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BIOMD0000000190 - Rodriguez-Caso2006_Polyamine_Metabolism

 

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Reference Publication
Publication ID: 16709566
Rodríguez-Caso C, Montañez R, Cascante M, Sánchez-Jiménez F, Medina MA.
Mathematical modeling of polyamine metabolism in mammals.
J. Biol. Chem. 2006 Aug; 281(31): 21799-21812
Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga E-29071, Spain.  [more]
Model
Original Model: BIOMD0000000190.origin
Submitter: Armando Reyes-Palomares
Submission ID: MODEL6812345601
Submission Date: 08 Sep 2008 12:35:49 UTC
Last Modification Date: 05 Jul 2012 14:37:34 UTC
Creation Date: 08 Sep 2008 15:27:37 UTC
Encoders:  Lukas Endler
   Armando Reyes-Palomares
   Carlos Rodríguez-Caso
   Raul Montañez
   Marta Cascante
   Francisca Sánchez-Jiménez
   Miguel A. Medina
set #1
bqbiol:isVersionOf Gene Ontology polyamine metabolic process
bqbiol:occursIn Taxonomy Rodentia
Taxonomy Mammalia
Notes

SBML creators: Armando Reyes-Palomares * , Carlos Rodríguez-Caso +, Raul Montañez * , Marta Cascante $, Francisca Sánchez-Jiménez * , Miguel A. Medina *

* ProCel Group, Department of Molecular Biology and Biochemistry, Faculty of Sciences, Campus de Teatinos, University of Malaga and CIBER de Enfermedades Raras (CIBER-ER). + Complex Systems Lab (ICREA-UPF), Barcelona Biomedical Research Park (PRBB-GRIB). $ Department of Biochemistry and Molecular Biology, Faculty of Biology, Universitat de Barcelona.

http://asp.uma.es

Metabolic modeling of polyamine metabolism in mammals.
Rodríguez-Caso,C et al.: J Biol Chem 2006 : 281:21799-812.
The model reproduces the dynamical behavior of the polyamine metabolism in mammals. In this model there are some additions and corrections to the publication. All perturbations and analysis have produced results very close to the published experiments. The model was successfully tested on CoPaSi v.4.4 (build 26).

Parameters not included in the publication:

1. Parameters for SSAT kinetic constants:

KmAcCoA = 1.5 µM

KmCoA = 40 µM

2. Parameters for equation MAT (table 1):

Vmax_MAT = 0.45 µM/min

Km_MAT = 41 µM

Ki_MET_MAT = 50 µM

3. Erratum.: The corrected ODE for time-dependent variable Antz is:

KsANTZ*(1-1/(1+Keq*0.01*([D]+[S])))-KdANTZ*[Antz]

According to these modifications the new steady-state analysis results are:

Metabolites:

[P]= 104.681 µM

[D]= 76.7492 µM

[S]= 58.0135 µM

[SAM]= 52.327 µM

[A]= 0.0101962 µM

[aS]= 0.0245375 µM

[aD]= 0.832236 µM

Time-dependent global parameters:

[Antz] = 0.574038 µM

Vmaxodc = 1.28315 µM/min

Vmaxssat = 0.673814 µM/min

Vmaxsamdc = 0.36829 µM/min


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.

Model
Publication ID: 16709566 Submission Date: 08 Sep 2008 12:35:49 UTC Last Modification Date: 05 Jul 2012 14:37:34 UTC Creation Date: 08 Sep 2008 15:27:37 UTC
Mathematical expressions
Reactions
Ornithine decarboxylase S-adenosylmethionine decarboxylase Spermidine/Spermine N1-acetyltransferase for S Spermidine/spermine N1-acetyltransferase for D
Polyamine oxidase for aD Polyamine oxidase for aS Spermidine synthase Spermine synthase
Methionine adenosyltransferase VCOA VACCOA Putrescine efflux
aD efflux      
Rules
Assignment Rule (variable: Kaccoa) Assignment Rule (variable: Kcoa) Rate Rule (variable: Vmaxodc) Rate Rule (variable: Vmaxssat)
Rate Rule (variable: Vmaxsamdc) Rate Rule (variable: Antz)    
Physical entities
Compartments Species
Cytosol S-adenosyl-L-methionine S-adenosylmethioninamine Putrescine
Spermine Spermidine N1-Acetylspermine
N1-Acetylspermidine Methionine L-Ornithine
Acetyl-CoA CoA  
Global parameters
Vmaxodc Vmaxssat Vmaxsamdc Antz
Keq KdODC KsODC KdSSAT
KsSSAT KdSAMDC KsSAMDC KdANTZ
KsANTZ R C Kaccoa
Kcoa      
Reactions (13)
 
