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BIOMD0000000062 - Bhartiya2003_Tryptophan_operon

 

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Reference Publication
Publication ID: 12787031
Bhartiya S, Rawool S, Venkatesh KV.
Dynamic model of Escherichia coli tryptophan operon shows an optimal structural design.
Eur. J. Biochem. 2003 Jun; 270(12): 2644-2651
Department of Chemical Engineering and School of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Mumbai, India.  [more]
Model
Original Model: JWS logo
Submitter: Nicolas Le Novère
Submission ID: MODEL6624111460
Submission Date: 01 Aug 2006 07:54:32 UTC
Last Modification Date: 16 May 2012 10:21:54 UTC
Creation Date: 04 Feb 2010 17:43:13 UTC
Encoders:  Jacky L Snoep
   Harish Dharuri
set #1
bqbiol:occursIn Taxonomy Escherichia coli
bqbiol:isVersionOf Gene Ontology tryptophan biosynthetic process
Notes

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.

Model
Publication ID: 12787031 Submission Date: 01 Aug 2006 07:54:32 UTC Last Modification Date: 16 May 2012 10:21:54 UTC Creation Date: 04 Feb 2010 17:43:13 UTC
Mathematical expressions
Reactions
Anthranilate synthase synthesis Enzyme dilution due to cell growth Tryptophan synthesis Tryptophan consumption for protein synthesis
Tryptophan dilution due to cell growth      
Rules
Assignment Rule (variable: exog. Trp) Assignment Rule (variable: Total tryptophan) Assignment Rule (variable: Enz_norm) Assignment Rule (variable: Ts_norm)
Assignment Rule (variable: Tt_norm) Assignment Rule (variable: To_norm)    
Physical entities
Compartments Species
cell Anthranilate synthase Synthesized tryptophan Total tryptophan
exog. Trp    
Global parameters
Tomax Tex e_val f_val
Ts_norm To_norm Tt_norm Enz_norm
Reactions (5)
 
 Anthranilate synthase synthesis  ↔ [Anthranilate synthase];   {Total tryptophan}
 
 Enzyme dilution due to cell growth [Anthranilate synthase] ↔ ;  
 
 Tryptophan synthesis  ↔ [Synthesized tryptophan];   {Anthranilate synthase} , {Total tryptophan}
 
 Tryptophan consumption for protein synthesis [Synthesized tryptophan] ↔ ;  
 
 Tryptophan dilution due to cell growth [Synthesized tryptophan] ↔ ;  
 
Rules (6)
 
 Assignment Rule (name: To) exog. Trp = Tomax*Tex/(Tex*(1+Ts/f_val)+e_val)
 
 Assignment Rule (name: Tt) Total tryptophan = To+Ts
 
 Assignment Rule (name: Enz_norm) Enz_norm = Enz/1
 
 Assignment Rule (name: Ts_norm) Ts_norm = Ts/82
 
 Assignment Rule (name: Tt_norm) Tt_norm = Tt/82
 
 Assignment Rule (name: To_norm) To_norm = To/82
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 Anthranilate synthase
Compartment: cell
Initial concentration: 0.0
 
 Synthesized tryptophan
Compartment: cell
Initial concentration: 0.0
 
  Total tryptophan
Compartment: cell
Initial concentration: 0.0
 
   exog. Trp
Compartment: cell
 
Global Parameters (8)
 
   Tomax
Value: 100.0   (Units: microM)
Constant
 
   Tex
Value: 0.14   (Units: microM)
Constant
 
   e_val
Value: 0.9   (Units: microM)
Constant
 
   f_val
Value: 380.0   (Units: microM)
Constant
 
   Ts_norm
Value: NaN   (Units: dimensionless)
 
   To_norm
Value: NaN   (Units: dimensionless)
 
   Tt_norm
Value: NaN   (Units: dimensionless)
 
   Enz_norm
Value: NaN   (Units: dimensionless)
 
Anthranilate synthase synthesis (4)
 
   k1
Value: 65.0   (Units: per_min)
Constant
 
   ki1
Value: 3.53   (Units: microM)
Constant
 
   nH
Value: 1.92   (Units: dimensionless)
Constant
 
   Ot
Value: 0.0033   (Units: microM)
Constant
 
Enzyme dilution due to cell growth (1)
 
   mu
Value: 0.01   (Units: per_min)
Constant
 
Tryptophan synthesis (2)
 
   k2
Value: 25.0   (Units: per_min)
Constant
 
   Ki2
Value: 810.0   (Units: microM)
Constant
 
Tryptophan consumption for protein synthesis (2)
 
   g
Value: 25.0   (Units: microM_per_min)
Constant
 
   Kg
Value: 0.2   (Units: microM)
Constant
 
Tryptophan dilution due to cell growth (1)
 
   mu
Value: 0.01   (Units: per_min)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000062

Curator's comment: (updated: 04 Feb 2010 20:19:39 GMT)

Reproduction of figure 3 of the original article using Copasi 4.5.

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