Determination of elasticities, concentration and flux control coefficients from transient metabolite data using linlog kinetics.
This paper presents a practical approach to estimate the kinetic parameters of a metabolic network from in vivo kinetics experiments. This method is based on the linlog kinetics format (Visser and Heijnen, 2003, Metab. Eng. 5(3), 164-176; Wu et al., 2004, Eur. J. Biochem. 271, 3348-3359), of which the kinetic parameters, called elasticities, are estimated by an iterative linear optimization followed by non-linear optimization, from transient metabolite concentration data which are directly obtainable from rapid pulse experiments. In this way, not only the parameters are estimated but also a full kinetic model, based on linlog kinetics, is developed. The obtained elasticities also allow immediate calculation of all control coefficients. As an in silico case study, the estimation of elasticities of a linear pathway is presented. The method is shown to be able to estimate the elasticities quite accurately and to be robust toward errors in the metabolite data originating from sampling and measurement inaccuracy. The method allows experimental redesign to get more accurate estimated parameters and accommodates various types of experimentally applied disturbances in the pathway: changes in independent metabolites, dependent metabolites or enzyme levels/activities.
Kresnowati
M T A Penia
MT
Department of Biotechnology, TU Delft, Julianalaan 67, 2628 BC Delft, The Netherlands. m.t.a.p.kresnowati@tnw.tudelft.nl
van Winden
Wouter A
WA
Heijnen
Joseph J
JJ
D003198:Computer Simulation; D004798:Enzymes / Q000737:chemistry*; D007700:Kinetics; D008954:Models, Biological
D004798:Enzymes