 Ornithine decarboxylase [L-Ornithine] → [Putrescine];  
 
 S-adenosylmethionine decarboxylase [S-adenosyl-L-methionine] → [S-adenosylmethioninamine];   {Spermine} , {Putrescine}
 
 Spermidine/Spermine N1-acetyltransferase for S [Spermine] + [Acetyl-CoA] → [N1-Acetylspermine] + [CoA];   {Spermidine}
 
 Spermidine/spermine N1-acetyltransferase for D [Spermidine] + [Acetyl-CoA] → [N1-Acetylspermidine] + [CoA];   {Spermine}
 
 Polyamine oxidase for aD [N1-Acetylspermidine] → [Putrescine];   {N1-Acetylspermine} , {Spermidine} , {Spermine}
 
 Polyamine oxidase for aS [N1-Acetylspermine] → [Spermidine];   {N1-Acetylspermidine} , {Spermine}
 
 Spermidine synthase [S-adenosylmethioninamine] + [Putrescine] → [Spermidine];  
 
 Spermine synthase [S-adenosylmethioninamine] + [Spermidine] → [Spermine];  
 
 Methionine adenosyltransferase [Methionine] → [S-adenosyl-L-methionine];  
 
 VCOA [Acetyl-CoA] → [CoA];  
 
 VACCOA [CoA] → [Acetyl-CoA];  
 
 Putrescine efflux [Putrescine] → ;  
 
 aD efflux [N1-Acetylspermidine] → ;  
 
Rules (6)
 
 Assignment Rule (name: Kaccoa) Kaccoa = R
 
 Assignment Rule (name: Kcoa) Kcoa = 3*R
 
 Rate Rule (name: Vmaxodc) d [ Vmaxodc] / d t= Ksodc/(1+Keq*(D+S))-Kdodc*Antz*Vmaxodc
 
 Rate Rule (name: Vmaxssat) d [ Vmaxssat] / d t= Ksssat*(1-1/(1+Keq*(D+S)))-Kdssat*1/(1+Keq*(D+S))*Vmaxssat
 
 Rate Rule (name: Vmaxsamdc) d [ Vmaxsamdc] / d t= Kssamdc*1/(1+Keq*(D+S))-Kdsamdc*Vmaxsamdc
 
 Rate Rule (name: Antz) d [ Antz] / d t= Ksantz*(1-1/(1+Keq*0.01*(D+S)))-Kdantz*Antz
 
 Cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 S-adenosyl-L-methionine
Compartment: Cytosol
Initial concentration: 0.01
 
 S-adenosylmethioninamine
Compartment: Cytosol
Initial concentration: 0.01
 
 Putrescine
Compartment: Cytosol
Initial concentration: 0.01
 
 Spermine
Compartment: Cytosol
Initial concentration: 0.01
 
 Spermidine
Compartment: Cytosol
Initial concentration: 0.01
 
 N1-Acetylspermine
Compartment: Cytosol
Initial concentration: 0.01
 
 N1-Acetylspermidine
Compartment: Cytosol
Initial concentration: 0.01
 
 Methionine
Compartment: Cytosol
Initial concentration: 50.0
Constant
 
 L-Ornithine
Compartment: Cytosol
Initial concentration: 300.0
Constant
 
 Acetyl-CoA
Compartment: Cytosol
Initial concentration: 39.5
Constant
 
 CoA
Compartment: Cytosol
Initial concentration: 160.0
Constant
 
Global Parameters (17)
 
   Vmaxodc
Value: 1.27905671844446   (Units: uMpermin)
 
   Vmaxssat
Value: 0.677298510125025   (Units: uMpermin)
 
   Vmaxsamdc
Value: 0.367465856805639   (Units: uMpermin)
 
   Antz
Value: 0.574589492832405   (Units: uMpermin)
 
