔ [citrate] + [coenzyme A];  
 
 aconitase [citrate] ↔ [isocitrate];  
 
 isocitrate dehydrogenase (NAD+) (alpha/beta/gamma) [isocitrate] + [NAD+] → [oxoglutarate] + [NADH];   {adenine diphosphate}
 
 oxoglutarate dehydrogenase complex [oxoglutarate] + [coenzyme A] + [NAD+] → [carbon dioxide] + [succinyl-CoA] + [NADH];  
 
 succinyl-CoA synthetase [guanosine diphosphate] + [succinyl-CoA] + [phosphate] ↔ [succinate] + [guanosine triphosphate] + [coenzyme A];  
 
 succinate dehydrogenase [succinate] + [ubiquinone] ↔ [fumarate] + [ubiquinol];  
 
 fumarase [fumarate] ↔ [malate];  
 
 malate dehydrogenase (mitochondrion) [malate] + [NAD+] ↔ [NADH] + [oxaloacetate];  
 
 alanine transaminase [slanine] + [oxoglutarate] ↔ [glutamate] + [pyruvate];  
 
 aspartate transaminase [oxaloacetate] + [glutamate] ↔ [aspartate] + [oxoglutarate];  
 
 aspartate/glutamate carrier [glutamate] + [aspartate] ↔ [aspartate] + [glutamate];  
 
 NADH:ubiquinone oxidoreductase [NADH] + [ubiquinone] ↔ [NAD+] + [ubiquinol];  
 
 ubiquinol:cytochrome c oxidoreductase [ubiquinol] + 2.0 × [ferrocytochrome c] → [ubiquinone] + 2.0 × [ferricytochrome c];  
 
 cytochrome c oxidase [ferricytochrome c] → [ferrocytochrome c];  
 
 citrate synthase [citrate] + [coenzyme A] ↔ [oxaloacetate] + [acetyl CoA];  
 
 ATPase complex [adenine diphosphate] + [phosphate] ↔ [adenine triphosphate] + [water];  
 
 aconitase [citrate] ↔ [isocitrate];  
 
 oxoglutarate carrier [malate] + [oxoglutarate] ↔ [oxoglutarate] + [malate];  
 
 malate dehydrogenase (cytosol) [NADH] + [oxaloacetate] → [malate] + [NAD];  
 
 aspartate transaminase [aspartate] + [oxoglutarate] ↔ [oxaloacetate] + [glutamate];  
 
 citrate carrier [citrate] + [malate] ↔ [malate] + [citrate];  
 
 ETF:Q oxidoreductase [electron transfer flavoprotein (reduced form)] + [ubiquinone] ↔ [electron transfer flavoprotein (oxidised form)] + [ubiquinol];  
 
 glutathione reductase [FADH2] + [electron transfer flavoprotein (oxidised form)] ↔ [electron transfer flavoprotein (reduced form)] + [FAD];  
 
 pyruvate decarboxylase [adenine triphosphate] + [carbon dioxide] + [pyruvate] ↔ [phosphate] + [adenine diphosphate] + [oxaloacetate];  
 
 glycerol-3-phosphate dehydrogenase (FAD dependent) [glycerol-3-phosphate] + [FAD] → [FADH2] + [dihydrohxyacetone-phosphate];  
 
 glycerol-3-phosphate dehydrogenase (NAD+ dependent) [NADH] + [dihydrohxyacetone-phosphate] → [glycerol-3-phosphate] + [NAD];  
 
 ATP/ADP carrier [adenine diphosphate] → [adenine diphosphate];  
 
 cytosolic isocitrate dehydrogenase [isocitrate] + [NADP] ↔ [oxoglutarate] + [NADPH];   {carbon dioxide}
 
 citrate carrier [isocitrate] + [malate] ↔ [malate] + [isocitrate];  
 
