Polyphosphate kinases in Sulfolobus acidocaldarius
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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.
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Created: 19th Sep 2025 at 09:40
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Projects: PSYSMO, MOSES, SysMO DB, SysMO-LAB, SulfoSys, SulfoSys - Biotec, Whole body modelling of glucose metabolism in malaria patients, FAIRDOM, Molecular Systems Biology, COMBINE Multicellular Modelling, HOTSOLUTE, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers, Project Coordination, WP 3: Drug release kinetics study, Glucose metabolism in cancer cell lines
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch, University of Manchester - Department of Computer Science, Stellenbosch University
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 ...
Projects: Whole body modelling of glucose metabolism in malaria patients, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications, Glucose metabolism in cancer cell lines
Web page: http://www.sun.ac.za/english/faculty/science/biochemistry/research/snoep-group
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.
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
PPK was isolated and it was kinetically characterized in initial rate kinetic experiments. A rate equation was parameterized and used to simulate enzyme incubations
Submitter: Jacky Snoep
Investigation: Polyphosphate kinases in Sulfolobus acidocaldarius
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.
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Initial Rate Experiment
Investigation: Polyphosphate kinases in Sulfolobus acidocaldarius
Study: PPK kinetics and 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.
Creator: Jacky Snoep
Submitter: Jacky Snoep
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.
Creator: Jacky Snoep
Submitter: Jacky Snoep
The excel file has two sheets, the first contains the initial rate kinetics data and the second sheet contains the NMR incubations data.
Creator: Jacky Snoep
Submitter: Jacky Snoep
