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BIOMD0000000053 - Ferreira2003_CML_generation2

 

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Reference Publication
Publication ID: 12911334
Ferreira AE, Ponces Freire AM, Voit EO.
A quantitative model of the generation of N(epsilon)-(carboxymethyl)lysine in the Maillard reaction between collagen and glucose.
Biochem. J. 2003 Nov; 376(Pt 1): 109-121
Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Bloco C8, Campo Grande, 1749-016 Lisboa, Portugal. aeferreira@fc.ul.pt  [more]
Model
Original Model: BIOMD0000000053.origin
Submitter: Harish Dharuri
Submission ID: MODEL0733584307
Submission Date: 09 Apr 2006 21:05:31 UTC
Last Modification Date: 09 Oct 2014 15:39:20 UTC
Creation Date: 09 Apr 2006 20:54:45 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:hasProperty Human Disease Ontology diabetes mellitus
Human Disease Ontology amyloidosis
set #2
bqbiol:hasPart Gene Ontology collagen binding
Gene Ontology peptidyl-lysine modification
bqbiol:occursIn Taxonomy cellular organisms
Notes

The model should reproduce the figure 2F of the article.

The equation 7 has been split into equations 7a-7c, in order to take into account the different flux rates of Lysine and CML formation from Schiff.

The model was tested in Jarnac (SBML L2 V1) and Copasi (SBML L2 V3).


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: 12911334 Submission Date: 09 Apr 2006 21:05:31 UTC Last Modification Date: 09 Oct 2014 15:39:20 UTC Creation Date: 09 Apr 2006 20:54:45 UTC
Mathematical expressions
Reactions
v1a v1b v2a v2b
v3 v4 v5 v5b
v6 v7a v7b v7c
Rules
Assignment Rule (variable: Fraction_Amadori) Assignment Rule (variable: Fraction_CML)    
Physical entities
Compartments Species
compartment Glucose Lysine Schiff
Amadori Glyoxal CML
Global parameters
Fraction_Amadori Fraction_CML    
Reactions (12)
 
 v1a [Lysine] + [Glucose] → [Schiff];  
 
 v1b [Schiff] → [Lysine] + [Glucose];  
 
 v2a [Schiff] → [Amadori];  
 
 v2b [Amadori] → [Schiff];  
 
 v3 [Glucose] → [Glyoxal];  
 
 v4 [Amadori] → [CML];  
 
 v5 [Lysine] + [Glyoxal] → [CML];  
 
 v5b [Glyoxal] → ;  
 
 v6 [Schiff] → [CML];  
 
 v7a  → [Lysine];   {Schiff}
 
 v7b  → [Glyoxal];   {Schiff}
 
 v7c [Schiff] → ;  
 
Rules (2)
 
 Assignment Rule (name: Fraction_Amadori) Fraction_Amadori = Amadori/0.0034
 
 Assignment Rule (name: Fraction_CML) Fraction_CML = CML/0.0034
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
 Glucose
Compartment: compartment
Initial concentration: 0.25
 
 Lysine
Compartment: compartment
Initial concentration: 0.0034
 
   Schiff
Compartment: compartment
Initial concentration: 0.0
 
   Amadori
Compartment: compartment
Initial concentration: 0.0
 
 Glyoxal
Compartment: compartment
Initial concentration: 0.0
 
   CML
Compartment: compartment
Initial concentration: 0.0
 
Global Parameters (2)
 
   Fraction_Amadori  
 
   Fraction_CML  
 
v1a (2)
 
   p1
Value: 0.115
Constant
 
   k1a
Value: 0.09
Constant
 
v1b (1)
 
   k1b
Value: 0.36
Constant
 
v2a (2)
 
   p2
Value: 0.75
Constant
 
   k2a
Value: 0.033
Constant
 
v2b (2)
 
   p2
Value: 0.75
Constant
 
   k2b
Value: 0.0012
Constant
 
v3 (3)
 
   ox
Value: 1.0
Constant
 
   p3
Value: 1.0
Constant
 
   k3
Value: 7.92E-7
Constant
 
v4 (3)
 
   ox
Value: 1.0
Constant
 
   p4
Value: 1.0
Constant
 
   k4
Value: 8.6E-5
Constant
 
v5 (3)
 
   ox
Value: 1.0
Constant
 
   p5
Value: 1.0
Constant
 
   k5
Value: 0.019
Constant
 
v5b (1)
 
   k5b
Value: 0.0017
Constant
 
v6 (3)
 
   ox
Value: 1.0
Constant
 
   p6
Value: 2.7
Constant
 
   k3
Value: 7.92E-7
Constant
 
v7a (3)
 
   ox
Value: 1.0
Constant
 
   p7
Value: 60.0
Constant
 
   k3
Value: 7.92E-7
Constant
 
v7b (3)
 
   ox
Value: 1.0
Constant
 
   p7
Value: 60.0
Constant
 
   k3
Value: 7.92E-7
Constant
 
v7c (3)
 
   ox
Value: 1.0
Constant
 
   p7
Value: 60.0
Constant
 
   k3
Value: 7.92E-7
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000053

Curator's comment: (updated: 27 Aug 2009 16:50:45 BST)

The model reproduces the time profiles of Amadori and CML for oxidative conditions as shown in Fig 2 F. Please note that the variables are expressed as a fraction of total lysine. Simulation result obtained with Copasi 4.5 (build 30).

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