BioModels Database logo

BioModels Database

spacer

BIOMD0000000390 - Arnold2011_Giersch1990_CalvinCycle

 

 |   |   |  Send feedback
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: BIOMD0000000390.origin
Submitter: Anne Arnold
Submission ID: MODEL1109270005
Submission Date: 27 Sep 2011 11:18:06 UTC
Last Modification Date: 20 Apr 2012 19:51:07 UTC
Creation Date: 19 Oct 2011 14:53:43 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 by Giersch et al. (1990, DOI:10.1007/BF00032595 ).

The parameter values are taken from Figure 4 and 5. 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 .

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team.
For more information see the terms of use .
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 22001849 Submission Date: 27 Sep 2011 11:18:06 UTC Last Modification Date: 20 Apr 2012 19:51:07 UTC Creation Date: 19 Oct 2011 14:53:43 UTC
Mathematical expressions
Reactions
RuBisCO PGA reduction TP reduction RuBP regeneration
TP translocator ATP synthesis    
Rules
Assignment Rule (variable: totRuBP)      
Physical entities
Compartments Species
chloroplast RuBP PGA TP
Ru5P Pi ATP
ADP RuBisCo totRuBP
     
cytosol TPc Pic  
Global parameters
V6 P_0    
Reactions (6)
 
 RuBisCO [totRuBP] + [RuBP] → 2.0 × [PGA];   {RuBisCo}
 
 PGA reduction [PGA] + [ATP] ↔ [ADP] + [TP] + [Pi];  
 
 TP reduction 5.0 × [TP] → 3.0 × [Ru5P] + 2.0 × [Pi];  
 
 RuBP regeneration [Ru5P] + [ATP] → [RuBP] + [ADP];   {Pi}
 
 TP translocator [TP] + [Pic] ↔ [TPc] + [Pi];  
 
 ATP synthesis [ADP] + [Pi] → [ATP];  
 
Rules (1)
 
 Assignment Rule (name: totRuBP) totRuBP = 1/2*(P_0-(PGA+TP+Ru5P+Pi+ATP))
 
Functions (6)
 
 PGA reduction lambda(Vm, S1, S2, P1, P2, P3, k, K1, K2, Vm*(S1*S2-P1*P2*P3/k)/(K1+S1*S2*K1/K2+P1*P2*P3/k))
 
 High Substrate MM - RuBisCO lambda(k, E, S, K, k/2*(E+S+K-((E+S+K)^2-4*E*S)^(0.5)))
 
 MM s1 - reg (TP reduction) lambda(Vm, S, K, Vm*S/(S+K))
 
 RuBP regeneration lambda(Vm, S1, S2, K1, K2, K3, R, Vm*S1*S2/(K1*K2+K2*S2+S1*S2+K3*R))
 
 MM s2 - reg (ATP synthesis) lambda(Vm, s1, s2, K1, K2, Vm*s1*s2/((s1+K1)*(s2+K2)))
 
 TP translocator lambda(S1, S2, P1, P2, K2, K1, Vm, Vm*(S1*S2-P1*P2)/((S1+P1)*K2+(S2+P2)*K1+K1*K2*(S1/K1+P2/K2)*(S2/K2+P1/K1)))
 
   chloroplast Spatial dimensions: 3.0  Compartment size: 1.0
 
 RuBP
Compartment: chloroplast
Initial concentration: 2.0
 
 PGA
Compartment: chloroplast
Initial concentration: 2.4
 
 TP
Compartment: chloroplast
Initial concentration: 0.5
 
 Ru5P
Compartment: chloroplast
Initial concentration: 0.0500747384155456
 
 Pi
Compartment: chloroplast
Initial concentration: 5.0
 
 ATP
Compartment: chloroplast
Initial concentration: 0.68
 
 ADP
Compartment: chloroplast
Initial concentration: 0.82
 
 RuBisCo
Compartment: chloroplast
Initial concentration: 3.56
Constant
 
   totRuBP
Compartment: chloroplast
Initial concentration: 3.68496263079223
 
   cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 TPc
Compartment: cytosol
Initial concentration: 0.2
Constant
 
 Pic
Compartment: cytosol
Initial concentration: 1.4
Constant
 
Global Parameters (2)
 
 V6
Value: 5.8801285588795
Constant
 
 P_0
Value: 16.0
Constant
 
RuBisCO (2)
 
 k
Value: 0.504
Constant
 
 K
Value: 0.04
Constant
 
PGA reduction (4)
 
 Vm
Value: 3.49
Constant
 
 k
Value: 14.0
Constant
 
 K1
Value: 1.0
Constant
 
 K2
Value: 1.0
Constant
 
TP reduction (2)
 
 Vm
Value: 1.06
Constant
 
 K
Value: 0.4
Constant
 
RuBP regeneration (4)
 
 Vm
Value: 4.81
Constant
 
 K1
Value: 0.05
Constant
 
 K2
Value: 0.5
Constant
 
 K3
Value: 0.05
Constant
 
TP translocator (3)
 
 K2
Value: 0.25
Constant
 
 K1
Value: 0.08
Constant
 
 Vm
Value: 3.3
Constant
 
ATP synthesis (2)
 
 K1
Value: 0.08
Constant
 
 K2
Value: 0.5
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000390

Curator's comment: (updated: 19 Oct 2011 15:46:03 BST)

The steady state concentration of the metabolites involved are reproduced here. This is the reproduction of the Table S7 (referring Giersch 1990) of the reference (supp. material) publication. The simulation was done using Copasi v4.7 (Build 34).

spacer
spacer