   Keq
Value: 1.0   (Units: peruM)
Constant
 
   KdODC
Value: 0.05   (Units: peruM)
Constant
 
   KsODC
Value: 5.0   (Units: uM(min)^-2)
Constant
 
   KdSSAT
Value: 0.2   (Units: permin)
Constant
 
   KsSSAT
Value: 0.0010   (Units: uM(min)^-2)
Constant
 
   KdSAMDC
Value: 0.02   (Units: permin)
Constant
 
   KsSAMDC
Value: 1.0   (Units: uM(min)^-2)
Constant
 
   KdANTZ
Value: 0.02   (Units: permin)
Constant
 
   KsANTZ
Value: 0.02   (Units: uM(min)^-2)
Constant
 
   R
Value: 0.0040   (Units: permin)
Constant
 
   C
Value: 4.44   (Units: dimensionless)
Constant
 
   Kaccoa
Value: 0.0040   (Units: permin)
 
   Kcoa
Value: 0.012   (Units: permin)
 
Ornithine decarboxylase (2)
 
   Kipodc
Value: 1300.0   (Units: microM)
Constant
 
   Kmodc
Value: 60.0   (Units: microM)
Constant
 
S-adenosylmethionine decarboxylase (4)
 
   Kapsamdc
Value: 0.5   (Units: microM)
Constant
 
   Kiasamdc
Value: 2.5   (Units: microM)
Constant
 
   Kissamdc
Value: 500.0   (Units: microM)
Constant
 
   Kmsamdc
Value: 50.0   (Units: microM)
Constant
 
Spermidine/Spermine N1-acetyltransferase for S (4)
 
   Kmaccoassat
Value: 1.5   (Units: microM)
Constant
 
   Kmcoassat
Value: 40.0   (Units: microM)
Constant
 
   Kmdssat
Value: 130.0   (Units: microM)
Constant
 
   Kmsssat
Value: 35.0   (Units: microM)
Constant
 
Spermidine/spermine N1-acetyltransferase for D (4)
 
   Kmaccoassat
Value: 1.5   (Units: microM)
Constant
 
   Kmcoassat
Value: 40.0   (Units: microM)
Constant
 
   Kmdssat
Value: 130.0   (Units: microM)
Constant
 
   Kmsssat
Value: 35.0   (Units: microM)
Constant
 
Polyamine oxidase for aD (5)
 
   Kmadpao
Value: 14.0   (Units: microM)
Constant
 
   Kmaspao
Value: 0.6   (Units: microM)
Constant
 
   Kmdpao
Value: 50.0   (Units: microM)
Constant
 
   Kmspao
Value: 15.0   (Units: microM)
Constant
 
   Vmpao
Value: 10.35   (Units: uMpermin)
Constant
 
Polyamine oxidase for aS (5)
 
   Kmadpao
Value: 14.0   (Units: microM)
Constant
 
   Kmaspao
Value: 0.6   (Units: microM)
Constant
 
   Kmdpao
Value: 50.0   (Units: microM)
Constant
 
   Kmspao
Value: 15.0   (Units: microM)
Constant
 
   Vmpao
Value: 10.35   (Units: uMpermin)
Constant
 
Spermidine synthase (5)
 
   KaSpds
Value: 0.3   (Units: microM)
Constant
 
   Kiaspds
Value: 0.8   (Units: microM)
Constant
 
   Kidspds
Value: 100.0   (Units: microM)
Constant
 
   Kpspds
Value: 40.0   (Units: microM)
Constant
 
   Vmspds
Value: 10.95   (Units: uMpermin)
Constant
 
Spermine synthase (5)
 
   Kaspms
Value: 0.1   (Units: microM)
Constant
 
   Kdspms
Value: 60.0   (Units: microM)
Constant
 
   Kiaspms
Value: 0.06   (Units: microM)
Constant
 
   Kisspms
Value: 25.0   (Units: microM)
Constant
 
   Vmspms
Value: 3.23   (Units: uMpermin)
Constant
 
Methionine adenosyltransferase (3)
 
   Kimetmat
Value: 50.0   (Units: microM)
Constant
 
   Kmmat
Value: 41.0   (Units: microM)
Constant
 
   Vmmat
Value: 0.45   (Units: uMpermin)
Constant
 
Putrescine efflux (1)
 
   Kpefflux
Value: 0.01   (Units: permin)
Constant
 
aD efflux (1)
 
   Kadefflux
Value: 0.01   (Units: permin)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000190

Curator's comment: (updated: 08 Sep 2008 12:53:28 BST)

reproduction of figures 3 and 5 from the original publication, the time courses differ slightly from the publication, due to corrections applied by one of the authors. See the model notes for further details

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