Research

Distinguishing enzymes using metabolome data for the hybrid dynamic/static method

Nobuyoshi Ishii¹ , Yoichi Nakayama^1,2 and Masaru Tomita¹

¹  Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0035, Japan

²  Network Biology Research Centre, Articell Systems Corporation, Keio Fujisawa Innovation Village, 4489 Endo, Fujisawa, 252-0816, Japan

author email corresponding author email

Theoretical Biology and Medical Modelling 2007, 4:19doi:10.1186/1742-4682-4-19

Published:	20 May 2007

Abstract

Background

In the process of constructing a dynamic model of a metabolic pathway, a large number of parameters such as kinetic constants and initial metabolite concentrations are required. However, in many cases, experimental determination of these parameters is time-consuming. Therefore, for large-scale modelling, it is essential to develop a method that requires few experimental parameters. The hybrid dynamic/static (HDS) method is a combination of the conventional kinetic representation and metabolic flux analysis (MFA). Since no kinetic information is required in the static module, which consists of MFA, the HDS method may dramatically reduce the number of required parameters. However, no adequate method for developing a hybrid model from experimental data has been proposed.

Results

In this study, we develop a method for constructing hybrid models based on metabolome data. The method discriminates enzymes into static modules and dynamic modules using metabolite concentration time series data. Enzyme reaction rate time series were estimated from the metabolite concentration time series data and used to distinguish enzymes optimally for the dynamic and static modules. The method was applied to build hybrid models of two microbial central-carbon metabolism systems using simulation results from their dynamic models.

Conclusion

A protocol to build a hybrid model using metabolome data and a minimal number of kinetic parameters has been developed. The proposed method was successfully applied to the strictly regulated central-carbon metabolism system, demonstrating the practical use of the HDS method, which is designed for computer modelling of metabolic systems.