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BIOMD0000000050 - Martins2003_AmadoriDegradation

 

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Reference Publication
Publication ID: 12873422
Martins SI, Van Boekel MA.
Kinetic modelling of Amadori N-(1-deoxy-D-fructos-1-yl)-glycine degradation pathways. Part II--kinetic analysis.
Carbohydr. Res. 2003 Jul; 338(16): 1665-1678
Department of Agrotechnology and Food Sciences, Product Design and Quality Management Group, Wageningen University, P.O. Box 8129, 6700 EV, Wageningen, The Netherlands.  [more]
Model
Original Model: BIOMD0000000050.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL7981660691
Submission Date: 18 Jan 2006 18:08:56 UTC
Last Modification Date: 04 Apr 2014 12:28:30 UTC
Creation Date: 18 Jan 2006 18:08:56 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:hasTaxon Taxonomy cellular organisms
set #2
bqbiol:isVersionOf Gene Ontology organic substance catabolic process
Notes

This a model from the article:
Kinetic modelling of Amadori N-(1-deoxy-D-fructos-1-yl)-glycine degradation pathways. Part II--kinetic analysis.
Martins SI, Van Boekel MA. Carbohydr Res2003 Jul;338(16):1665-78. 12873422,
Abstract:
A kinetic model for N-(1-deoxy-Image -fructos-1-yl)-glycine (DFG) thermal decomposition was proposed. Two temperatures (100 and 120 °C) and two pHs (5.5 and 6.8) were studied. The measured responses were DFG, 3-deoxyosone, 1-deoxyosone, methylglyoxal, acetic acid, formic acid, glucose, fructose, mannose and melanoidins. For each system the model parameters, the rate constants, were estimated by non-linear regression, via multiresponse modelling. The determinant criterion was used as the statistical fit criterion. Model discrimination was performed by both chemical insight and statistical tests (Posterior Probability and Akaike criterion). Kinetic analysis showed that at lower pH DFG 1,2-enolization is favoured whereas with increasing pH 2,3-enolization becomes a more relevant degradation pathway. The lower amount observed of 1-DG is related with its high reactivity. It was shown that acetic acid, a main degradation product from DFG, was mainly formed through 1-DG degradation. Also from the estimated parameters 3-DG was found to be the main precursor in carbohydrate fragments formation, responsible for colour formation. Some indication was given that as the reaction proceeded other compounds besides DFG become reactants themselves with the formation among others of methylglyoxal. The multiresponse kinetic analysis was shown to be both helpful in deriving relevant kinetic parameters as well as in obtaining insight into the reaction mechanism.

Model was intially tested in Jarnac.

The model was recently updated on 9th July 2010. The reference publication has reported two models M1 and M2, where the parameter values are given for conditions A) 100oC, pH5.5, B) 120oC, pH5.5, C) 100oC, pH6.8 and D) 120oC, pH6.8.

This model corresponds to the model M2 with condition 100oC, pH6.8

The model reproduces Figure 6 of the reference publication. The curation figure was recently added

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: 12873422 Submission Date: 18 Jan 2006 18:08:56 UTC Last Modification Date: 04 Apr 2014 12:28:30 UTC Creation Date: 18 Jan 2006 18:08:56 UTC
Mathematical expressions
Reactions
v1 v2 v3 v4
v5 v6 v7 v8
v9 v10 v11 v12
v13 v14 v15 v16
Physical entities
Compartments Species
compartment DFG E1 E2
Cn Gly _3DG
FA _1DG AA
Man Glu MG
Mel Fru  
Reactions (16)
 
 v1 [DFG] → [E1];  
 
 v2 [DFG] → [E2];  
 
 v3 [DFG] → [Gly] + [Cn];  
 
 v4 [E1] → [Gly] + [_3DG];  
 
 v5 [_3DG] → [Cn];  
 
 v6 [_3DG] → [FA];  
 
 v7 [E2] → [Gly] + [_1DG];  
 
 v8 [_1DG] → [Cn];  
 
 v9 [_1DG] → [AA];  
 
 v10 [E1] → [Gly] + [Man];  
 
 v11 [E1] → [Gly] + [Glu];  
 
 v12 [Man] → [Glu];  
 
 v13 [Glu] → [_3DG];  
 
 v14 [Gly] + [Cn] → [Mel];  
 
 v15 [Cn] → [AA] + [FA] + [MG];  
 
 v16 [E2] → [Gly] + [Fru];  
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
   DFG
Compartment: compartment
Initial concentration: 9.0
 
   E1
Compartment: compartment
Initial concentration: 0.0
 
   E2
Compartment: compartment
Initial concentration: 0.0
 
 Cn
Compartment: compartment
Initial concentration: 0.0
 
 Gly
Compartment: compartment
Initial concentration: 0.0
 
   _3DG
Compartment: compartment
Initial concentration: 0.0
 
 FA
Compartment: compartment
Initial concentration: 0.0
 
   _1DG
Compartment: compartment
Initial concentration: 0.0
 
 AA
Compartment: compartment
Initial concentration: 0.0
 
 Man
Compartment: compartment
Initial concentration: 0.0
 
 Glu
Compartment: compartment
Initial concentration: 0.0
 
 MG
Compartment: compartment
Initial concentration: 0.0
 
   Mel
Compartment: compartment
Initial concentration: 0.0
 
 Fru
Compartment: compartment
Initial concentration: 0.0
 
v1 (1)
 
   k1
Value: 0.0057
Constant
 
v2 (1)
 
   k2
Value: 0.0156
Constant
 
v3 (1)
 
   k3
Value: 0.0155
Constant
 
v4 (1)
 
   k4
Value: 0.0794
Constant
 
v5 (1)
 
   k5
Value: 0.0907
Constant
 
v6 (1)
 
   k6
Value: 0.0274
Constant
 
v7 (1)
 
   k7
Value: 0.2125
Constant
 
v8 (1)
 
   k8
Constant
 
v9 (1)
 
   k9
Value: 1.9085
Constant
 
v10 (1)
 
   k10
Value: 0.0707
Constant
 
v11 (1)
 
   k11
Value: 0.1131
Constant
 
v12 (1)
 
   k12
Value: 8.0E-4
Constant
 
v13 (1)
 
   k13
Value: 0.0022
Constant
 
v14 (1)
 
   k14
Value: 0.0034
Constant
 
v15 (1)
 
   k15
Value: 0.0159
Constant
 
v16 (1)
 
   k16
Value: 0.0134
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000050

Curator's comment: (updated: 09 Jul 2010 14:16:11 BST)

The model reproduces figure 6 of the reference publication. This model corresponds to the model M2 with conditions 100C and pH 6.8. The model was integrated and simulated using Copasi 4.5.31.

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