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BIOMD0000000482 - Noguchi2013 - Insulin dependent glucose metabolism

 

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Reference Publication
Publication ID: 23670537
Noguchi R, Kubota H, Yugi K, Toyoshima Y, Komori Y, Soga T, Kuroda S.
The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns.
Mol. Syst. Biol. 2013; 9: 664
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.  [more]
Model
Original Model: BIOMD0000000482.origin
Submitter: Rei Noguchi
Submission ID: MODEL1301020001
Submission Date: 02 Jan 2013 19:42:57 UTC
Last Modification Date: 10 Oct 2014 11:31:41 UTC
Creation Date: 23 Sep 2013 12:08:14 UTC
Encoders:  Vijayalakshmi Chelliah
   Rei Noguchi
set #1
bqbiol:hasProperty Human Disease Ontology diabetes mellitus
set #2
bqbiol:hasTaxon Taxonomy Rattus
set #3
bqmodel:isDerivedFrom BioModels Database Kubota2012_InsulinAction_AKTpathway
set #4
bqbiol:isVersionOf Gene Ontology regulation of insulin secretion involved in cellular response to glucose stimulus
set #5
bqbiol:occursIn Brenda Tissue Ontology hepatoma cell
set #6
bqbiol:hasProperty Mathematical Modelling Ontology ordinary differential equation model
Notes
Model
Publication ID: 23670537 Submission Date: 02 Jan 2013 19:42:57 UTC Last Modification Date: 10 Oct 2014 11:31:41 UTC Creation Date: 23 Sep 2013 12:08:14 UTC
Mathematical expressions
Reactions
v1 v2 v3 v4
v5 v6 v7 v8
v9 metabolicENZ1 reaction1 reaction2
reaction3 reaction4 reaction5 reaction6
reaction7 reaction8 reaction9 reaction10
reaction11 reaction12 reaction13 reaction14
reaction15 reactionPEP1 reactionPEP2 reaction16
metabolicENZ2      
Physical entities
Compartments Species
default GP pGP mRNA
PEPCK IRS p1IRS
p2IRS p1p2IRS Akt
pAkt mTOR pmTOR
Foxo pFoxo  
Vex PYRout GLCex  
Vin F16P PYRin LAC
OAA GLY G1P
G6P    
Global parameters
V1 K1 V2_G6P K2_G6P
V2_F16P K2_F16P V3 K3
V6 K6 V7 K7
V4_PYR K4_PYR V4_LAC K4_LAC
V8_G6P K8_G6P V8_G1P K8_G1P
V5 K5 V9_G1P K9_G1P
V9_GLY K9_GLY k3 k4
s1 s4 s2 s3
k1_PEPCK k2_PEPCK k3_PEPCK k4_PEPCK
k5_PEPCK k6_PEPCK param1 param2
param3 param4 param5 param6
param7 param8 param9 param10
param11 param12 param13 param14
param15 param16 proIRS insulin
Reactions (29)
 