 ATP/ADP carrier [adenine triphosphate] → [adenine triphosphate];  
 
 malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) [malate] + [NADP] ↔ [NADPH] + [pyruvate];  
 
 malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) [malate] + [NADP+] ↔ [NADPH] + [pyruvate];  
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 glucose
Compartment: cytoplasm
Initial concentration: 1.12817E-5
 
 fructose-6-phosphate
Compartment: cytoplasm
Initial concentration: 6.5939E-4
 
 fructose-1,6-bisphosphate
Compartment: cytoplasm
Initial concentration: 7.70135E-6
 
 glyceraldehyde 3-phosphate
Compartment: cytoplasm
Initial concentration: 1.90919E-6
 
 1,2-bisphospho-D-glycerate
Compartment: cytoplasm
Initial concentration: 2.99109E-4
 
 phosphoenolpyruvate
Compartment: cytoplasm
Initial concentration: 2.1125E-6
 
 pyruvate
Compartment: cytoplasm
Initial concentration: 4.22702E-6
 
 adenine monophosphate
Compartment: cytoplasm
Initial concentration: 2.61149E-6
 
 lactate
Compartment: cytoplasm
Initial concentration: 3.3981E-4
 
 glycerol-3-phosphate
Compartment: cytoplasm
Initial concentration: 0.0076925
 
 dihydrohxyacetone-phosphate
Compartment: cytoplasm
Initial concentration: 0.0076925
 
 oxaloacetate
Compartment: cytoplasm
Initial concentration: 4.0E-6
 
 aspartate
Compartment: cytoplasm
Initial concentration: 0.00114
 
 glutamate
Compartment: cytoplasm
Initial concentration: 0.00303
 
 oxoglutarate
Compartment: cytoplasm
Initial concentration: 2.1E-5
 
 malate
Compartment: cytoplasm
Initial concentration: 5.0E-4
 
 acetyl CoA
Compartment: cytoplasm
Initial concentration: 3.0E-5
 
 coenzyme A
Compartment: cytoplasm
Initial concentration: 2.72E-4
 
 isocitrate
Compartment: cytoplasm
Initial concentration: 4.2E-4
 
 citrate
Compartment: cytoplasm
Initial concentration: 4.2E-4
 
 adenine triphosphate
Compartment: cytoplasm
Initial concentration: 0.00449064
 
 adenine diphosphate
Compartment: cytoplasm
Initial concentration: 1.08367E-4
 
 NAD
Compartment: cytoplasm
Initial concentration: 0.00362057
 
 NADH
Compartment: cytoplasm
Initial concentration: 6.16118E-4
 
 NADP
Compartment: cytoplasm
Initial concentration: 0.00362057
 
 NADPH
Compartment: cytoplasm
Initial concentration: 6.16118E-4
 
 mitochondrial intermembrane space Spatial dimensions: 3.0  Compartment size: 1.0
 
 ubiquinone
Compartment: mitochondrial intermembrane space
Initial concentration: 0.026
 
 ubiquinol
Compartment: mitochondrial intermembrane space
Initial concentration: 0.028
 
 ferrocytochrome c
Compartment: mitochondrial intermembrane space
Initial concentration: 0.003
 
 ferricytochrome c
Compartment: mitochondrial intermembrane space
Initial concentration: 1.1E-4
 
 mitochondrial inner membrane Spatial dimensions: 3.0  Compartment size: 1.0
 mitochondrial matrix Spatial dimensions: 3.0  Compartment size: 1.0
 
 pyruvate
Compartment: mitochondrial matrix
Initial concentration: 0.001025
 
 carbon dioxide
Compartment: mitochondrial matrix
Initial concentration: 0.00163
 
 coenzyme A
Compartment: mitochondrial matrix
Initial concentration: 2.72E-4
 
 acetyl CoA
Compartment: mitochondrial matrix
Initial concentration: 3.0E-5
 
 phosphate
Compartment: mitochondrial matrix
Initial concentration: 0.004
 
 fumarate
Compartment: mitochondrial matrix
Initial concentration: 6.5E-5
 
 succinyl-CoA
Compartment: mitochondrial matrix
Initial concentration: 2.941E-4
 
 succinate
Compartment: mitochondrial matrix
Initial concentration: 0.00295
 
 guanosine triphosphate
Compartment: mitochondrial matrix
Initial concentration: 0.0045
 
