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BIOMD0000000387 - Arnold2011_Damour2007_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: BIOMD0000000387.origin
Submitter: Anne Arnold
Submission ID: MODEL1109270003
Submission Date: 27 Sep 2011 11:16:11 UTC
Last Modification Date: 20 Apr 2012 19:52:02 UTC
Creation Date: 19 Oct 2011 14:52:11 UTC
Encoders:  Vijayalakshmi Chelliah
   Anne Arnold
   Zoran Nikoloski
set #1
bqbiol:encodes Gene Ontology reductive pentose-phosphate cycle
set #2
bqbiol:occursIn 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 Damour and Urban (2007, [for PDF click here] ).

The parameter values are partly taken from Farquhar et al. (1980, DOI:10.1007/BF00386231 ) and Urban et al. (2003, DOI:10.1093/treephys/23.5.289 ). 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 11:16:11 UTC Last Modification Date: 20 Apr 2012 19:52:02 UTC Creation Date: 19 Oct 2011 14:52:11 UTC
Mathematical expressions
Reactions
PGA production - v_c PGA production - v_o PGA consumption NADPH production
Rules
Assignment Rule (variable: Gamma) Assignment Rule (variable: Cst) Assignment Rule (variable: phi) Assignment Rule (variable: Vc)
Assignment Rule (variable: Vp) Assignment Rule (variable: NADP) Assignment Rule (variable: J) Assignment Rule (variable: Vj)
Physical entities
Compartments Species
chloroplast RuBP PGA NADPH
CO2 O2 NADP
starch    
Global parameters
Rp Nt alpha J
Jmax Gamma Q Vcmax
Kc Ko Vj phi
Vc Vp TPU Cst
a      
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 (8)
 
 Assignment Rule (name: Gamma) Gamma = O2/(2*exp(-7.458+37830/(8.3143*298.15)))
 
 Assignment Rule (name: Cst) Cst = exp((-0.0398)*starch*a)
 
 Assignment Rule (name: phi) phi = 0.21*O2/Ko/CO2/Kc
 
 Assignment Rule (name: Vc) Vc = Vcmax*CO2/((1+O2/Ko)*(CO2+Kc))
 
 Assignment Rule (name: Vp) Vp = 3*TPU/(1-Gamma/CO2)
 
 Assignment Rule (name: NADP) NADP = Nt-NADPH
 
 Assignment Rule (name: J) J = Cst*alpha*0.9*Q/(1+(alpha*0.9*Q/Jmax)^2)^(0.5)/(65*0.5)
 
 Assignment Rule (name: Vj) Vj = J/4*CO2/(CO2+2*Gamma)
 
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)
 
 Carboxylation lambda(Vc, Vj, Vp, ((Vc+Vj-abs(Vc-Vj))/2+Vp-abs((Vc+Vj-abs(Vc-Vj))/2-Vp))/2)
 
 NADPH production lambda(j, S1, Nt, j/2*S1/Nt)
 
 PGA consumption lambda(S1, Rp, R, Nt, Vc, S1/Rp*R/Nt*Vc)
 
   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: 21000.0
Constant
 
  NADP
Compartment: chloroplast
Initial concentration: 0.29
 
 starch
Compartment: chloroplast
Initial concentration: 0.5
Constant
 
Global Parameters (17)
 
 Rp
Value: 3.2
Constant
 
 Nt
Value: 0.5
Constant
 
 alpha
Value: 0.24
Constant
 
  J
Value: 3.64863790509821
 
 Jmax
Value: 142.047003854271
Constant
 
  Gamma
Value: 4.29040862748855
 
 Q
Value: 1000.0
Constant
 
 Vcmax
Value: 1.91141270310584
Constant
 
 Kc
Value: 26.7125313821435
Constant
 
 Ko
Value: 187891.032274486
Constant
 
  Vj
Value: 0.675554869049198
 
  phi
Value: 0.025590660664217
 
  Vc
Value: 0.822489884906092
 
  Vp
Value: 0.942054655190967
 
 TPU
Value: 0.259027750094988
Constant
 
  Cst
Value: 0.999136712846952
 
 a
Value: 0.0434
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000387

Curator's comment: (updated: 19 Oct 2011 15:44:25 BST)

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

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