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BIOMD0000000013 - Poolman2004_CalvinCycle

 

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Reference Publication
Publication ID: 15073223
Poolman MG, Assmus HE, Fell DA.
Applications of metabolic modelling to plant metabolism.
J. Exp. Bot. 2004 May; 55(400): 1177-1186
School of Biology and Molecular Science, Oxford Brookes University, Headington, Oxford OX3 OBP, UK. mgpoolman@brookes.ac.uk  [more]
Model
Original Model: BIOMD0000000013.xml.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL6615594069
Submission Date: 13 Sep 2005 13:03:34 UTC
Last Modification Date: 16 May 2012 14:15:01 UTC
Creation Date: 25 Jun 2008 15:14:01 UTC
Encoders:  Nicolas Le Novère
   Herbert Sauro
   Mark Poolman
   Lukas Endler
set #1
bqbiol:isVersionOf Gene Ontology photosynthesis
Gene Ontology reductive pentose-phosphate cycle
bqbiol:occursIn Taxonomy Nicotiana tabacum
Notes

This a model from the article:
Applications of metabolic modelling to plant metabolism.
Poolman MG ,Assmus HE, Fell DA J. Exp. Bot. [2004 May; Volume: 55 (Issue: 400 )]: 1177-86 15073223 ,
Abstract:
In this paper some of the general concepts underpinning the computer modelling of metabolic systems are introduced. The difference between kinetic and structural modelling is emphasized, and the more important techniques from both, along with the physiological implications, are described. These approaches are then illustrated by descriptions of other work, in which they have been applied to models of the Calvin cycle, sucrose metabolism in sugar cane, and starch metabolism in potatoes.



This model describes the non oxidative Calvin cycle as depicted in Poolman et al; J Exp Bot (2004) 55:1177-1186, fig 2. Reaction E20: E4P + F6P ↔ S7P + GAP, is depicted in the figure, but not included in the model. The light reaction: ADP + P i → ATP, is included in the model, but only mentioned in the figure caption. The parameters and initial concentrations are the same as in Poolman, 1999, Computer Modelling Applied to the Calvin Cycle, PhD Thesis, Oxford Brookes University, Appendix A (available at at http://mudshark.brookes.ac.uk/index.php/Publications/Theses/Mark )

© Mark Poolman (mgpoolman@brookes.ac.uk) 1995-2002
Based on a description by Pettersson 1988, Eur. J. Biochem. 175, 661-672
Differences are:
1 - Reactions assumed by Pettersson to be in equilibrium have fast mass action kinetics.
2 - Introduction of the parameter PGAxpMult to modulate PGA export through TPT.
3 - Introduction of Starch phosphorylase reaction.
This file may be freely copied or translated into other formats provided:
1 - This notice is reproduced in its entirety
2 - Published material making use of (information gained from) this model cites at least:
(a) Poolman, 1999, Computer Modelling Applied to the Calvin Cycle, PhD Thesis, Oxford Brookes University
(b) Poolman, Fell, and Thomas. 2000, Modelling Photosynthesis and its control, J. Exp. Bot. 51, 319-328
or
(c) Poolman et al. 2001, Computer modelling and experimental evidence for two steady states in the photosynthetic Calvin cycle. Eur. J. Biochem. 268, 2810-2816
Further related information may be found at http://mudshark.brookes.ac.uk .

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: 15073223 Submission Date: 13 Sep 2005 13:03:34 UTC Last Modification Date: 16 May 2012 14:15:01 UTC Creation Date: 25 Jun 2008 15:14:01 UTC
Mathematical expressions
Reactions
E1 E2 E3 E4
E5 E6 E7 E8
E9 E10 E11 E12
E13 E14 E15 light_reaction
E16 E17 E18_DHAP E18_PGA
E18_GAP      
Physical entities
Compartments Species
chloroplast x_CO2 RuBP_ch PGA_ch
ATP_ch BPGA_ch x_NADPH_ch
GAP_ch Pi_ch DHAP_ch
FBP_ch F6P_ch E4P_ch
X5P_ch SBP_ch S7P_ch
R5P_ch Ru5P_ch G6P_ch
x_NADP_ch ADP_ch x_Proton_ch
G1P_ch x_Starch_ch  
cytosol x_Pi_cyt x_GAP_cyt x_PGA_cyt
x_DHAP_cyt    
Global parameters
Light_on      
Reactions (21)
 
 E1 [RuBP_ch] + [x_CO2] → 2.0 × [PGA_ch];   {FBP_ch} , {SBP_ch} , {Pi_ch} , {x_NADPH_ch}
 
 E2 [PGA_ch] + [ATP_ch] → [BPGA_ch] + [ADP_ch];  
 
 E3 [x_NADPH_ch] + [BPGA_ch] + [x_Proton_ch] → [x_NADP_ch] + [GAP_ch] + [Pi_ch];  
 
 E4 [GAP_ch] ↔ [DHAP_ch];  
 
 E5 [GAP_ch] + [DHAP_ch] ↔ [FBP_ch];  
 
