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BIOMD0000000384 - Arnold2011_Medlyn2002_RuBisCO-CalvinCycle

 

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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: BIOMD0000000384.xml.origin
Submitter: Anne Arnold
Submission ID: MODEL1109270000
Submission Date: 27 Sep 2011 11:13:38 UTC
Last Modification Date: 20 Apr 2012 19:53:00 UTC
Creation Date: 19 Oct 2011 14:50:44 UTC
Encoders:  Vijayalakshmi Chelliah
   Anne Arnold
   Zoran Nikoloski
set #1
bqbiol:occursIn Taxonomy Viridiplantae
set #2
bqbiol:encodes 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 Science 2011 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 with focus on the RuBisCO reaction by Medlyn et al. (2002, DOI:10.1046/j.1365-3040.2002.00891.x ).

The parameter values are widely taken from Farquhar et al. (1980, DOI:10.1007/BF00386231 ). 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 11:13:38 UTC Last Modification Date: 20 Apr 2012 19:53:00 UTC Creation Date: 19 Oct 2011 14:50:44 UTC
Mathematical expressions
Reactions
PGA production - v_c PGA production - v_o PGA consumption NADPH production
Rules
Assignment Rule (variable: J) Assignment Rule (variable: Vj) Assignment Rule (variable: Vc) Assignment Rule (variable: NADP)
Assignment Rule (variable: Vomax) Assignment Rule (variable: phi)    
Physical entities
Compartments Species
chloroplast RuBP PGA NADPH
CO2 O2 NADP
Global parameters
Rp Nt alpha Q
J Gamma teta Vcmax
Vomax Kc Ko Vj
phi Vc    
Reactions (4)
 
 PGA production - v_c [RuBP] + [CO2] + 2.0 × [NADPH] → 2.0 × [PGA];  
 
 PGA production - v_o [RuBP] + [O2] + 2.0 × [NADPH] → 1.5 × [PGA];  
 
 PGA consumption [PGA] → [RuBP];   {NADPH}
 
 NADPH production [NADP] → [NADPH];  
 
Rules (6)
 
 Assignment Rule (name: J) J = alpha*Q/(10-9*teta)/(65*0.5)
 
 Assignment Rule (name: Vj) Vj = J/4*CO2/(CO2+2*Gamma)
 
 Assignment Rule (name: Vc) Vc = Vcmax*CO2/((1+O2/Ko)*Kc+CO2)
 
 Assignment Rule (name: NADP) NADP = Nt-NADPH
 
 Assignment Rule (name: Vomax) Vomax = 0.21*Vcmax
 
 Assignment Rule (name: phi) phi = 0.21*O2/Ko/CO2/Kc
 
Functions (4)
 
 PGA consumption lambda(S1, Rp, R, Nt, Vc, S1/Rp*R/Nt*Vc)
 
 NADPH production lambda(j, S1, Nt, j/2*S1/Nt)
 
 Carboxylation lambda(Vc, Vj, (Vc+Vj-abs(Vc-Vj))/2)
 
 Oxygenation lambda(phi, Vc, Vj, phi*(Vc+Vj-abs(Vc-Vj))/2)
 
   chloroplast Spatial dimensions: 3.0  Compartment size: 1.0
 
 RuBP
Compartment: chloroplast
Initial concentration: 2.0
Constant
 
 PGA
Compartment: chloroplast
Initial concentration: 2.4
 
 NADPH
Compartment: chloroplast
Initial concentration: 0.21
 
 CO2
Compartment: chloroplast
Initial concentration: 245.0
Constant
 
 O2
Compartment: chloroplast
Initial concentration: 210.0
Constant
 
  NADP
Compartment: chloroplast
Initial concentration: 0.29
 
Global Parameters (14)
 
   Rp
Value: 3.2
Constant
 
 Nt
Value: 0.5
Constant
 
 alpha
Value: 0.3
Constant
 
 Q
Value: 1000.0
Constant
 
  J
Value: 4.8582995951417
 
 Gamma
Value: 42.8926627111176
Constant
 
 teta
Value: 0.9
Constant
 
 Vcmax
Value: 2.53232284114507
Constant
 
   Vomax
Value: 0.531787796640465
 
 Kc
Value: 406.066146391504
Constant
 
 Ko
Value: 276.900084789612
Constant
 
  Vj
Value: 0.899589030506691
 
  phi
Value: 0.263964911408408
 
  Vc
Value: 0.646926785453086
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000384

Curator's comment: (updated: 19 Oct 2011 15:39:54 BST)

The steady state concentrations of the metabolites involved are reproduced here. This is the reproduction of the Table S7 (referring Medlyn 2002) of the reference (supp. material) publication. The simulation was done using Copasi v4.7 (Build 34).

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