 guanosine diphosphate
Compartment: mitochondrial matrix
Initial concentration: 4.5E-4
 
 slanine
Compartment: mitochondrial matrix
Initial concentration: 0.00344
 
 aspartate
Compartment: mitochondrial matrix
Initial concentration: 0.00114
 
 glutamate
Compartment: mitochondrial matrix
Initial concentration: 0.00303
 
 water
Compartment: mitochondrial matrix
Initial concentration: 0.001
 
 electron transfer flavoprotein (reduced form)
Compartment: mitochondrial matrix
Initial concentration: 3.1E-4
 
 electron transfer flavoprotein (oxidised form)
Compartment: mitochondrial matrix
Initial concentration: 3.2E-4
 
 FADH2
Compartment: mitochondrial matrix
Initial concentration: 7.2E-5
 
 FAD
Compartment: mitochondrial matrix
Initial concentration: 0.00101
 
 oxoglutarate
Compartment: mitochondrial matrix
Initial concentration: 2.1E-5
 
 malate
Compartment: mitochondrial matrix
Initial concentration: 5.0E-4
 
 oxaloacetate
Compartment: mitochondrial matrix
Initial concentration: 4.0E-6
 
 citrate
Compartment: mitochondrial matrix
Initial concentration: 4.2E-4
 
 isocitrate
Compartment: mitochondrial matrix
Initial concentration: 4.2E-4
 
 adenine triphosphate
Compartment: mitochondrial matrix
Initial concentration: 0.0045
 
 adenine diphosphate
Compartment: mitochondrial matrix
Initial concentration: 4.5E-4
 
 NADP+
Compartment: mitochondrial matrix
Initial concentration: 0.0101
 
 NADPH
Compartment: mitochondrial matrix
Initial concentration: 7.2E-5
 
 NAD+
Compartment: mitochondrial matrix
Initial concentration: 0.0101
 
 NADH
Compartment: mitochondrial matrix
Initial concentration: 7.2E-4
 
Global Parameters (1)
 
   flow
Value: 0.011
Constant
 
GLCflow (1)
 
   Glc_F
Value: 64.941
Constant
 
glucokinase (3)
 
   V1
Value: 5.0E-4
Constant
 
   K1GLC
Value: 1.0E-4
Constant
 
   K1ATP
Value: 6.3E-5
Constant
 
6-phosphofructokinase (4)
 
   V2
Value: 0.0015
Constant
 
   K2
Value: 1.6E-9
Constant
 
   k2
Value: 0.017
Constant
 
   K2ATP
Value: 1.0E-5
Constant
 
fructose-bisphosphate aldolase (2)
 
   k3f
Value: 1.0
Constant
 
   k3b
Value: 0.05
Constant
 
glyceraldehyde 3-phosphate dehydrogenase (3)
 
   V4
Value: 0.01
Constant
 
   K4GAP
Value: 0.001
Constant
 
   K4NAD
Value: 0.001
Constant
 
bisphosphoglycerate phosphotase (1/2) (2)
 
   k5f
Value: 1000.0
Constant
 
   k5b
Value: 500.0
Constant
 
pyruvate kinase (3)
 
   V6
Value: 0.01
Constant
 
   K6PEP
Value: 2.0E-4
Constant
 
   K6ADP
Value: 3.0E-4
Constant
 
lactate dehydrogenase (2)
 
   k8f
Value: 1000.0
Constant
 
   k8b
Value: 0.143
Constant
 
hidden_1 (2)
 
   k9f
Value: 10000.0
Constant
 
   k9b
Value: 10000.0
Constant
 
pyruvate carrier (3)
 
   V
Value: 1.0E-8
Constant
 
   K
Value: 1.5E-7
Constant
 
   PYC
Value: 3.3211E-4
Constant
 
pyruvate dehydrogenase complex (13)
 