 v1 [GLCex] ↔ [G6P];   {GLCex} , {G6P}
 
 v2 [pAkt] + [G6P] ↔ [pAkt] + [F16P];   {pAkt} , {G6P} , {F16P}
 
 v3 [F16P] → [PYRin];   {F16P}
 
 v4 [PYRin] ↔ [LAC];   {PYRin} , {LAC}
 
 v5 [PYRout] ↔ [PYRin];   {PYRout} , {PYRin}
 
 v6 [PYRin] → [OAA];   {PYRin}
 
 v7 [PEPCK] + [OAA] → [PEPCK] + [F16P];   {PEPCK} , {OAA}
 
 v8 [pAkt] + [G6P] ↔ [pAkt] + [G1P];   {pAkt} , {G6P} , {G1P}
 
 v9 [pGP] + [G1P] ↔ [pGP] + [GLY];   {G1P} , {pGP} , {GLY}
 
 metabolicENZ1 [pGP] + [G6P] → [GP] + [G6P];   {pGP} , {G6P}
 
 reaction1  → [IRS];   {IRS}
 
 reaction2 [IRS] ↔ [p1IRS];   {IRS} , {p1IRS}
 
 reaction3 [p1IRS] → ;   {p1IRS}
 
 reaction4 [p1IRS] + [pmTOR] → [p1p2IRS] + [pmTOR];   {p1IRS} , {pmTOR}
 
 reaction5 [p1p2IRS] → [p1IRS];   {p1p2IRS}
 
 reaction6 [IRS] + [pmTOR] → [p2IRS] + [pmTOR];   {IRS} , {pmTOR}
 
 reaction7 [p2IRS] → [IRS];   {p2IRS}
 
 reaction8 [p2IRS] → ;   {p2IRS}
 
 reaction9 [p2IRS] ↔ [p1p2IRS];   {p2IRS} , {p1p2IRS}
 
 reaction10 [p1p2IRS] → ;   {p1p2IRS}
 
 reaction11 [Akt] + [p1IRS] → [pAkt] + [p1IRS];   {p1IRS} , {Akt}
 
 reaction12 [pAkt] → [Akt];   {pAkt}
 
 reaction13 [mTOR] + [pAkt] → [pmTOR] + [pAkt];   {mTOR} , {pAkt}
 
 reaction14 [pmTOR] → [mTOR];   {pmTOR}
 
 reaction15 [Foxo] + [pAkt] → [pFoxo] + [pAkt];   {pAkt} , {Foxo}
 
 reactionPEP1 [Foxo] → [mRNA] + [Foxo];   {Foxo} , {mRNA}
 
 reactionPEP2 [mRNA] → [PEPCK] + [mRNA];   {mRNA} , {PEPCK}
 
 reaction16 [pFoxo] → [Foxo];   {pFoxo}
 
 metabolicENZ2 [GP] → [pGP];   {GP}
 
 default Spatial dimensions: 3.0  Compartment size: 1.0
 
 GP
Compartment: default
Initial amount: 0.4726
 
 pGP
Compartment: default
Initial amount: 0.1723
 
 mRNA
Compartment: default
Initial amount: 2.905
 
 PEPCK
Compartment: default
Initial amount: 0.7686
 
 IRS
Compartment: default
Initial amount: 888.77
 
 p1IRS
Compartment: default
Initial amount: 0.0
 
 p2IRS
Compartment: default
Initial amount: 0.0
 
 p1p2IRS
Compartment: default
Initial amount: 0.0
 
 Akt
Compartment: default
Initial amount: 1.1182
 
 pAkt
Compartment: default
Initial amount: 0.0
 
 mTOR
Compartment: default
Initial amount: 880.25
 
 pmTOR
Compartment: default
Initial amount: 0.0
 
 Foxo
Compartment: default
Initial amount: 1.069E-5
 
 pFoxo
Compartment: default
Initial amount: 0.0
 
 Vex Spatial dimensions: 3.0  Compartment size: 0.004  (Units: litre)
 
 PYRout
Compartment: Vex
Initial amount: 137.5
 
 GLCex
Compartment: Vex
Initial amount: 114.9
 
 Vin Spatial dimensions: 3.0  Compartment size: 2.64E-5  (Units: litre)
 
 F16P
Compartment: Vin
Initial amount: 9.571
 
 PYRin
Compartment: Vin
Initial amount: 0.9872
 
 LAC
Compartment: Vin
Initial amount: 1001.0
 
 OAA
Compartment: Vin
Initial amount: 0.0022
 
 GLY
Compartment: Vin
Initial amount: 4.8248
 
 G1P
Compartment: Vin
Initial amount: 5.303
 
   G6P
Compartment: Vin
Initial amount: 0.5188
 
Global Parameters (56)
 
   V1
Value: 8.97
Constant
 
   K1
Value: 0.0451
Constant
 
   V2_G6P
Value: 7.71
Constant
 
   K2_G6P
Value: 925.0
Constant
 
   V2_F16P
Value: 0.0839
Constant
 
   K2_F16P
Value: 0.597
Constant
 
   V3
Value: 0.00229
Constant
 
   K3
Value: 2.92
Constant
 
   V6
Value: 0.00247
Constant
 
   K6
Value: 0.996
Constant
 
   V7
Value: 2.84E-5
Constant
 
   K7
Value: 8.43
Constant
 
   V4_PYR
Value: 23.6
Constant
 
   K4_PYR
Value: 56.4
Constant
 
   V4_LAC
Value: 1.2E-6
Constant
 
   K4_LAC
Value: 0.0154
Constant
 
   V8_G6P
Value: 2.02E-5
Constant
 
   K8_G6P
Value: 0.791
Constant
 
   V8_G1P
Value: 0.04
Constant
 
   K8_G1P
Value: 69.8
Constant
 
   V5
Value: 0.00112
Constant
 
   K5
Value: 0.228
Constant
 
   V9_G1P
Value: 0.488
Constant
 
   K9_G1P
Value: 2.69
Constant
 
   V9_GLY
Value: 1.02E-6
Constant
 
   K9_GLY
Value: 6.23E-4
Constant
 
   k3
Value: 112.76
Constant
 
   k4
Value: 1.9448
Constant
 
   s1
Value: 1.722
Constant
 
   s4
Value: 214.7
Constant
 
   s2
Value: 46.54
Constant
 
   s3
Value: 1.19
Constant
 
   k1_PEPCK
Value: 0.12225
Constant
 
   k2_PEPCK
Value: 0.0045985
Constant
 
   k3_PEPCK
Value: 486.28
Constant
 
   k4_PEPCK
Value: 0.0046101
Constant
 
   k5_PEPCK
Value: 1.0958E-4
Constant
 
   k6_PEPCK
Value: 0.0018592
Constant
 
   param1
Value: 5.5702
Constant
 
   param2
Value: 2.3969
Constant
 
   param3
Value: 0.020934
Constant
 
   param4
Value: 1.214E-5
Constant
 
   param5
Value: 0.2751
Constant
 
   param6
Value: 0.0072509
Constant
 
   param7
Value: 758.12
Constant
 
   param8
Value: 0.91758
Constant
 
   param9
Value: 0.041292
Constant
 
   param10
Value: 1.3032E-4
Constant
 
   param11
Value: 1.92E-4
Constant
 
   param12
Value: 0.029311
Constant
 
   param13
Value: 4.4307E-5
Constant
 
   param14
Value: 0.35211
Constant
 
   param15
Value: 3.1385E-5
Constant
 
   param16
Value: 0.0095934
Constant
 
   proIRS
Value: 888.77
Constant
 
   insulin
Value: 100.0   (Units: nanomole/litre)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000482

Curator's comment: (updated: 23 Sep 2013 12:09:56 GMT)

Figure 2 that corresponds to pAKT, at varying insulin concentrations (0, 1, 100nM) has been reproduced here.
The model was simulated using Copasi v4.8 (Build 55) and the plot was generated using Gnuplot.

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