 E6 [FBP_ch] → [F6P_ch] + [Pi_ch];  
 
 E7 [GAP_ch] + [F6P_ch] ↔ [X5P_ch] + [E4P_ch];  
 
 E8 [DHAP_ch] + [E4P_ch] ↔ [SBP_ch];  
 
 E9 [SBP_ch] → [Pi_ch] + [S7P_ch];  
 
 E10 [S7P_ch] + [GAP_ch] ↔ [R5P_ch] + [X5P_ch];  
 
 E11 [R5P_ch] ↔ [Ru5P_ch];  
 
 E12 [X5P_ch] ↔ [Ru5P_ch];  
 
 E13 [Ru5P_ch] + [ATP_ch] → [RuBP_ch] + [ADP_ch];   {PGA_ch} , {Pi_ch}
 
 E14 [F6P_ch] ↔ [G6P_ch];  
 
 E15 [G6P_ch] ↔ [G1P_ch];  
 
 light_reaction [Pi_ch] + [ADP_ch] → [ATP_ch];  
 
 E16 [ATP_ch] + [G1P_ch] → [x_Starch_ch] + [ADP_ch] + 2.0 × [Pi_ch];   {PGA_ch} , {F6P_ch} , {FBP_ch}
 
 E17 [x_Starch_ch] + [Pi_ch] → [G1P_ch];  
 
 E18_DHAP [x_Pi_cyt] + [DHAP_ch] → [x_DHAP_cyt] + [Pi_ch];   {PGA_ch} , {GAP_ch}
 
 E18_PGA [x_Pi_cyt] + [PGA_ch] → [x_PGA_cyt] + [Pi_ch];   {DHAP_ch} , {GAP_ch}
 
 E18_GAP [x_Pi_cyt] + [GAP_ch] → [x_GAP_cyt] + [Pi_ch];   {PGA_ch} , {DHAP_ch}
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 x_CO2
Compartment: chloroplast
Initial concentration: 1.0
 
 RuBP_ch
Compartment: chloroplast
Initial concentration: 0.33644
 
 PGA_ch
Compartment: chloroplast
Initial concentration: 3.35479
 
 ATP_ch
Compartment: chloroplast
Initial concentration: 0.49806
 
 BPGA_ch
Compartment: chloroplast
Initial concentration: 0.14825
 
 x_NADPH_ch
Compartment: chloroplast
Initial concentration: 0.21
 
 GAP_ch
Compartment: chloroplast
Initial concentration: 0.01334
 
 Pi_ch
Compartment: chloroplast
Initial concentration: 1.5662
 
 DHAP_ch
Compartment: chloroplast
Initial concentration: 0.29345
 
 FBP_ch
Compartment: chloroplast
Initial concentration: 0.02776
 
 F6P_ch
Compartment: chloroplast
Initial concentration: 1.36481
 
 E4P_ch
Compartment: chloroplast
Initial concentration: 0.41021
 
 X5P_ch
Compartment: chloroplast
Initial concentration: 0.00363
 
 SBP_ch
Compartment: chloroplast
Initial concentration: 1.56486
 
 S7P_ch
Compartment: chloroplast
Initial concentration: 0.00541
 
 R5P_ch
Compartment: chloroplast
Initial concentration: 0.00599
 
 Ru5P_ch
Compartment: chloroplast
Initial concentration: 0.00235
 
 G6P_ch
Compartment: chloroplast
Initial concentration: 3.1396
 
 x_NADP_ch
Compartment: chloroplast
Initial concentration: 0.29
 
 ADP_ch
Compartment: chloroplast
Initial concentration: 0.00149
 
 x_Proton_ch
Compartment: chloroplast
Initial concentration: 2.512E-5
 
 G1P_ch
Compartment: chloroplast
Initial concentration: 0.18206
 
 x_Starch_ch
Compartment: chloroplast
Initial concentration: 1.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 x_Pi_cyt
Compartment: cytosol
Initial concentration: 0.5
 
 x_GAP_cyt
Compartment: cytosol
Initial concentration: 1.0
 
 x_PGA_cyt
Compartment: cytosol
Initial concentration: 1.0
 
 x_DHAP_cyt
Compartment: cytosol
Initial concentration: 1.0
 
Global Parameters (1)
 
   Light_on
Value: 1.0
Constant
 
E1 (7)
 
   Rbco_vm
Value: 340.0
Constant
 
   Rbco_km
Value: 0.02
Constant
 
   Rbco_KiPGA
Value: 0.84
Constant
 
   Rbco_KiFBP
Value: 0.04
Constant
 
   Rbco_KiSBP
Value: 0.075
Constant
 
   Rbco_KiPi
Value: 0.9
Constant
 
   Rbco_KiNADPH
Value: 0.07
Constant
 
E2 (2)
 
   PGK_v
Value: 5.0E8
Constant
 
   q2
Value: 3.1E-4
Constant
 
E3 (2)
 
   G3Pdh_v
Value: 5.0E8
Constant
 
   q3
Value: 1.6E7
Constant
 
E4 (2)
 