   KmA
Value: 2.5E-5
Constant
 
   KmB
Value: 1.3E-5
Constant
 
   KmC
Value: 5.0E-5
Constant
 
   KmP
Value: 5.9E-7
Constant
 
   KmR
Value: 6.9E-7
Constant
 
   Kia
Value: 5.5E-4
Constant
 
   Kib
Value: 3.0E-4
Constant
 
   Kic
Value: 1.8E-4
Constant
 
   Kip
Value: 6.0E-5
Constant
 
   Kiq
Value: 3.5E-5
Constant
 
   Kir
Value: 3.6E-5
Constant
 
   KcF
Value: 856.0
Constant
 
   PDC
Value: 3.8617E-7
Constant
 
citrate synthase (6)
 
   V
Value: 0.005267
Constant
 
   Ka
Value: 1.18E-5
Constant
 
   Kb
Value: 4.8E-6
Constant
 
   Kia
Value: 1.0E-5
Constant
 
   Kib
Value: 4.0E-6
Constant
 
   CS
Value: 3.8617E-7
Constant
 
aconitase (5)
 
   Ks
Value: 5.0E-4
Constant
 
   Kp
Value: 1.1E-4
Constant
 
   KcF
Value: 20.47
Constant
 
   KcR
Value: 31.44
Constant
 
   ACO
Value: 3.8617E-7
Constant
 
isocitrate dehydrogenase (NAD+) (alpha/beta/gamma) (7)
 
   KcF
Value: 105.0
Constant
 
   b
Value: 29.6
Constant
 
   c
Value: 2.3E-4
Constant
 
   d
Value: 7.8E-5
Constant
 
   e
Value: 6.4E-4
Constant
 
   f
Value: 3.6E-4
Constant
 
   IDHa
Value: 3.8617E-7
Constant
 
oxoglutarate dehydrogenase complex (13)
 
   KmA
Value: 2.2E-4
Constant
 
   KmB
Value: 2.5E-5
Constant
 
   KmC
Value: 5.0E-5
Constant
 
   KmP
Value: 3.0E-4
Constant
 
   KmR
Value: 6.0E-4
Constant
 
   Kia
Value: 7.2E-4
Constant
 
   Kib
Value: 7.4E-4
Constant
 
   Kic
Value: 1.0E-4
Constant
 
   Kip
Value: 1.1E-6
Constant
 
   Kiq
Value: 8.1E-5
Constant
 
   Kir
Value: 2.5E-5
Constant
 
   KcF
Value: 177.0
Constant
 
   OGDC
Value: 3.8617E-7
Constant
 
succinyl-CoA synthetase (17)
 
   KmA
Value: 5.0E-6
Constant
 
   KmB
Value: 3.5E-5
Constant
 
   KmC
Value: 4.5E-4
Constant
 
   KmP
Value: 6.0E-4
Constant
 
   KmQ
Value: 7.5E-6
Constant
 
   KmC2
Value: 4.5E-4
Constant
 
   KmP2
Value: 6.0E-4
Constant
 
   Keq
Value: 8.375
Constant
 
   Kia
Value: 4.0E-4
Constant
 
   Kib
Value: 2.0E-5
Constant
 
   Kic
Value: 3.0E-5
Constant
 
   Kip
Value: 0.07
Constant
 
   Kiq
Value: 5.0E-6
Constant
 
   Kir
Value: 6.7E-6
Constant
 
   Kc1
Value: 100.0
Constant
 
   Kc2
Value: 100.0
Constant
 
   SCS
Value: 3.8617E-7
Constant
 
succinate dehydrogenase (10)
 
   KmS1
Value: 3.0E-5
Constant
 
   KmS2
Value: 6.9E-5
Constant
 
   KmP1
Value: 3.0E-7
Constant
 
   KmP2
Value: 1.5E-6
Constant
 
   KiS1
Value: 4.1E-6
Constant
 
   KiP2
Value: 5.6E-6
Constant
 
   Keq
Value: 0.037
Constant
 
   KcF
Value: 69.3
Constant
 
   KcR
Value: 1.73
Constant
 
   SDH
Value: 9.9211E-5
Constant
 
fumarase (5)
 
   Kp
Value: 2.5E-5
Constant
 
   Ks
Value: 5.0E-6
Constant
 
   KcF
Value: 800.0
Constant
 
   KcR
Value: 900.0
Constant
 
   FM
Value: 3.8617E-7
Constant
 
malate dehydrogenase (mitochondrion) (11)
 
