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BIOMD0000000391 - Arnold2011_Poolman2000_CalvinCycle_Starch

 

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Reference Publication
Publication ID: 22001849
Arnold A, Nikoloski Z.
A quantitative comparison of Calvin-Benson cycle models.
Trends Plant Sci. 2011 Dec; 16(12): 676-683
Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.  [more]
Model
Original Model: BIOMD0000000391.origin
Submitter: Anne Arnold
Submission ID: MODEL1109270007
Submission Date: 27 Sep 2011 11:19:45 UTC
Last Modification Date: 08 Apr 2016 17:11:43 UTC
Creation Date: 16 Sep 2011 14:50:04 UTC
Encoders:  Vijayalakshmi Chelliah
   Anne Arnold
   Zoran Nikoloski
set #1
bqbiol:hasTaxon Taxonomy Viridiplantae
set #2
bqmodel:is Gene Ontology reductive pentose-phosphate cycle
Notes

This model is from the article:
A quantitative comparison of Calvin–Benson cycle models
Anne Arnold, Zoran Nikoloski Trends in Plant Science2011 Oct 14. 22001849,
Abstract:
The Calvin-Benson cycle (CBC) provides the precursors for biomass synthesis necessary for plant growth. The dynamic behavior and yield of the CBC depend on the environmental conditions and regulation of the cellular state. Accurate quantitative models hold the promise of identifying the key determinants of the tightly regulated CBC function and their effects on the responses in future climates. We provide an integrative analysis of the largest compendium of existing models for photosynthetic processes. Based on the proposed ranking, our framework facilitates the discovery of best-performing models with regard to metabolomics data and of candidates for metabolic engineering.

Note: Model of the Calvin cycle and the related end-product pathway to starch synthesis by Poolman et al. (2000, DOI:10.1093/jexbot/51.suppl_1.319).

The parameter values are widely taken from Pettersson and Ryde-Pettersson (1988, DOI:10.1111/j.1432-1033.1988.tb14242.x) and Poolman (1999, [click here for PDF]). The initial metabolite values are chosen from the data set of Zhu et al. (2007, DOI:10.1104/pp.107.103713). A detailed description of all modifications is given in the model described by Arnold and Nikoloski (2011, PMID:22001849.
Model
Publication ID: 22001849 Submission Date: 27 Sep 2011 11:19:45 UTC Last Modification Date: 08 Apr 2016 17:11:43 UTC Creation Date: 16 Sep 2011 14:50:04 UTC
Mathematical expressions
Reactions
RuBisCo PGA kinase GAP dehydrogenase TP isomerase
FBP aldolase FBP ase F6P transketolase SBP aldolase
SBP ase S7P transketolase R5P isomerase Ru5P epimerase
Ru5P kinase PG isomerase PG mutase starch synthase
starch phosphorylase ATP synthetase TPT - PGA TPT - GAP
TPT - DHAP      
Rules
Assignment Rule (variable: Pi) Assignment Rule (variable: ADP)    
Physical entities
Compartments Species
chloroplast RuBP PGA DPGA
GAP DHAP FBP
F6P E4P SBP
S7P X5P R5P
Ru5P G6P G1P
ATP ADP NADPH
NADP H Pi
     
cytosol Pext    
Reactions (21)
 
 RuBisCo [RuBP] → 2.0 × [PGA];   {PGA} , {FBP} , {SBP} , {Pi} , {NADPH}
 
 PGA kinase [PGA] + [ATP] ↔ [DPGA] + [ADP];  
 
 GAP dehydrogenase [DPGA] + [NADPH] + [H] ↔ [GAP] + [NADP] + [Pi];  
 
 TP isomerase [GAP] ↔ [DHAP];  
 
 FBP aldolase [DHAP] + [GAP] ↔ [FBP];  
 
 FBP ase [FBP] → [F6P] + [Pi];   {F6P} , {Pi}
 
 F6P transketolase [GAP] + [F6P] ↔ [X5P] + [E4P];  
 
 SBP aldolase [DHAP] + [E4P] ↔ [SBP];  
 
 SBP ase [SBP] → [S7P] + [Pi];   {Pi}
 
 S7P transketolase [GAP] + [S7P] ↔ [X5P] + [R5P];  
 
 R5P isomerase [R5P] ↔ [Ru5P];  
 
 Ru5P epimerase [X5P] ↔ [Ru5P];  
 
 Ru5P kinase [Ru5P] + [ATP] → [RuBP] + [ADP];   {PGA} , {RuBP} , {Pi} , {ADP}
 
 PG isomerase [F6P] ↔ [G6P];  
 