   TPI_v
Value: 5.0E8
Constant
 
   q4
Value: 22.0
Constant
 
E5 (2)
 
   F_Aldo_v
Value: 5.0E8
Constant
 
   q5
Value: 7.1
Constant
 
E6 (4)
 
   FBPase_ch_vm
Value: 200.0
Constant
 
   FBPase_ch_km
Value: 0.03
Constant
 
   FBPase_ch_KiF6P
Value: 0.7
Constant
 
   FBPase_ch_KiPi
Value: 12.0
Constant
 
E7 (2)
 
   F_TKL_v
Value: 5.0E8
Constant
 
   q7
Value: 0.084
Constant
 
E8 (2)
 
   E_Aldo_v
Value: 5.0E8
Constant
 
   q8
Value: 13.0
Constant
 
E9 (3)
 
   SBPase_ch_vm
Value: 40.0
Constant
 
   SBPase_ch_km
Value: 0.013
Constant
 
   SBPase_ch_KiPi
Value: 12.0
Constant
 
E10 (2)
 
   G_TKL_v
Value: 5.0E8
Constant
 
   q10
Value: 0.85
Constant
 
E11 (2)
 
   R5Piso_v
Value: 5.0E8
Constant
 
   q11
Value: 0.4
Constant
 
E12 (2)
 
   X5Pepi_v
Value: 5.0E8
Constant
 
   q12
Value: 0.67
Constant
 
E13 (8)
 
   Ru5Pk_ch_vm
Value: 10000.0
Constant
 
   Ru5Pk_ch_km1
Value: 0.05
Constant
 
   Ru5Pk_ch_KiPGA
Value: 2.0
Constant
 
   Ru5Pk_ch_KiRuBP
Value: 0.7
Constant
 
   Ru5Pk_ch_KiPi
Value: 4.0
Constant
 
   Ru5Pk_ch_KiADP1
Value: 2.5
Constant
 
   Ru5Pk_ch_km2
Value: 0.05
Constant
 
   Ru5Pk_ch_KiADP2
Value: 0.4
Constant
 
E14 (2)
 
   PGI_v
Value: 5.0E8
Constant
 
   q14
Value: 2.3
Constant
 
E15 (2)
 
   PGM_v
Value: 5.0E8
Constant
 
   q15
Value: 0.058
Constant
 
light_reaction (3)
 
   LR_vm
Value: 3500.0
Constant
 
   LR_kmADP
Value: 0.014
Constant
 
   LR_kmPi
Value: 0.3
Constant
 
E16 (7)
 
   StSyn_vm
Value: 40.0
Constant
 
   stsyn_ch_km1
Value: 0.08
Constant
 
   stsyn_ch_Ki
Value: 10.0
Constant
 
   stsyn_ch_km2
Value: 0.08
Constant
 
   stsyn_ch_ka1
Value: 0.1
Constant
 
   stsyn_ch_ka2
Value: 0.02
Constant
 
   stsyn_ch_ka3
Value: 0.02
Constant
 
E17 (3)
 
   StPase_Vm
Value: 40.0
Constant
 
   StPase_km
Value: 0.1
Constant
 
   StPase_kiG1P
Value: 0.05
Constant
 
E18_DHAP (6)
 
   TP_Piap_vm
Value: 250.0
Constant
 
   TP_Piap_kDHAP_ch
Value: 0.077
Constant
 
   TP_Piap_kPi_cyt
Value: 0.74
Constant
 
   TP_Piap_kPi_ch
Value: 0.63
Constant
 
   TP_Piap_kPGA_ch
Value: 0.25
Constant
 
   TP_Piap_kGAP_ch
Value: 0.075
Constant
 
E18_PGA (7)
 
   PGA_xpMult
Value: 0.75
Constant
 
   TP_Piap_vm
Value: 250.0
Constant
 
   TP_Piap_kPGA_ch
Value: 0.25
Constant
 
   TP_Piap_kPi_cyt
Value: 0.74
Constant
 
   TP_Piap_kPi_ch
Value: 0.63
Constant
 
   TP_Piap_kDHAP_ch
Value: 0.077
Constant
 
   TP_Piap_kGAP_ch
Value: 0.075
Constant
 
E18_GAP (6)
 
   TP_Piap_vm
Value: 250.0
Constant
 
   TP_Piap_kGAP_ch
Value: 0.075
Constant
 
   TP_Piap_kPi_cyt
Value: 0.74
Constant
 
   TP_Piap_kPi_ch
Value: 0.63
Constant
 
   TP_Piap_kPGA_ch
Value: 0.25
Constant
 
   TP_Piap_kDHAP_ch
Value: 0.077
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000013

Curator's comment: (updated: 26 Jun 2008 09:15:02 BST)

Simulation of the steady state flux of starch as in fig. 3 A of the publication. All calculations where performed using SBMLodeSolver (20080507). For Pi_cyt concentrations lower than 0.08 mM an initial G1P concentration of 10 mM had to be given to get the right steady state.

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