   KmS1
Value: 7.2E-5
Constant
 
   KmS2
Value: 1.1E-4
Constant
 
   KmP1
Value: 0.0016
Constant
 
   KmP2
Value: 1.7E-4
Constant
 
   KiS1
Value: 1.1E-5
Constant
 
   KiS2
Value: 1.0E-4
Constant
 
   KiP1
Value: 0.0071
Constant
 
   KiP2
Value: 0.0019
Constant
 
   KcF
Value: 0.39
Constant
 
   KcR
Value: 0.04
Constant
 
   MDH
Value: 3.8617E-7
Constant
 
alanine transaminase (10)
 
   KmS1
Value: 0.002
Constant
 
   KmS2
Value: 4.0E-4
Constant
 
   KmP1
Value: 0.032
Constant
 
   KmP2
Value: 4.0E-4
Constant
 
   KiS1
Value: 0.0087
Constant
 
   KiP2
Value: 0.012
Constant
 
   Keq
Value: 0.69
Constant
 
   KcF
Value: 337.0
Constant
 
   KcR
Value: 0.15
Constant
 
   AlaTA
Value: 3.8617E-7
Constant
 
aspartate transaminase (10)
 
   KmS1
Value: 9.0E-4
Constant
 
   KmS2
Value: 1.0E-4
Constant
 
   KmP1
Value: 4.0E-5
Constant
 
   KmP2
Value: 0.004
Constant
 
   KiS1
Value: 0.002
Constant
 
   KiP2
Value: 0.0083
Constant
 
   Keq
Value: 6.2
Constant
 
   KcF
Value: 300.0
Constant
 
   KcR
Value: 1000.0
Constant
 
   AspTA
Value: 3.8617E-7
Constant
 
aspartate/glutamate carrier (11)
 
   KiS1
Value: 8.0E-5
Constant
 
   KiS2
Value: 0.0032
Constant
 
   KiP1
Value: 1.8E-4
Constant
 
   KiP2
Value: 0.0028
Constant
 
   KcF
Value: 10.0
Constant
 
   KcR
Value: 10.0
Constant
 
   alpha
Value: 1.0
Constant
 
   beta
Value: 1.0
Constant
 
   gamma
Value: 1.0
Constant
 
   delta
Value: 1.0
Constant
 
   AGC
Value: 3.3211E-4
Constant
 
NADH:ubiquinone oxidoreductase (10)
 
   KmS1
Value: 9.2E-6
Constant
 
   KmS2
Value: 2.6E-4
Constant
 
   KmP1
Value: 9.9E-6
Constant
 
   KmP2
Value: 5.9E-5
Constant
 
   KiS1
Value: 2.1E-8
Constant
 
   KiP2
Value: 9.8E-8
Constant
 
   Keq
Value: 407.9
Constant
 
   KcF
Value: 498.0
Constant
 
   KcR
Value: 229.0
Constant
 
   Complex_I
Value: 3.3211E-4
Constant
 
ubiquinol:cytochrome c oxidoreductase (9)
 
   KmA
Value: 2.8E-5
Constant
 
   KmB
Value: 3.0E-6
Constant
 
   Kb1
Value: 5.4E-6
Constant
 
   Kb2
Value: 5.7E-6
Constant
 
   Kq1
Value: 2.8E-6
Constant
 
   Kq2
Value: 1.9E-6
Constant
 
   k8
Value: 622.1
Constant
 
   KcF
Value: 426.8
Constant
 
   Complex_III
Value: 9.963E-9
Constant
 
cytochrome c oxidase (3)
 
   Ks
Value: 1.1E-4
Constant
 
   KcF
Value: 9.35E-4
Constant
 
   Complex_IV
Value: 0.002325
Constant
 
citrate synthase (9)
 
