Regensburg 2010 – scientific programme

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SOE: Fachverband Physik sozio-ökonomischer Systeme

SOE 20: Networks: From Topology to Dynamics V (with BP, DY)

SOE 20.4: Talk

Thursday, March 25, 2010, 16:45–17:00, H44

Linking Molecular Simulations and Systemic Modelling — •Tihamer Geyer and Volkhard Helms — Zentrum für Bioinformatik, Universität des Saarlandes, D-66123 Saarbrücken

When modeling biological systems there is a gap of scales between the systemic models that try to describe the metabolism of a complete cell and the molecular biological descriptions focussing on the detailed processes of a single enzyme. We therefore proposed an agent based approch that allows to bridge between the two regimes.

For this, we set up the individual enzymes from their microscopic elementary reactions like the binding of a metabolite molecule to a binding site or the transfer of an electron from one site inside the protein to another. The respective numbers of these protein "building blocks" are then connected to metabolite pools via standardized connectors to set up the metabolic system under consideration. This pools-and-proteins model can thus be used to "convert" detailed molecular biological knowledge into a systems biological model for analyzis of the complete system.

To develop and test our approach we used the bacterial photosynthetic apparatus. But even for the "boringly" well-known system, many of the detailed kinetic constants were unknown. By comparing the behavior of the complete system to time-dependent experiments, we could determine the values and sensitivities of all parameters of our model. The thus parametrized protein modules allowed for new insights into their inner working and can be re-used to set up other, related systems.