Hanke 200804

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Computational approaches are increasingly used to analyse complex biological systems such as cellular metabolism and signalling pathways. In order to yield reliable results computations have to rest on a correct representation of individual phenomena such as diffusion, binding interactions, enzyme catalysis, membrane transport/partitioning, and compartmentalisation. For instance, binding and catalytic parameters obtained in traditional experimantal setups (in dilute solutions) do not always correctly translate to those obtained in a crowded milieu such as the cell interior. Although in vitro experiments including ``crowding agents can be used to obtain more relevant parameters in vitro, a description of the ``real behaviour of molecules in the interior of the cell is clearly the ultimate goal.

The present investigations are motivated by a collaboration between the NA group at KTH and a research group at Karolinska Institutet. In an experiment, the distribution and reaction of carcinogenic polycyclic aromatic hydrocarbons and reactive metabolites derived thereof are used as intracellular probes of diffusion, enzymatic and non-enzymatic reactions. Given that numerous polycyclic aromatic hydrocarbons exist and that a good deal of metabolic studies have been performed in cellular systems the stage is set for a comprehensive computational approach that can be refined against exact measurements of enzyme and molecular behaviour in cells.

In this talk, we report about the modelling approach, the results obtained so far, and future directions of investigations.

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