Dataset Information

Olsen2003_peroxidase

ABSTRACT: Notes of the BioModels curators: The current model reproduce the figure 7, panel B of the paper. Note that there is a typo in the figure. The ordinates represent the concentration of peroxyde, as stated in the legend, and not of oxygen. The model has been tested in COPASI (http://www.copasi.org/, build 13). Notes of the original version of the SBML file: 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.

SUBMITTER: Nicolas Le Novère

PROVIDER: BIOMD0000000046 | BioModels | 2024-09-02

REPOSITORIES: BioModels

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Dataset's files

Source:

			Action	DRS
	BIOMD0000000046?filename=BIOMD0000000046-biopax2.owl	Owl
	BIOMD0000000046?filename=BIOMD0000000046-biopax3.owl	Owl
	BIOMD0000000046?filename=BIOMD0000000046-matlab.m	Other
	BIOMD0000000046?filename=BIOMD0000000046-octave.m	Other
	BIOMD0000000046?filename=BIOMD0000000046.m	Other

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Publications

Mechanism of protection of peroxidase activity by oscillatory dynamics.

Olsen Lars F LF Hauser Marcus J B MJ Kummer Ursula U

European journal of biochemistry 20030701 13

The peroxidase-oxidase reaction is known to involve reactive oxygen species as intermediates. These intermediates inactivate many types of biomolecules, including peroxidase itself. Previously, we have shown that oscillatory dynamics in the peroxidase-oxidase reaction seem to protect the enzyme from inactivation. It was suggested that this is due to a lower average concentration of reactive oxygen species in the oscillatory state compared to the steady state. Here, we studied the peroxidase-oxid ...[more]

PMID: 12823550

Publication: 1/2

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Project description:This a model from the article: Modelling the dynamics of the yeast pheromone pathway. Kofahl B, Klipp E Yeast[2004 Jul; Volume: 21 (Issue: 10 )] Page info: 831-50 15300679, Abstract: We present a mathematical model of the dynamics of the pheromone pathways in haploid yeast cells of mating type MATa after stimulation with pheromone alpha-factor. The model consists of a set of differential equations and describes the dynamics of signal transduction from the receptor via several steps, including a G protein and a scaffold MAP kinase cascade, up to changes in the gene expression after pheromone stimulation in terms of biochemical changes (complex formations, phosphorylations, etc.). The parameters entering the models have been taken from the literature or adapted to observed time courses or behaviour. Using this model we can follow the time course of the various complex formation processes and of the phosphorylation states of the proteins involved. Furthermore, we can explain the phenotype of more than a dozen well-characterized mutants and also the graded response of yeast cells to varying concentrations of the stimulating pheromone. The model was updated on 21st October 2010, by Vijayalakshmi Chelliah. The following changes were made: 1) The model has been converted to SBML l2v4. 2) The model has been recurated and the curation figure was updated (units are in nanoMolar; but the publication has units in microMolar). Simulations were done using Copasi v4.6 (Build 32). 3) Notes have been added. 4) Annotation for one of the species has been corrected (Complex M). 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 The following are the four major differences between the original publication by Kofahl et al and the model that actually is able to replicate the results as depicted in the publication (those corrections have been made in agreement with the authors): 1. Bar1 is the inactive protease present inside the cell but the publication wrongly mentions that Bar1 is also the protease that is present on the extracellular surface. The model correctly names the protease in it's different forms by calling inactive Bar1 within the cell as Bar1, active Bar1 within the cell as Bar1a and extracellular Bar1 as Bar1aex 2. The initial amount of Alpha-factor is given as 1000nM but the model uses a value of 100nM. 3. The value of the paramenter k8 is given as 0.33 but the model uses a value of 0.033. 4. The value of the paramenter k41 is given as 0.002 but the model uses a value of 0.02. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/).(http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net Team. For more information see the terms of use. 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.