title: Computer controlled automated assay for comprehensive studies of enzyme kinetic parameters.
abstract: Stability and biological activity of proteins is highly dependent on their physicochemical environment. The development of realistic models of biological systems necessitates quantitative information on the response to changes of external conditions like pH, salinity and concentrations of substrates and allosteric modulators. Changes in just a few variable parameters rapidly lead to large numbers of experimental conditions, which go beyond the experimental capacity of most research groups. We implemented a computer-aided experimenting framework ("robot lab assistant") that allows us to parameterize abstract, human-readable descriptions of micro-plate based experiments with variable parameters and execute them on a conventional 8 channel liquid handling robot fitted with a sensitive plate reader. A set of newly developed R-packages translates the instructions into machine commands, executes them, collects the data and processes it without user-interaction. By combining script-driven experimental planning, execution and data-analysis, our system can react to experimental outcomes autonomously, allowing outcome-based iterative experimental strategies. The framework was applied in a response-surface model based iterative optimization of buffer conditions and investigation of substrate, allosteric effector, pH and salt dependent activity profiles of pyruvate kinase (PYK). A diprotic model of enzyme kinetics was used to model the combined effects of changing pH and substrate concentrations. The 8 parameters of the model could be estimated from a single two-hour experiment using nonlinear least-squares regression. The model with the estimated parameters successfully predicted pH and PEP dependence of initial reaction rates, while the PEP concentration dependent shift of optimal pH could only be reproduced with a set of manually tweaked parameters. Differences between model-predictions and experimental observations at low pH suggest additional protonation-sites at the enzyme or substrates critical for enzymatic activity. The developed framework is a powerful tool to investigate enzyme reaction specifics and explore biological system behaviour in a wide range of experimental conditions.
authors.affiliation: Department of Biology, Institute for Pharmacy and Molecular Biotechnology, Ruperto-Carola University of Heidelberg, Heidelberg, Germany.
authors.forename: Felix
authors.initials: F
authors.lastname: Bonowski
authors.forename: Ana
authors.initials: A
authors.lastname: Kitanovic
authors.forename: Peter
authors.initials: P
authors.lastname: Ruoff
authors.forename: Jinda
authors.initials: J
authors.lastname: Holzwarth
authors.forename: Igor
authors.initials: I
authors.lastname: Kitanovic
authors.forename: Van Ngoc
authors.initials: VN
authors.lastname: Bui
authors.forename: Elke
authors.initials: E
authors.lastname: Lederer
authors.forename: Stefan
authors.initials: S
authors.lastname: Wölfl
mesh_terms: D001331:Automation / Q000379:methods*; D002021:Buffers; D003198:Computer Simulation; D057075:Enzyme Assays / Q000379:methods*; D005635:Fructosediphosphates / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008958:Models, Molecular; D010728:Phosphoenolpyruvate / Q000378:metabolism; D011770:Pyruvate Kinase / Q000378:metabolism; D013379:Substrate Specificity; D013499:Surface Properties
chemical_list: D002021:Buffers; D005635:Fructosediphosphates; D010728:Phosphoenolpyruvate; D011770:Pyruvate Kinase; C029063:fructose-1,6-diphosphate