Simulation of a Petri net-based Model of the Terpenoid Biosynthesis Pathway

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Background: The development and simulation of dynamic models of terpenoid biosynthesis has yielded a systems perspective that provides new insights into how the structure of this biochemical pathway affects compound synthesis. These insights may eventually help identify reactions that could be experimentally manipulated to amplify terpenoid production. In this study, a dynamic model of the terpenoid biosynthesis pathway was constructed based on the Hybrid Functional Petri Net (HFPN) technique. This technique is a fusion of three other extended Petri net techniques, namely Hybrid Petri Net (HPN), Dynamic Petri Net (HDN) and Functional Petri Net (FPN).Results: The biological data needed to construct the terpenoid metabolic model were gathered from the literature and from biological databases. These data were used as building blocks to create an HFPNe model and to generate parameters that govern the global behaviour of the model. The dynamic model was simulated and validated against known experimental data obtained from extensive literature searches. The model successfully simulated metabolite concentration changes over time (pt) and the observations correlated with known data. Interactions between the intermediates that affect the production of terpenes could be observed through the introduction of inhibitors that established feedback loops within and crosstalk between the pathways.Conclusions: Although this metabolic model is only preliminary, it will provide a platform for analysing various high-throughput data, and it should lead to a more holistic understanding of terpenoid biosynthesis.

Original languageEnglish
Article number83
JournalBMC Bioinformatics
Volume11
DOIs
Publication statusPublished - 9 Feb 2010

Fingerprint

Biosynthesis
Terpenes
Petri nets
Petri Nets
Pathway
Dynamic models
Dynamic Model
Simulation
Correlated Observations
Model
Crosstalk
Feedback Loop
Metabolites
Building Blocks
High Throughput
Inhibitor
Fusion
Fusion reactions
Throughput
Experimental Data

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Structural Biology
  • Applied Mathematics

Cite this

Simulation of a Petri net-based Model of the Terpenoid Biosynthesis Pathway. / Hawari, Aliah H.; Mohamed Hussein, Zeti Azura.

In: BMC Bioinformatics, Vol. 11, 83, 09.02.2010.

Research output: Contribution to journalArticle

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