Project description:Messiha2013 - Pentose phosphate pathway model This model describes the dynamic behaviour of the pentose phosphate pathway with the inclusion of various enzymes involved in the pathway. The model's predictions are compared with experimental observations of transient metabolite concentrations following a glucose pulse. This model is described in the article: Enzyme characterisation and kinetic modelling of pentose phosphate pathway in yeast. Hanan L. Messiha, Edward Kent, Naglis Malys, Kathleen M. Carroll, Pedro Mendes, Kieran Smallbone PeerJ PrePrints 1:e146v2 Abstract: We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows for the predicting changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis one to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardized enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network models by merging smaller pathway models. This model is hosted on BioModels Database and identified by: BIOMD0000000502 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description:This is the model with unfitted parameters described in the article Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress Markus Ralser, Mirjam M Wamelink, Axel Kowald, Birgit Gerisch, Gino Heeren, Eduard A Struys, Edda Klipp, Cornelis Jakobs, Michael Breitenbach, Hans Lehrach and Sylvia Krobitsch, J Biol 2007 6(4):10; PMID: 18154684 , doi: 10.1186/jbiol61 Abstract: BACKGROUND: Eukaryotic cells have evolved various response mechanisms to counteract the deleterious consequences of oxidative stress. Among these processes, metabolic alterations seem to play an important role. RESULTS: We recently discovered that yeast cells with reduced activity of the key glycolytic enzyme triosephosphate isomerase exhibit an increased resistance to the thiol-oxidizing reagent diamide. Here we show that this phenotype is conserved in Caenorhabditis elegans and that the underlying mechanism is based on a redirection of the metabolic flux from glycolysis to the pentose phosphate pathway, altering the redox equilibrium of the cytoplasmic NADP(H) pool. Remarkably, another key glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), is known to be inactivated in response to various oxidant treatments, and we show that this provokes a similar redirection of the metabolic flux. CONCLUSION: The naturally occurring inactivation of GAPDH functions as a metabolic switch for rerouting the carbohydrate flux to counteract oxidative stress. As a consequence, altering the homoeostasis of cytoplasmic metabolites is a fundamental mechanism for balancing the redox state of eukaryotic cells under stress conditions. Different realtive enzyme velocities can be simulated by varying the parameters k_rel_TPI and k_rel_GAPDH . This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team. For more information see the terms of use . To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

			Action	DRS
	BIOMD0000000503?filename=BIOMD0000000503-biopax2.owl	Owl
	BIOMD0000000503?filename=BIOMD0000000503-biopax3.owl	Owl
	BIOMD0000000503?filename=BIOMD0000000503-matlab.m	Other
	BIOMD0000000503?filename=BIOMD0000000503-octave.m	Other
	BIOMD0000000503?filename=BIOMD0000000503.m	Other

Dataset Information

Messiha2013 - combined glycolysis and pentose phosphate pathway model

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets