PPK kinetics and incubations

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 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.

In the mathematica notebook the parameterized rate equation from the first model file is now simulated for several enzyme incubations with different initial conditions. The NMR data for the same incubations are imported in the notebook (save both files in the same directory), and plotted together with the model simulations. The incubation figures in the manuscript are reproduced in the notebook.

The mathematica notebook reads in the data from the excel file (save both files in the same directory), and the kinetic rate equation in the notebook is fitted on the data. Figures as published in the manuscript are reproduced in the notebook.

The excel file has two sheets, the first contains the initial rate kinetics data and the second sheet contains the NMR incubations data.