Abstract
For reactions using thiamine diphosphate (ThDP)‐dependent enzymes many empirically‐derived kinetic models exist. However, there is a lack of mechanistic kinetic models. This is especially true for the synthesis of symmetric 2‐hydroxy ketones from two identical aldehydes, with one substrate acting as the donor and the other as the acceptor. In this contribution, a systematic approach for deriving such a kinetic model for thiamine diphosphate (ThDP)‐dependent enzymes is presented. The derived mechanistic kinetic model takes this donor–acceptor principle into account by containing two K~m~‐values even for identical substrate molecules. As example the stereoselective carbon–carbon coupling of two 3,5‐dimethoxy‐benzaldehyde molecules to (R)‐3,3′,5,5′‐tetramethoxy‐benzoin using benzaldehyde lyase (EC 4.1.2.38) from Pseudomonas fluorescens is studied. The model is derived using a model‐based experimental analysis method which includes parameter estimation, model analysis, optimal experimental design, in silico experiments, sensitivity analysis and model revision. It is shown that this approach leads to a robust kinetic model with accurate parameter estimates and an excellent prediction capability. Biotechnol. Biotechnol. Bioeng. 2008;101: 27–38. © 2008 Wiley Periodicals, Inc.