   V
Value: 0.004833
Constant
 
   Ka
Value: 5.0E-6
Constant
 
   Kb
Value: 4.5E-6
Constant
 
   Kc
Value: 3.9E-5
Constant
 
   Kia
Value: 5.0E-6
Constant
 
   Kib
Value: 4.5E-6
Constant
 
   Kid
Value: 0.0043
Constant
 
   Keq
Value: 1.8E7
Constant
 
   CS
Value: 3.8617E-7
Constant
 
ATPase complex (4)
 
   V
Value: 0.075
Constant
 
   Km
Value: 0.0045
Constant
 
   Ki
Value: 0.047
Constant
 
   Complex_V
Value: 0.0033211
Constant
 
aconitase (5)
 
   Ks
Value: 5.0E-4
Constant
 
   Kp
Value: 1.1E-4
Constant
 
   KcF
Value: 20.47
Constant
 
   KcR
Value: 31.44
Constant
 
   ACO
Value: 3.8617E-7
Constant
 
oxoglutarate carrier (11)
 
   KiS1
Value: 3.0E-4
Constant
 
   KiS2
Value: 7.0E-4
Constant
 
   KiP1
Value: 0.0014
Constant
 
   KiP2
Value: 1.7E-4
Constant
 
   KcF
Value: 3.675
Constant
 
   KcR
Value: 4.83
Constant
 
   alpha
Value: 1.0
Constant
 
   beta
Value: 1.0
Constant
 
   gamma
Value: 1.0
Constant
 
   delta
Value: 1.0
Constant
 
   OGC
Value: 3.3211E-4
Constant
 
malate dehydrogenase (cytosol) (9)
 
   k1
Value: 3.4E7
Constant
 
   k2
Value: 3.5E7
Constant
 
   k3
Value: 4650.0
Constant
 
   k4
Value: 214.0
Constant
 
   kminus1
Value: 26.0
Constant
 
   kminus2
Value: 1400.0
Constant
 
   kminus3
Value: 570000.0
Constant
 
   kminus4
Value: 260000.0
Constant
 
   MDH
Value: 3.8617E-7
Constant
 
aspartate transaminase (10)
 
   KmS1
Value: 9.0E-4
Constant
 
   KmS2
Value: 1.0E-4
Constant
 
   KmP1
Value: 4.0E-5
Constant
 
   KmP2
Value: 0.004
Constant
 
   KiS1
Value: 0.002
Constant
 
   KiP2
Value: 0.0083
Constant
 
   Keq
Value: 6.2
Constant
 
   KcF
Value: 300.0
Constant
 
   KcR
Value: 1000.0
Constant
 
   AspTA
Value: 3.8617E-7
Constant
 
citrate carrier (11)
 
   KiS1
Value: 1.3E-4
Constant
 
   KiS2
Value: 4.4E-4
Constant
 
   KiP1
Value: 3.3E-4
Constant
 
   KiP2
Value: 4.18E-5
Constant
 
   KcF
Value: 5.6
Constant
 
   KcR
Value: 3.5
Constant
 
   alpha
Value: 1.0
Constant
 
   beta
Value: 1.0
Constant
 
   gamma
Value: 1.0
Constant
 
   delta
Value: 1.0
Constant
 
   CIC
Value: 3.3211E-4
Constant
 
ETF:Q oxidoreductase (10)
 
   KmS1
Value: 3.1E-7
Constant
 
   KmS2
Value: 3.9E-7
Constant
 
   KmP1
Value: 3.2E-7
Constant
 
   KmP2
Value: 4.2E-9
Constant
 
   KiS1
Value: 3.1E-7
Constant
 
   KiP2
Value: 3.0E-7
Constant
 
   Keq
Value: 0.66
Constant
 
   KcF
Value: 78.0
Constant
 
   KcR
Value: 101.0
Constant
 
   v34_ETF_QO
Value: 3.3211E-5
Constant
 
glutathione reductase (12)
 
   KmS1
Value: 3.9E-5
Constant
 
   KmS2
Value: 1.2E-7
Constant
 
   KmP1
Value: 1.08E-6
Constant
 
   KmP2
Value: 2.42E-5
Constant
 
   KiS1
Value: 7.6E-5
Constant
 
   KiS2
Value: 2.4E-7
Constant
 
   KiP1
Value: 7.53E-5
Constant
 
   KiP2
Value: 1.19E-5
Constant
 
   Keq
Value: 8.99
Constant
 
   KcF
Value: 2.18
Constant
 
   KcR
Value: 0.3
Constant
 
   v35_ACD
Value: 3.3211E-5
Constant
 
pyruvate decarboxylase (16)
 
