title: Parameter optimization and sensitivity analysis for large kinetic models using a real-coded genetic algorithm.
abstract: Dynamic modeling is a powerful tool for predicting changes in metabolic regulation. However, a large number of input parameters, including kinetic constants and initial metabolite concentrations, are required to construct a kinetic model. Therefore, it is important not only to optimize the kinetic parameters, but also to investigate the effects of their perturbations on the overall system. We investigated the efficiency of the use of a real-coded genetic algorithm (RCGA) for parameter optimization and sensitivity analysis in the case of a large kinetic model involving glycolysis and the pentose phosphate pathway in Escherichia coli K-12. Sensitivity analysis of the kinetic model using an RCGA demonstrated that the input parameter values had different effects on model outputs. The results showed highly influential parameters in the model and their allowable ranges for maintaining metabolite-level stability. Furthermore, it was revealed that changes in these influential parameters may complement one another. This study presents an efficient approach based on the use of an RCGA for optimizing and analyzing parameters in large kinetic models.
authors.affiliation: Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shig 525-8577, Japan. yukako@sk.ritsumei.ac.jp
authors.forename: Yukako
authors.initials: Y
authors.lastname: Tohsato
authors.forename: Kunihiko
authors.initials: K
authors.lastname: Ikuta
authors.forename: Akitaka
authors.initials: A
authors.lastname: Shionoya
authors.forename: Yusaku
authors.initials: Y
authors.lastname: Mazaki
authors.forename: Masahiro
authors.initials: M
authors.lastname: Ito
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D048168:Escherichia coli K12 / Q000235:genetics* / Q000378:metabolism*; D006019:Glycolysis; D007700:Kinetics; D008957:Models, Genetic; D010427:Pentose Phosphate Pathway