Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module

Syst Biol (Stevenage). 2005 Dec;152(4):229-42. doi: 10.1049/ip-syb:20050014.

Abstract

Biochemical systems embed complex networks and hence development and analysis of their detailed models pose a challenge for computation. Coarse-grained biochemical models, called reduced-order models (ROMs), consisting of essential biochemical mechanisms are more useful for computational analysis and for studying important features of a biochemical network. The authors present a novel method to model-reduction by identifying potentially important parameters using multidimensional sensitivity analysis. A ROM is generated for the GTPase-cycle module of m1 muscarinic acetylcholine receptor, Gq, and regulator of G-protein signalling 4 (a GTPase-activating protein or GAP) starting from a detailed model of 48 reactions. The resulting ROM has only 17 reactions. The ROM suggested that complexes of G-protein coupled receptor (GPCR) and GAP--which were proposed in the detailed model as a hypothesis--are required to fit the experimental data. Models previously published in the literature are also simulated and compared with the ROM. Through this comparison, a minimal ROM, that also requires complexes of GPCR and GAP, with just 15 parameters is generated. The proposed reduced-order modelling methodology is scalable to larger networks and provides a general framework for the reduction of models of biochemical systems.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Animals
  • Biochemistry / methods
  • Cell Physiological Phenomena*
  • Computer Simulation
  • GTP Phosphohydrolases / metabolism*
  • GTPase-Activating Proteins / metabolism*
  • Humans
  • Models, Biological*
  • Signal Transduction / physiology*
  • Systems Biology / methods*

Substances

  • GTPase-Activating Proteins
  • GTP Phosphohydrolases