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BIOMD0000000386 - Arnold2011_Sharkey2007_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: BIOMD0000000386.origin
Submitter: Anne Arnold
Submission ID: MODEL1109270002
Submission Date: 27 Sep 2011 11:15:25 UTC
Last Modification Date: 20 Apr 2012 19:52:27 UTC
Creation Date: 19 Oct 2011 14:51:41 UTC
Encoders:  Vijayalakshmi Chelliah
   Anne Arnold
   Zoran Nikoloski
set #1
bqmodel:is Gene Ontology reductive pentose-phosphate cycle
set #2
bqbiol:hasTaxon Taxonomy Viridiplantae
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 Sharkey et al. (2007, DOI:10.1111/j.1365-3040.2007.01710.x ).

The parameter values are partly taken from Farquhar et al. (1980, DOI:10.1007/BF00386231 ) and Medlyn et al. (2002, DOI:10.1046/j.1365-3040.2002.00891.x ). 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 11:15:25 UTC Last Modification Date: 20 Apr 2012 19:52:27 UTC Creation Date: 19 Oct 2011 14:51:41 UTC
Mathematical expressions
Reactions
PGA production - v_c PGA production - v_o PGA consumption NADPH production
Rules
Assignment Rule (variable: Vj) Assignment Rule (variable: NADP) Assignment Rule (variable: Vp) Assignment Rule (variable: Vc)
Assignment Rule (variable: v_c) Assignment Rule (variable: phi)    
Physical entities
Compartments Species
chloroplast RuBP PGA NADPH
CO2 O2 NADP
Global parameters
Rp Nt Rd J
gm Gamma Vcmax Kc
Ko phi TPU v_c
Vj Vp Vc  
Reactions (4)
 
 PGA production - v_c [RuBP] + [CO2] + 2.0 × [NADPH] → 2.0 × [PGA];   {O2}
 
 PGA production - v_o [RuBP] + [O2] + 2.0 × [NADPH] → 1.5 × [PGA];   {CO2}
 
 PGA consumption [PGA] → [RuBP];   {NADPH}
 
 NADPH production [NADP] → [NADPH];  
 
Rules (6)
 
 Assignment Rule (name: Vj) Vj = J/4*(CO2-1/2*((CO2+2*Gamma+(J-4*Rd)/(4*gm))-((CO2+2*Gamma+(J-4*Rd)/(4*gm))^2+4/gm*(Rd*(CO2+2*Gamma)+J/4*(Gamma-CO2)))^(0.5)))/((CO2-1/2*((CO2+2*Gamma+(J-4*Rd)/(4*gm))-((CO2+2*Gamma+(J-4*Rd)/(4*gm))^2+4/gm*(Rd*(CO2+2*Gamma)+J/4*(Gamma-CO2)))^(0.5)))+2*Gamma)
 
 Assignment Rule (name: NADP) NADP = Nt-NADPH
 
 Assignment Rule (name: Vp) Vp = 3*TPU*(CO2-(3*TPU-Rd)/gm)/((CO2-(3*TPU-Rd)/gm)-Gamma)
 
 Assignment Rule (name: Vc) Vc = Vcmax*(CO2-1/2*((CO2+Kc*(1+O2/Ko)+(Vcmax-Rd)/gm)-((CO2+Kc*(1+O2/Ko)+(Vcmax-Rd)/gm)^2+4/gm*(Rd*(CO2+Kc*(1+O2/Ko))+Vcmax*(Gamma-CO2)))^(0.5)))/((CO2-1/2*((CO2+Kc*(1+O2/Ko)+(Vcmax-Rd)/gm)-((CO2+Kc*(1+O2/Ko)+(Vcmax-Rd)/gm)^2+4/gm*(Rd*(CO2+Kc*(1+O2/Ko))+Vcmax*(Gamma-CO2)))^(0.5)))+Kc*(1+O2/Ko))
 
 Assignment Rule (name: v_c) v_c = (abs((abs(Vc+Vj)-abs(Vc-Vj))/2+Vp)-abs((abs(Vc+Vj)-abs(Vc-Vj))/2-Vp))/2
 
 Assignment Rule (name: phi) phi = 0.21*gm*O2/Ko/(((gm*CO2-v_c)+Rd)/Kc)
 
Functions (4)
 
 Oxygenation lambda(phi, Vc, Vj, Vp, phi*((((Vc+Vj)-abs(Vc-Vj))/2+Vp)-abs(((Vc+Vj)-abs(Vc-Vj))/2-Vp))/2)
 
 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, Vp, ((((Vc+Vj)-abs(Vc-Vj))/2+Vp)-abs(((Vc+Vj)-abs(Vc-Vj))/2-Vp))/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: 24.5
Constant
 
 O2
Compartment: chloroplast
Initial concentration: 21.0
Constant
 
  NADP
Compartment: chloroplast
Initial concentration: 0.29
 
Global Parameters (15)
 
 Rp
Value: 3.2
Constant
 
 Nt
Value: 0.5
Constant
 
 Rd
Value: 0.0307674936008629
Constant
 
 J
Value: 0.0307678189755062
Constant
 
 gm
Value: 0.0307740792044142
Constant
 
 Gamma
Value: 3.74116898182615
Constant
 
 Vcmax
Value: 0.0307602623029146
Constant
 
 Kc
Value: 27.2372124161502
Constant
 
 Ko
Value: 16.5788431231261
Constant
 
  phi
Value: 0.286292104000314
 
 TPU
Value: 0.0307585098788555
Constant
 
  v_c
Value: 0.00593820961819415
 
  Vj
Value: 0.00593820961819415
 
  Vp
Value: 0.110677228404984
 
  Vc
Value: 0.00892944491541968
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000386

Curator's comment: (updated: 19 Oct 2011 15:43:51 BST)

The steady state concentration of the metabolites involved are reproduced here. This is the reproduction of the Table S7 (referring Sharkey 2007) of the reference (supp. material) publication. The simulation was done using Copasi v4.7 (Build 34).

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