ferreira1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000053) Biomodels 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). 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. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.

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A quantitative model of the generation of N(epsilon)-(carboxymethyl)lysine in the Maillard reaction between collagen and glucose.

  • António E N Ferreira
  • Ana M J Ponces Freire
  • Eberhard O Voit
Biochem. J. 2003; 376 : 109-121
Abstract
The Maillard reaction between reducing sugars and amino groups of biomolecules generates complex structures known as AGEs (advanced glycation endproducts). These have been linked to protein modifications found during aging, diabetes and various amyloidoses. To investigate the contribution of alternative routes to the formation of AGEs, we developed a mathematical model that describes the generation of CML [ N(epsilon)-(carboxymethyl)lysine] in the Maillard reaction between glucose and collagen. Parameter values were obtained by fitting published data from kinetic experiments of Amadori compound decomposition and glycoxidation of collagen by glucose. These raw parameter values were subsequently fine-tuned with adjustment factors that were deduced from dynamic experiments taking into account the glucose and phosphate buffer concentrations. The fine-tuned model was used to assess the relative contributions of the reaction between glyoxal and lysine, the Namiki pathway, and Amadori compound degradation to the generation of CML. The model suggests that the glyoxal route dominates, except at low phosphate and high glucose concentrations. The contribution of Amadori oxidation is generally the least significant at low glucose concentrations. Simulations of the inhibition of CML generation by aminoguanidine show that this compound effectively blocks the glyoxal route at low glucose concentrations (5 mM). Model results are compared with literature estimates of the contributions to CML generation by the three pathways. The significance of the dominance of the glyoxal route is discussed in the context of possible natural defensive mechanisms and pharmacological interventions with the goal of inhibiting the Maillard reaction in vivo.

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
3600.0 second
Id Name Spatial dimensions Size
compartment 3.0 1.0
Id Name Initial quantity Compartment Fixed
Amadori 0.0 compartment
CML 0.0 compartment
Glucose 0.25 compartment
Glyoxal 0.0 compartment
Lysine 0.0034 compartment
Schiff 0.0 compartment

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
v1a Lysine + Glucose > Schiff

compartment * p1 * k1a * Glucose * Lysine
v1b Schiff > Lysine + Glucose

compartment * k1b * Schiff
v2a Schiff > Amadori

compartment * p2 * k2a * Schiff
v2b Amadori > Schiff

compartment * p2 * k2b * Amadori
v3 Glucose > Glyoxal

compartment * ox * p3 * k3 * pow(Glucose / 0.25, 0.36)
v4 Amadori > CML

compartment * ox * p4 * k4 * Amadori
v5 Lysine + Glyoxal > CML

compartment * ox * p5 * k5 * Glyoxal * Lysine
v5b Glyoxal > ∅

compartment * k5b * Glyoxal
v6 Schiff > CML

compartment * ox * p6 * k3 * pow(Schiff / 0.25, 0.36)
v7a ∅ > Lysine

compartment * 0.05 * ox * p7 * k3 * pow(Schiff / 0.25, 0.36)
v7b ∅ > Glyoxal

compartment * 0.005 * ox * p7 * k3 * pow(Schiff / 0.25, 0.36)
v7c Schiff > ∅

compartment * ox * p7 * k3 * pow(Schiff / 0.25, 0.36)

Global parameters

Id Value
Fraction_Amadori 0.0
Fraction_CML 0.0

Local parameters

Id Value Reaction
p1 0.115 v1a
k1a 0.09 v1a
k1b 0.36 v1b
p2 0.75 v2a
k2a 0.033 v2a
p2 0.75 v2b
k2b 0.0012 v2b
ox 1.0 v3
p3 1.0 v3
k3 0.000000792 v3
ox 1.0 v4
p4 1.0 v4
k4 0.000086 v4
ox 1.0 v5
p5 1.0 v5
k5 0.019 v5
k5b 0.0017 v5b
ox 1.0 v6
p6 2.7 v6
k3 0.000000792 v6
ox 1.0 v7a
p7 60.0 v7a
k3 0.000000792 v7a
ox 1.0 v7b
p7 60.0 v7b
k3 0.000000792 v7b
ox 1.0 v7c
p7 60.0 v7c
k3 0.000000792 v7c

Assignment rules

Definition
Fraction_Amadori = Amadori / 0.0034
Fraction_CML = CML / 0.0034

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments