Modelling the Krebs cycle and oxidative phosphorylation

The Krebs cycle and oxidative phosphorylation are the two most important sets of reactions in a eukaryotic cell that meet the major part of the total energy demands of a cell. In this paper, we present a computer simulation of the coupled reactions using open source tools for simulation. We also sho...

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Bibliographic Details
Published in:Journal of biomolecular structure & dynamics 2014-02, Vol.32 (2), p.242-256
Main Authors: Korla, Kalyani, Mitra, Chanchal K.
Format: Article
Language:English
Subjects:
Animals
ATP synthesis
Citric Acid Cycle
Computer Simulation
Electron Transport
electron transport chain
Energy Metabolism
ETC
Eukaryotic Cells - enzymology
Eukaryotic Cells - metabolism
Humans
kinetic simulation
Krebs cycle
Models, Biological
Models, Molecular
Oxidative Phosphorylation
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Summary:The Krebs cycle and oxidative phosphorylation are the two most important sets of reactions in a eukaryotic cell that meet the major part of the total energy demands of a cell. In this paper, we present a computer simulation of the coupled reactions using open source tools for simulation. We also show that it is possible to model the Krebs cycle with a simple black box with a few inputs and outputs. However, the kinetics of the internal processes has been modelled using numerical tools. We also show that the Krebs cycle and oxidative phosphorylation together can be combined in a similar fashion - a black box with a few inputs and outputs. The Octave script is flexible and customisable for any chosen set-up for this model. In several cases, we had no explicit idea of the underlying reaction mechanism and the rate determining steps involved, and we have used the stoichiometric equations that can be easily changed as and when more detailed information is obtained. The script includes the feedback regulation of the various enzymes of the Krebs cycle. For the electron transport chain, the pH gradient across the membrane is an essential regulator of the kinetics and this has been modelled empirically but fully consistent with experimental results. The initial conditions can be very easily changed and the simulation is potentially very useful in a number of cases of clinical importance.
ISSN:0739-1102
1538-0254
DOI:10.1080/07391102.2012.762723