   KmA
Value: 1.1E-4
Constant
 
   KmB
Value: 0.00163
Constant
 
   KmC
Value: 3.7E-4
Constant
 
   KmP
Value: 0.016
Constant
 
   KmQ
Value: 2.4E-4
Constant
 
   KmR
Value: 5.1E-5
Constant
 
   Keq
Value: 9.0
Constant
 
   Kia
Value: 1.5E-4
Constant
 
   Kib
Value: 0.0016
Constant
 
   Kic
Value: 1.3E-4
Constant
 
   Kip
Value: 0.0079
Constant
 
   Kiq
Value: 1.9E-4
Constant
 
   Kir
Value: 2.4E-4
Constant
 
   KcF
Value: 200.0
Constant
 
   KcR
Value: 20.0
Constant
 
   PC
Value: 3.8617E-7
Constant
 
glycerol-3-phosphate dehydrogenase (FAD dependent) (3)
 
   K
Value: 3.4E-5
Constant
 
   V
Value: 3.99E-8
Constant
 
   Glycerol-3-phosphate dehydrogenase
Value: 0.001
Constant
 
glycerol-3-phosphate dehydrogenase (NAD+ dependent) (3)
 
   K
Value: 34.0
Constant
 
   V
Value: 0.0399
Constant
 
   Glycerol-3-phosphate dehydrogenase
Value: 0.001
Constant
 
ATP/ADP carrier (3)
 
   V
Value: 0.1667
Constant
 
   K
Value: 0.012
Constant
 
   AAC
Value: 3.3211E-4
Constant
 
cytosolic isocitrate dehydrogenase (13)
 
   phi0
Value: 0.051
Constant
 
   phi1
Value: 9.5E-8
Constant
 
   phi2
Value: 9.6E-7
Constant
 
   phi12
Value: 9.0E-8
Constant
 
   phir0
Value: 0.066
Constant
 
   phir1
Value: 3.7E-7
Constant
 
   phir2
Value: 2.9E-5
Constant
 
   phir3
Value: 2.5E-4
Constant
 
   phir12
Value: 6.0E-12
Constant
 
   phir13
Value: 1.3E-10
Constant
 
   phir23
Value: 9.4E-8
Constant
 
   phir123
Value: 4.6E-14
Constant
 
   IDHc
Value: 3.8617E-7
Constant
 
citrate carrier (11)
 
   KiS1
Value: 1.3E-4
Constant
 
   KiS2
Value: 4.4E-4
Constant
 
   KiP1
Value: 3.3E-4
Constant
 
   KiP2
Value: 4.18E-5
Constant
 
   KcF
Value: 5.6
Constant
 
   KcR
Value: 3.5
Constant
 
   alpha
Value: 1.0
Constant
 
   beta
Value: 1.0
Constant
 
   gamma
Value: 1.0
Constant
 
   delta
Value: 1.0
Constant
 
   CIC
Value: 3.3211E-4
Constant
 
ATP/ADP carrier (3)
 
   V
Value: 1.11667
Constant
 
   K
Value: 0.005
Constant
 
   AAC
Value: 3.3211E-4
Constant
 
malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) (4)
 
   Kcat
Value: 0.333
Constant
 
   Kmal
Value: 1.25E-4
Constant
 
   Knadp
Value: 0.011
Constant
 
   MDH
Value: 3.8617E-7
Constant
 
malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) (3)
 
   Kcat
Value: 130.5
Constant
 
   Km
Value: 0.01295
Constant
 
   MDH
Value: 3.8617E-7
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000239

Curator's comment: (updated: 01 Dec 2009 16:35:08 GMT)

The model reproduces figure 2 of the reference publication. The model was integrated and simulated using Copasi v4.5 (Build 30).

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