Hybrid dynamic/static method for large-scale simulation of metabolism

Katsuyuki Yugi, Yoichi Nakayama, Ayako Kinoshita, Masaru Tomita

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

Background: Many computer studies have employed either dynamic simulation or metabolic flux analysis (MFA) to predict the behaviour of biochemical pathways. Dynamic simulation determines the time evolution of pathway properties in response to environmental changes, whereas MFA provides only a snapshot of pathway properties within a particular set of environmental conditions. However, owing to the large amount of kinetic data required for dynamic simulation, MFA, which requires less information, has been used to manipulate large-scale pathways to determine metabolic outcomes. Results: Here we describe a simulation method based on cooperation between kinetics-based dynamic models and MFA-based static models. This hybrid method enables quasi-dynamic simulations of large-scale metabolic pathways, while drastically reducing the number of kinetics assays needed for dynamic simulations. The dynamic behaviour of metabolic pathways predicted by our method is almost identical to that determined by dynamic kinetic simulation. Conclusion: The discrepancies between the dynamic and the hybrid models were sufficiently small to prove that an MFA-based static module is capable of performing dynamic simulations as accurately as kinetic models. Our hybrid method reduces the number of biochemical experiments required for dynamic models of large-scale metabolic pathways by replacing suitable enzyme reactions with a static module.

Original languageEnglish
Article number42
JournalTheoretical Biology and Medical Modelling
Volume2
DOIs
Publication statusPublished - 2005 Oct 4

ASJC Scopus subject areas

  • Modelling and Simulation
  • Health Informatics

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