KETCHUP

KETCHUP parameterizes kinetic models of cell-free systems using time-series data, extending existing methods to improve accuracy and predictive power for metabolic simulations.

Key Features:

• Time-series parameterization: KETCHUP parameterizes kinetic models using time-course data across various initial conditions rather than relying solely on steady-state flux measurements.
• Measurement time-lag error reconciliation: An implemented extension allows for the reconciliation of measurement time-lag errors present in datasets to parameterize multiple datasets.
• Single-enzyme to multi-enzyme extrapolation: Kinetic parameters fitted to the dynamics of single-enzyme assays remain accurate for the simulation of multi-enzyme cell-free systems.
• Semi-automatic kinetic construction: KETCHUP provides semi-automatic kinetic construction and parameterization functionality.
• Steady-state data pilot: The tool utilizes steady-state data as a pilot for the parameterization of single-enzyme cell-free time-course data.

Scientific Applications:

• Cell-free enzymatic cascade simulation: KETCHUP enables accurate simulation of enzymatic cascade reactions such as binary FDH-BDH systems where steady-state is not applicable because all measured metabolite concentrations vary with time.
• Metabolic engineering: The tool supports the metabolic engineering of microorganisms for sustainable and renewable industrial scale production of commodity chemicals by improving predictive accuracy and strain design.
• Multi-enzyme system recapitulation: KETCHUP successfully recapitulates metabolite profiles for two-enzyme systems when simulating a kinetic model with parameters derived from single-enzyme assays.

Methodology:

KETCHUP uses Pyomo for parameterization and extends existing methods to incorporate temporal data; it fits kinetic parameters to single-enzyme assay dynamics and combines these parameters to simulate multi-enzyme systems, with an extension for reconciling measurement time-lag errors in datasets.