 PG mutase [G6P] ↔ [G1P];  
 
 starch synthase [G1P] + [ATP] → ;   {ADP} , {Pi} , {PGA} , {F6P} , {FBP}
 
 starch phosphorylase [Pi] → [G1P];   {G1P}
 
 ATP synthetase [ADP] + [Pi] → [ATP];  
 
 TPT - PGA [PGA] → ;   {Pext} , {Pi} , {GAP} , {DHAP}
 
 TPT - GAP [GAP] → ;   {Pext} , {Pi} , {PGA} , {DHAP}
 
 TPT - DHAP [DHAP] → ;   {Pext} , {Pi} , {PGA} , {GAP}
 
Rules (2)
 
 Assignment Rule (name: Pi) Pi = (15-2*(RuBP+DPGA+FBP+SBP))-(PGA+GAP+DHAP+F6P+E4P+S7P+X5P+R5P+Ru5P+G6P+G1P+ATP)
 
 Assignment Rule (name: ADP) ADP = 1.5-ATP
 
Functions (7)
 
 MM s1 + reg 2*c (FBPase) lambda(Vm, S, K, R1, KR1, R2, KR2, Vm*S/(S+K*(1+R1/KR1+R2/KR2)))
 
 MM s1 + reg A,3*c (TPT) lambda(Vm, S, KA, A, K, R1, KR1, R2, KR2, R3, KR3, Vm*S/(S*(1+KA/A)+K*(1+(1+KA/A)*(R1/KR1+R2/KR2+R3/KR3))))
 
 MM s2 + reg 3*c-s1,1*m-s2 (Ru5P kinase) lambda(Vm, S1, S2, K1, R1, KR1, R2, KR2, R3, KR3, R4, KR41, K2, KR42, Vm*S1*S2/((S1+K1*(1+R1/KR1+R2/KR2+R3/KR3))*(S2*(1+R4/KR41)+K2*(1+R4/KR42))))
 
 MM s2 - reg (ATP synth) lambda(Vm, s1, s2, K1, K2, Vm*s1*s2/((s1+K1)*(s2+K2)))
 
 MM s1 + reg 5*c (RuBisCO) lambda(Vm, S, K, R1, KR1, R2, KR2, R3, KR3, R4, KR4, R5, KR5, Vm*S/(S+K*(1+R1/KR1+R2/KR2+R3/KR3+R4/KR4+R5/KR5)))
 
 MM s1 + reg 1*c (SBPase, starch phos) lambda(Vm, S, K, R1, KR1, Vm*S/(S+K*(1+R1/KR1)))
 
 starch synthase lambda(Vm, S1, S2, K1, K2, R1, KR1, R2, KA1, A1, KA2, A2, KA3, A3, Vm*S1*S2/((S1+K1)*(1+R1/KR1)*(S2+K2*(1+K2*R2/(KA1*A1+KA2*A2+KA3*A3)))))
 
   chloroplast Spatial dimensions: 3.0  Compartment size: 1.0
 
 RuBP
Compartment: chloroplast
Initial concentration: 2.0
 
 PGA
Compartment: chloroplast
Initial concentration: 2.4
 
 DPGA
Compartment: chloroplast
Initial concentration: 0.0011
 
 GAP
Compartment: chloroplast
Initial concentration: 0.02
 
 DHAP
Compartment: chloroplast
Initial concentration: 0.48
 
 FBP
Compartment: chloroplast
Initial concentration: 0.669999999999999
 
 F6P
Compartment: chloroplast
Initial concentration: 0.640764257004719
 
 E4P
Compartment: chloroplast
Initial concentration: 0.05
 
 SBP
Compartment: chloroplast
Initial concentration: 0.3
 
 S7P
Compartment: chloroplast
Initial concentration: 2.0
 
 X5P
Compartment: chloroplast
Initial concentration: 0.0747384155455904
 
 R5P
Compartment: chloroplast
Initial concentration: 0.125186846038864
 
 Ru5P
Compartment: chloroplast
Initial concentration: 0.0500747384155456
 
 G6P
Compartment: chloroplast
Initial concentration: 1.47375779111085
 
 G1P
Compartment: chloroplast
Initial concentration: 0.0854779518844294
 
 ATP
Compartment: chloroplast
Initial concentration: 0.68
 
  ADP
Compartment: chloroplast
Initial concentration: 0.82
 
 NADPH
Compartment: chloroplast
Initial concentration: 0.21
Constant
 
 NADP
Compartment: chloroplast
Initial concentration: 0.29
Constant
 
 H
Compartment: chloroplast
Initial concentration: 1.25892541179417E-5
Constant
 
  Pi
Compartment: chloroplast
Initial concentration: 0.977800000000002
 
   cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 Pext
Compartment: cytosol
Initial concentration: 0.5
Constant
 
