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BIOMD0000000388 - Arnold2011_Zhu2009_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: BIOMD0000000388.xml.origin
Submitter: Anne Arnold
Submission ID: MODEL1109270004
Submission Date: 27 Sep 2011 11:17:22 UTC
Last Modification Date: 20 Apr 2012 19:51:44 UTC
Creation Date: 19 Oct 2011 14:52:42 UTC
Encoders:  Vijayalakshmi Chelliah
   Anne Arnold
   Zoran Nikoloski
set #1
bqbiol:occursIn Taxonomy Viridiplantae
set #2
bqmodel:is KEGG Pathway ko00710
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 by Zhu et al. (2009, DOI:10.1016/j.nonrwa.2008.01.021 ).

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 11:17:22 UTC Last Modification Date: 20 Apr 2012 19:51:44 UTC Creation Date: 19 Oct 2011 14:52:42 UTC
Mathematical expressions
Reactions
RuBisCO PGA kinase GAP dehydrogenase GAP to Ru5P
Ru5P kinase PGA to sink GAP to sink  
Rules
Assignment Rule (variable: Pi)      
Physical entities
Compartments Species
chloroplast RuBP PGA DPGA
GAP Ru5P ADP
ATP Pi  
Reactions (7)
 
 RuBisCO [RuBP] → 2.0 × [PGA];  
 
 PGA kinase [PGA] + [ATP] → [ADP] + [DPGA];  
 
 GAP dehydrogenase [DPGA] → [GAP] + [Pi];  
 
 GAP to Ru5P [GAP] → 0.6 × [Ru5P];  
 
 Ru5P kinase [Ru5P] + [ATP] → [RuBP] + [ADP];  
 
 PGA to sink [PGA] → ;  
 
 GAP to sink [GAP] → ;  
 
Rules (1)
 
 Assignment Rule (name: Pi) Pi = 15-2*(RuBP+DPGA+ATP)-(PGA+GAP+Ru5P+ADP)
 
Functions (2)
 
 Henri-Michaelis-Menten (irreversible) lambda(substrate, Km, V, V*substrate/(Km+substrate))
 
 MM s2 - reg lambda(Vm, s1, s2, K1, K2, Vm*s1*s2/((s1+K1)*(s2+K2)))
 
   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
 
 Ru5P
Compartment: chloroplast
Initial concentration: 0.0501
 
 ADP
Compartment: chloroplast
Initial concentration: 0.82
Constant
 
 ATP
Compartment: chloroplast
Initial concentration: 0.68
Constant
 
  Pi
Compartment: chloroplast
Initial concentration: 6.3477
 
RuBisCO (2)
 
 Km
Value: 1.0
Constant
 
 V
Value: 3.78
Constant
 
PGA kinase (3)
 
 Vm
Value: 11.75
Constant
 
 K1
Value: 0.24
Constant
 
 K2
Value: 0.39
Constant
 
GAP dehydrogenase (2)
 
 Km
Value: 0.5
Constant
 
 V
Value: 5.04
Constant
 
GAP to Ru5P (2)
 
 Km
Value: 0.84
Constant
 
 V
Value: 3.05
Constant
 
Ru5P kinase (3)
 
 Vm
Value: 8.0
Constant
 
 K1
Value: 0.15
Constant
 
 K2
Value: 0.059
Constant
 
PGA to sink (2)
 
 Km
Value: 0.75
Constant
 
 V
Value: 3.0
Constant
 
GAP to sink (2)
 
 Km
Value: 5.0
Constant
 
 V
Value: 0.1
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000388

Curator's comment: (updated: 19 Oct 2011 15:45:17 BST)

The steady state concentration of the metabolites involved are reproduced here. This is the reproduction of the Table S7 (referring Zhu 2009) of the reference (supp. material) publication. The simulation was done using Copasi v4.7 (Build 34).

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