model file for PPK kinetics

Version 1

The Snoep Lab’s core research efforts are in Computational Systems Biology; a combined experimental, modeling and theoretical approach to quantitatively understand the functional behavior of Biological Systems resulting from the characteristics of their components. Our main focus is on metabolism, of human pathogens such as Plasmodium falciparum, Mycobacterium tuberculosis, but also of breast cancer cell lines, and on modelling disease states such as glucose homeostatis in type 2 diabetes, and ...

The goal of the project is to establish a new biotechnological platform for the production of hydroxy-amino acids, since the current production of these important building blocks is very expensive. Enzyme engineering, systems biotechnology and metabolic engineering will be used in a synthetic biology approach.

The polyphosphate kinase (PPK) of the crenarchaeal organism Sulfolobus acidocaldarius is kinetically characterised and polyphosphate synthesis and degradation in incubations of the enzyme were simulated with a kinetic model.

PPK was isolated and it was kinetically characterized in initial rate kinetic experiments. A rate equation was parameterized and used to simulate enzyme incubations

PPK kinetic data for initial rate experiments and for enzyme incubations are linked and available in an Excel file. In addition a model file is available as Mathematica notebook for the parameterization of a rate equation for the enzyme, and for simulation of the enzyme incubations.