Poolman2004_CalvinCycle

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Short description

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.

Format
SBML (L2V1)
Related Publication
  • Applications of metabolic modelling to plant metabolism.
  • Poolman MG, Assmus HE, Fell DA
  • Journal of experimental botany , 5/ 2004 , Volume 55 , pages: 1177-1186
  • School of Biology and Molecular Science, Oxford Brookes University, Headington, Oxford OX3 OBP, UK. mgpoolman@brookes.ac.uk
  • 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.
Contributors
Nicolas Le Novère

Metadata information

is
BioModels Database MODEL6615594069
BioModels Database BIOMD0000000013
isDescribedBy
PubMed 15073223
hasTaxon
isVersionOf
Curation status
Curated
  • Model originally submitted by : Nicolas Le Novère
  • Submitted: 13-Sep-2005 14:03:34
  • Last Modified: 23-Feb-2017 10:47:25
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 23-Feb-2017 10:47:25
    • Submitted by: Nicolas Le Novère
    • With comment: Current version of Poolman2004_CalvinCycle
  • Version: 1 public model Download this version
    • Submitted on: 13-Sep-2005 14:03:34
    • Submitted by: Nicolas Le Novère
    • With comment: Original import of Poolman2004_CalvinCycle
Curator's comment:
(added: 26 Jun 2008, 09:15:02, updated: 26 Jun 2008, 09:15:02)
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.