Dataset Information

Bhartiya2003_Tryptophan_operon

ABSTRACT: SBML level 2 code originaly generated for the JWS Online project by Jacky Snoep using PySCeS Run this model online at http://jjj.biochem.sun.ac.za To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based modelling using JWS Online , Bioinformatics, 20:2143-2144 BioModels Curation : The model reproduces Fig 3 of the publication. By substituting a value of 1.4 for Tex it is possible to reproduce Fig 3C and 3D(iii), Fig 3A and 3D(i), are obtained by setting Tex=0. Also, note that the tryptophan concentrations have been normalized by 82 micromolar in the figures; the normalized concetrations can be obtained via the parameters To/s/t_norm. The model was successfully tested on MathSBML and Copasi. 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.

SUBMITTER: Nicolas Le Novère

PROVIDER: BIOMD0000000062 | BioModels | 2010-02-04

REPOSITORIES: BioModels

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Publications

Dynamic model of Escherichia coli tryptophan operon shows an optimal structural design.

Bhartiya Sharad S Rawool Subodh S Venkatesh K V KV

European journal of biochemistry 20030601 12

A mathematical model has been developed to study the effect of external tryptophan on the trp operon. The model accounts for the effect of feedback repression by tryptophan through the Hill equation. We demonstrate that the trp operon maintains an intracellular steady-state concentration in a fivefold range irrespective of extracellular conditions. Dynamic behavior of the trp operon corresponding to varying levels of extracellular tryptophan illustrates the adaptive nature of regulation. Dependi ...[more]

PMID: 12787031

Publication: 1/2

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Project description:The model reproduces Figures 4,5 and 6 of the publication. The analytical functions for cometabolites Catp, Camp, Cnadph, and Cnadp slightly differ from the equations given in the paper. These changes were made in consultation with Dr. Christophe Chassagnole and are essential for reproducing the figures. The dependency of the rate of change of extracellular glucose concentration on the ratio of biomass concentration to specific weight of biomass (Cx*rPTS/Rhox) is taken into account by appropriately adjusting the stoichiometries of the species involved in the phosphotransferase system (rPTS). The rmax values for the various reactions are obtained from experiments and are not provided in the paper. However, these were personally communicated to the JWS repository. The model has been successfully tested on MathSBML. SBML level 2 code generated for the JWS Online project by Jacky Snoep using PySCeS Run this model online at http://jjj.biochem.sun.ac.za To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based modelling using JWS Online , Bioinformatics, 20:2143-2144 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.

Project description:. . . SBML level 2 code generated for the JWS Online project by Jacky Snoep using PySCeS Run this model online at http://jjj.biochem.sun.ac.za To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based modelling using JWS Online , Bioinformatics, 20:2143-2144 . . Biomodels Curation: The paper refers to the model equations present in Bakker et al's " Glycolysis in bloodstream from Trypanosoma brucei can be understood in terms of the kinetics of glycolytic enzymes" (Pubmed ID: 9013556), also, the authors claim that some of the modifications in these equations were made based on the experimental results from the paper "Contribution of glucose transport in the control of glycolytic flux in Trypanosoma brucei" (Pubmed ID: 10468568). The model reproduces the various flux values in Fig 3 for 100% TPI activity. It also matches with the values provided in Table 2 of the paper. The model was successfully tested with Copasi and SBML ODE Solver. The volumes are set to the values containing 1 mg of total protein per microlitre total cell volume. To change the protein concentration use Vt , the total cell volume in micro litre per mg protein. To change the TPI activity use the global parameter TPIact . 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.

Dataset Information

Bhartiya2003_Tryptophan_operon

Publications

Dynamic model of Escherichia coli tryptophan operon shows an optimal structural design.

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