title: Modelling the Krebs cycle and oxidative phosphorylation.
abstract: 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.
authors.affiliation: a School of Life Sciences, University of Hyderabad , Hyderabad 500046 , India .
authors.forename: Kalyani
authors.initials: K
authors.lastname: Korla
authors.forename: Chanchal K
authors.initials: CK
authors.lastname: Mitra
mesh_terms: D000818:Animals; D002952:Citric Acid Cycle; D003198:Computer Simulation; D004579:Electron Transport; D004734:Energy Metabolism; D005057:Eukaryotic Cells / Q000201:enzymology* / Q000378:metabolism*; D006801:Humans; D008954:Models, Biological; D008958:Models, Molecular; D010085:Oxidative Phosphorylation