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Messiha2013 - Pentose phosphate pathway model

ABSTRACT: 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.

SUBMITTER: Kieran Smallbone

PROVIDER: BIOMD0000000502 | BioModels | 2011-11-09

REPOSITORIES: BioModels

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Project description:Messiha2013 - combined glycolysis and pentose phosphate pathway model BIOMD0000000502 and MODEL1303260018 are combined to examine the response to oxidative stress. 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: BIOMD0000000503 . 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:Model as described in: In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae Vaseghi S, Baumeister A, Rizzi M, Reuss M. Metab Eng. 1999 Apr;1(2):128-40. PMID: 10935926 , doi: 10.1006/mben.1998.0110 ; Abstract: The in vivo dynamics of the pentose phosphate pathway has been studied with transient experiments in continuous culture of Saccharomyces cerevisiae. Rapid sampling was performed with a special sampling device after disturbing the steady state with a pulse of glucose. The time span of observation was 120 s after the pulse. During this short time period the dynamic effect of protein biosynthesis can be neglected. The metabolites of interest (glucose 6-phosphate, NADP, NADPH, 6-phosphogluconate, and MgATP2-) we determined with enzymatic assays and HPLC. The experimental observations were then used for the identification of kinetic rate equations and parameters under in vivo conditions. In accordance with results from in vitro studies the in vivo diagnosis supports an ordered Bi-Bi mechanism with noncompetitive inhibition by MgATP2- for the enzyme glucose-6-phosphate dehydrogenase. In the case of 6-phosphogluconate dehydrogenase an ordered Bi-Ter mechanism with a competitive inhibition by MgATP2- has been found. Because the MgATP2- concentration decreases abruptly after the pulse of glucose the inhibitory effect vanishes and the flux through the pentose phosphate pathway increases. This regulation phenomenon guarantees the balance of fluxes through glycolysis and pentose phosphate pathway during the dynamic time period. Typographical errors found and corrected from the original manuscript: rMax given for 6GPDH and 6PGDH are reversed (by solving their defining equations) Eq (52) should read C_NADPH(t) = 0.16 + ... (from Fig. 2) While the model is identical to the one described in the article, it cannot reproduce all time courses displayed in the article. The time courses for S7P and X5P differ from fig 5 and some of the reaction rates show slightly different dynamics than in fig 7. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. 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. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. . 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.

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Messiha2013 - Pentose phosphate pathway model

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