Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe

Authors:
Alexander Ullrich;Christoph Flamm
Affiliations:
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria A-1090;Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria A-1090
Venue:
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Year:
2008

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Abstract

The origin and evolution of metabolism is an interesting field of research with many unsolved questions. Simulation approaches, even though mostly very abstract and specific, have proven to be helpful in explaining properties and behavior observed in real world metabolic reaction networks, such as the occurrence of hub-metabolites. We propose here a more complex and intuitive graph-based model combined with an artificial chemistry. Instead of differential equations, enzymes are represented as graph rewriting rules and reaction rates are derived from energy calculations of the involved metabolite graphs. The generated networks were shown to possess the typical properties and further studied using our metabolic pathway analysis tool implemented for the observation of system properties such as robustness and modularity. The analysis of our simulations also leads to hypotheses about the evolution of catalytic molecules and its effect on the emergence of the properties mentioned above.