RuBisCo (7)
 
 Vm
Value: 340.0
Constant
 
 K
Value: 0.02
Constant
 
 KR1
Value: 0.84
Constant
 
 KR2
Value: 0.04
Constant
 
 KR3
Value: 0.0075
Constant
 
 KR4
Value: 0.9
Constant
 
 KR5
Value: 0.07
Constant
 
PGA kinase (2)
 
 k1
Value: 5.0E8
Constant
 
 k2
Value: 1.6129E12
Constant
 
GAP dehydrogenase (2)
 
 k1
Value: 5.0E8
Constant
 
 k2
Value: 31.25
Constant
 
TP isomerase (2)
 
 k1
Value: 5.0E8
Constant
 
 k2
Value: 2.2727E7
Constant
 
FBP aldolase (2)
 
 k1
Value: 5.0E8
Constant
 
 k2
Value: 7.0423E7
Constant
 
FBP ase (4)
 
 Vm
Value: 200.0
Constant
 
 K
Value: 0.03
Constant
 
 KR1
Value: 0.7
Constant
 
 KR2
Value: 12.0
Constant
 
F6P transketolase (2)
 
 k1
Value: 5.0E8
Constant
 
 k2
Value: 5.9524E9
Constant
 
SBP aldolase (2)
 
 k1
Value: 5.0E8
Constant
 
 k2
Value: 3.84615E7
Constant
 
SBP ase (3)
 
 Vm
Value: 40.0
Constant
 
 K
Value: 0.02
Constant
 
 KR1
Value: 12.0
Constant
 
S7P transketolase (2)
 
 k1
Value: 5.0E8
Constant
 
 k2
Value: 5.8824E8
Constant
 
R5P isomerase (2)
 
 k1
Value: 5.0E8
Constant
 
 k2
Value: 1.25E9
Constant
 
Ru5P epimerase (2)
 
 k1
Value: 5.0E8
Constant
 
 k2
Value: 7.46269E8
Constant
 
Ru5P kinase (8)
 
 Vm
Value: 1000.0
Constant
 
 K1
Value: 0.05
Constant
 
 KR1
Value: 2.0
Constant
 
 KR2
Value: 0.7
Constant
 
 KR3
Value: 4.0
Constant
 
 KR41
Value: 2.5
Constant
 
 K2
Value: 0.05
Constant
 
 KR42
Value: 0.4
Constant
 
PG isomerase (2)
 
 k1
Value: 5.0E8
Constant
 
 k2
Value: 2.174E8
Constant
 
PG mutase (2)
 
 k1
Value: 5.0E8
Constant
 
 k2
Value: 8.621E9
Constant
 
starch synthase (7)
 
 Vm
Value: 40.0
Constant
 
 K1
Value: 0.08
Constant
 
 K2
Value: 0.08
Constant
 
 KR1
Value: 10.0
Constant
 
 KA1
Value: 0.1
Constant
 
 KA2
Value: 0.02
Constant
 
 KA3
Value: 0.02
Constant
 
starch phosphorylase (3)
 
 Vm
Value: 40.0
Constant
 
 K
Value: 0.1
Constant
 
 KR1
Value: 0.05
Constant
 
ATP synthetase (3)
 
 Vm
Value: 350.0
Constant
 
 K1
Value: 0.014
Constant
 
   K2
Value: 0.3
Constant
 
TPT - PGA (6)
 
   Vm
Value: 250.0
Constant
 
   KA
Value: 0.74
Constant
 
   K
Value: 0.25
Constant
 
   KR1
Value: 0.63
Constant
 
   KR2
Value: 0.075
Constant
 
   KR3
Value: 0.077
Constant
 
TPT - GAP (6)
 
   Vm
Value: 250.0
Constant
 
   KA
Value: 0.74
Constant
 
   K
Value: 0.075
Constant
 
 KR1
Value: 0.63
Constant
 
   KR2
Value: 0.25
Constant
 
 KR3
Value: 0.077
Constant
 
TPT - DHAP (6)
 
   Vm
Value: 250.0
Constant
 
   KA
Value: 0.74
Constant
 
   K
Value: 0.077
Constant
 
   KR1
Value: 0.63
Constant
 
   KR2
Value: 0.25
Constant
 
   KR3
Value: 0.075
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000391

Curator's comment: (updated: 19 Oct 2011 15:47:07 BST)

The steady state concentration of the metabolites involved are reproduced here. This is the reproduction of the Table S7 (referring Poolman 2000) of the reference (supp. material) publication. The simulation was done using Copasi v4.7 (Build 34).

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