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BIOMD0000000415 - Mellor2012_LipooxygenasePathway

 

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Reference Publication
Publication ID: 21535565
Mellor N, Bligh F, Chandler I, Hodgman C.
Reduction of off-flavor generation in soybean homogenates: a mathematical model.
J. Food Sci. 2010 Sep; 75(7): R131-8
CPIB, Multidisciplinary Centre for Integrative Biology, School of Biosciences, the Univ. of Nottingham, Sutton Bonington Campus, LE12 5RD, UK.  [more]
Model
Original Model: BIOMD0000000415.origin
Submitter: Nathan Mellor
Submission ID: MODEL1203230000
Submission Date: 23 Mar 2012 10:15:29 UTC
Last Modification Date: 22 May 2014 19:03:16 UTC
Creation Date: 10 Apr 2012 13:24:24 UTC
Encoders:  Vijayalakshmi Chelliah
   Nathan Mellor
set #1
bqbiol:occursIn Taxonomy Glycine max
set #2
bqbiol:isVersionOf Gene Ontology lipoxygenase pathway
Notes

This model is from the article:
Reduction of off-flavor generation in soybean homogenates: a mathematical model.
Mellor N , Bligh F , Chandler I , Hodgman C J. Food Sci.2010 Sep; 75(7): R131-8; PMID: 2153556,
Abstract:
The generation of off-flavors in soybean homogenates such as n-hexanal via the lipoxygenase (LOX) pathway can be a problem in the processed food industry. Previous studies have examined the effect of using soybean varieties missing one or more of the 3 LOX isozymes on n-hexanal generation. A dynamic mathematical model of the soybean LOX pathway using ordinary differential equations was constructed using parameters estimated from existing data with the aim of predicting how n-hexanal generation could be reduced. Time-course simulations of LOX-null beans were run and compared with experimental results. Model L(2), L(3), and L(12) beans were within the range relative to the wild type found experimentally, with L(13) and L(23) beans close to the experimental range. Model L(1) beans produced much more n-hexanal relative to the wild type than those in experiments. Sensitivity analysis indicates that reducing the estimated K(m) parameter for LOX isozyme 3 (L-3) would improve the fit between model predictions and experimental results found in the literature. The model also predicts that increasing L-3 or reducing L-2 levels within beans may reduce n-hexanal generation. PRACTICAL APPLICATION: This work describes the use of mathematics to attempt to quantify the enzyme-catalyzed conversions of compounds in soybean homogenates into undesirable flavors, primarily from the compound n-hexanal. The effect of different soybean genotypes and enzyme kinetic constants was also studied, leading to recommendations on which combinations might minimize off-flavor levels and what further work might be carried out to substantiate these conclusions.

Model
Publication ID: 21535565 Submission Date: 23 Mar 2012 10:15:29 UTC Last Modification Date: 22 May 2014 19:03:16 UTC Creation Date: 10 Apr 2012 13:24:24 UTC
Mathematical expressions
Reactions
LOX1 LOX2 LOX3 HPL
HPL(RZE)      
Rules
Assignment Rule (variable: Vm(HPL-RZE))      
Physical entities
Compartments Species
compartment LA 13HOD-S(Z,E) 13HOD-R(Z,E)
13HOD-S(E,E) 13HOD-R(E,E) 9HOD-S(Z,E)
9HOD-R(Z,E) 9HOD-S(E,E) 9HOD-R(E,E)
nHexanal    
Global parameters
Km(L1) Vm(L1) Km(L2) Vm(L2)
Km(L3) Vm(L3) Km(HPL) Vm(HPL-SZE)
Vm(HPL-RZE)      
Reactions (5)
 
 LOX1 [LA] → 0.574 × [13HOD-S(Z,E)] + 0.144 × [13HOD-R(Z,E)] + 0.05 × [13HOD-S(E,E)] + 0.012 × [13HOD-R(E,E)] + 0.162 × [9HOD-S(Z,E)] + 0.04 × [9HOD-R(Z,E)] + 0.014 × [9HOD-S(E,E)] + 0.0040 × [9HOD-R(E,E)];  
 
 LOX2 [LA] → 0.751 × [13HOD-S(Z,E)] + 0.023 × [13HOD-R(Z,E)] + 0.025 × [13HOD-S(E,E)] + 0.015 × [13HOD-R(E,E)] + 0.127 × [9HOD-S(Z,E)] + 0.026 × [9HOD-R(Z,E)] + 0.018 × [9HOD-S(E,E)] + 0.016 × [9HOD-R(E,E)];  
 
 LOX3 [LA] → 0.068 × [13HOD-S(Z,E)] + 0.059 × [13HOD-R(Z,E)] + 0.136 × [13HOD-S(E,E)] + 0.107 × [13HOD-R(E,E)] + 0.218 × [9HOD-S(Z,E)] + 0.218 × [9HOD-R(Z,E)] + 0.098 × [9HOD-S(E,E)] + 0.097 × [9HOD-R(E,E)];  
 
 HPL [13HOD-S(Z,E)] → [nHexanal];  
 
 HPL(RZE) [13HOD-R(Z,E)] → [nHexanal];  
 
Rules (1)
 
 Assignment Rule (name: parameter_9) Vm(HPL-RZE) = 0.135*parameter_8
 
Functions (1)
 
 Henri-Michaelis-Menten (irreversible) lambda(substrate, Km, V, V*substrate/(Km+substrate))
 
 compartment Spatial dimensions: 3.0  Compartment size: 1000.0
 
 LA
Compartment: compartment
Initial concentration: 6.69999967735732E-5
 
 13HOD-S(Z,E)
Compartment: compartment
Initial concentration: 0.0
 
 13HOD-R(Z,E)
Compartment: compartment
Initial concentration: 0.0
 
 13HOD-S(E,E)
Compartment: compartment
Initial concentration: 0.0
 
 13HOD-R(E,E)
Compartment: compartment
Initial concentration: 0.0
 
 9HOD-S(Z,E)
Compartment: compartment
Initial concentration: 0.0
 
 9HOD-R(Z,E)
Compartment: compartment
Initial concentration: 0.0
 
 9HOD-S(E,E)
Compartment: compartment
Initial concentration: 0.0
 
 9HOD-R(E,E)
Compartment: compartment
Initial concentration: 0.0
 
 nHexanal
Compartment: compartment
Initial concentration: 0.0
 
Global Parameters (9)
 
   Km(L1)
Value: 0.49
Constant
 
   Vm(L1)
Value: 0.00825
Constant
 
   Km(L2)
Value: 0.49
Constant
 
   Vm(L2)
Value: 0.039
Constant
 
   Km(L3)
Value: 0.49
Constant
 
   Vm(L3)
Value: 0.00255
Constant
 
   Km(HPL)
Value: 0.05
Constant
 
   Vm(HPL-SZE)
Value: 0.285
Constant
 
   Vm(HPL-RZE)
Value: 0.038475
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000415

Curator's comment: (updated: 10 Apr 2012 14:24:08 BST)

n-hexanal concentration (relative to the maximum wild-type value (4.89e-005)) i.e. Figure 3A of the reference publication has been reproduced here. The model corresponds to the wild-type (L123) beans and reproduces the plot that corresponds to L123 (blue) in the figure. In order to obtain the plots for the mutants the following changes are to be made in the model.
L23 ; set Km(L1)& Vm(L1) to "0"
L13 ; set Km(L2)& Vm(L2) to "0"
L12 ; set Km(L3)& Vm(L3) to "0"
L2 ; set Km(L1), Vm(L1), Km(L3) & Vm(L3) to "0".

The model was simulated using SBMLsimulator 1.0.

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