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

Abstract

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.