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BIOMD0000000389 - Arnold2011_Hahn1986_CalvinCycle_Starch_Sucrose

 

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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: BIOMD0000000389.origin
Submitter: Anne Arnold
Submission ID: MODEL1109270006
Submission Date: 27 Sep 2011 11:19:01 UTC
Last Modification Date: 20 Apr 2012 19:51:27 UTC
Creation Date: 19 Oct 2011 14:53:17 UTC
Encoders:  Vijayalakshmi Chelliah
   Anne Arnold
   Zoran Nikoloski
set #1
bqbiol:hasTaxon 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 and the related end-product pathways to starch and sucrose synthesis by Hahn (1986, [click here for abstract] ).

The parameter values are taken from Hahn (1984, [click here for abstract] ). 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 11:19:01 UTC Last Modification Date: 20 Apr 2012 19:51:27 UTC Creation Date: 19 Oct 2011 14:53:17 UTC
Mathematical expressions
Reactions
RuBisCO PGA reduction FBP ald + ase F6P trans I
SBP ald + ase S7P trans I + R5P iso trans II + Ru5P epi Ru5P kinase
ATP synthase starch synthetase starch phosphorylase TP translocator
FBPc ald + ase sucrose synthetase UTP synthase respiration rate
diffusion rate translocation rate    
Rules
Assignment Rule (variable: v(15))      
Physical entities
Compartments Species
chloroplast RuBP PGA TP
HeP TPGA E4P
S7P Ru5P GG
ATP ADP UTP
UDP Pi CO2
Resp    
cytosol TPc HePc Suc
Pic    
vacuole SucV    
phloem E    
Global parameters
r D phi v(15)
Reactions (18)
 
 RuBisCO [RuBP] + [CO2] → 2.0 × [PGA];  
 
 PGA reduction [PGA] + [ATP] → [TP] + [ADP] + [Pi];  
 
 FBP ald + ase 2.0 × [TP] ↔ [HeP] + [Pi];  
 
 F6P trans I [HeP] → [TPGA] + [E4P];  
 
 SBP ald + ase [E4P] + [TP] → [S7P] + [Pi];  
 
 S7P trans I + R5P iso [S7P] → [TPGA] + [Ru5P];  
 
 trans II + Ru5P epi [TPGA] + [TP] → [Ru5P];  
 
 Ru5P kinase [Ru5P] + [ATP] → [RuBP] + [ADP];  
 
 ATP synthase [ADP] + [Pi] → [ATP];  
 
 starch synthetase [ATP] + [HeP] → [GG] + [ADP] + 2.0 × [Pi];  
 
 starch phosphorylase [GG] + [Pi] → [HeP];  
 
 TP translocator [TP] + [Pic] → [TPc] + [Pi];  
 
 FBPc ald + ase 2.0 × [TPc] → [HePc] + [Pic];  
 
 sucrose synthetase 2.0 × [HePc] + [UTP] → [Suc] + [UDP] + 3.0 × [Pic];  
 
 UTP synthase [UDP] + [Pic] → [UTP];  
 
 respiration rate [Suc] → [Resp];  
 
 diffusion rate [Suc] ↔ [SucV];  
 
 translocation rate [Suc] ↔ [E];  
 
Rules (1)
 
 Assignment Rule (name: v_15) v(15) = 0.0258*HePc*UTP
 
Functions (1)
 
 irreversilbe Constant flux (Suc synth) lambda(v, v)
 
   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
 
 HeP
Compartment: chloroplast
Initial concentration: 2.2
 
 TPGA
Compartment: chloroplast
Initial concentration: 0.2
 
 E4P
Compartment: chloroplast
Initial concentration: 0.05
 
 S7P
Compartment: chloroplast
Initial concentration: 2.0
 
 Ru5P
Compartment: chloroplast
Initial concentration: 0.05
 
 GG
Compartment: chloroplast
Initial concentration: 99.9999999999999
 
 ATP
Compartment: chloroplast
Initial concentration: 3.875
 
 ADP
Compartment: chloroplast
Initial concentration: 0.53
 
 UTP
Compartment: chloroplast
Initial concentration: 3.871
 
 UDP
Compartment: chloroplast
Initial concentration: 1.613
 
 Pi
Compartment: chloroplast
Initial concentration: 2.5
 
 CO2
Compartment: chloroplast
Initial concentration: 31.0
Constant
 
   Resp
Compartment: chloroplast
Initial concentration: 1.0
Constant
 
   cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 TPc
Compartment: cytosol
Initial concentration: 0.114
 
 HePc
Compartment: cytosol
Initial concentration: 0.1
 
 Suc
Compartment: cytosol
Initial concentration: 77.31
 
 Pic
Compartment: cytosol
Initial concentration: 0.8
 
   vacuole Spatial dimensions: 3.0  Compartment size: 1.0
 
 SucV
Compartment: vacuole
Initial concentration: 77.31
 
   phloem Spatial dimensions: 3.0  Compartment size: 1.0
 
 E
Compartment: phloem
Initial concentration: 0.5
Constant
 
Global Parameters (4)
 
 r
Value: 3.0E-5
Constant
 
 D
Value: 1.0E-4
Constant
 
 phi
Value: 1.0E-4
Constant
 
  v(15)
Value: 0.00998718
 
RuBisCO (1)
 
 k1
Value: 0.006
Constant
 
PGA reduction (1)
 
 k1
Value: 0.0207
Constant
 
FBP ald + ase (2)
 
 k1
Value: 4.0
Constant
 
 k2
Constant
 
F6P trans I (1)
 
 k1
Value: 0.031
Constant
 
SBP ald + ase (1)
 
 k1
Value: 3.1
Constant
 
S7P trans I + R5P iso (1)
 
 k1
Value: 0.31
Constant
 
trans II + Ru5P epi (1)
 
 k1
Value: 6.2
Constant
 
Ru5P kinase (1)
 
 k1
Value: 0.031
Constant
 
ATP synthase (1)
 
 k1
Value: 0.279
Constant
 
starch synthetase (1)
 
 k1
Value: 0.002
Constant
 
starch phosphorylase (1)
 
 k1
Value: 4.0E-5
Constant
 
TP translocator (1)
 
 k1
Value: 0.5
Constant
 
FBPc ald + ase (1)
 
 k1
Value: 1.55
Constant
 
UTP synthase (1)
 
 k1
Value: 0.00755
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000389

Curator's comment: (updated: 19 Oct 2011 15:46:38 BST)

The steady state concentration of the metabolites involved are reproduced here. This is the reproduction of the Table S7 (referring Hahn 1986) of the reference (supp. material) publication. The simulation was done using Copasi v4.7 (Build 34).

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