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Application of Petri Net Theory for Modelling and Validation of Menthol Biosynthesis

An essential step in network modelling is to validate the network
model. Petri net theory provides algorithms and methods, which can
be applied directly to metabolic network modelling and analysis in
order to validate the model. This paper describes the thriving application
of Petri net theory for model validation of biosynthesis of menthol
using the well-established Petri net analysis technique of place and
transition invariants. Because of the complexity of metabolic networks
and their regulation, formal modelling is a useful method to improve
the understanding of these systems. A petri net representation, its
validation and simulation of biosynthesis of menthol from geranyl
diphosphate (GPP) has been performed with the objective of understating
new insights of the structure of this pathway affecting the
synthesis of menthol. The model has been validated for its P-invariant
and T-invariant. T-invariant analysis suggest absence of any loop in
the net which restore the initial state suggesting all reactions to be only
forward. The net is covered by positive P-invariants and bounded. The
net is utilized to simulate the time (pt) with concentrations of GPP, (−)-
limonene, (+)-pulegone, (−)-menthone and (−)-menthol. Dimethylallyl
diphosphate and isopentenyl diphosphate were the main precursors
for this biosynthesis. Biological data needed for simulation where
obtained from extensive survey of literature. The results were shown
graphically and the nature of graphs represent the variation of
concentrations with time.