Simulating signaling pathways: the motile photoresponse of H. salinarum as a case study.

The simulation of signaling pathways is an important current challenge in Systems Biology, since it shows some characteristics that are difficult to manage by means of the simulation approaches usually adopted for constitutive metabolic pathways. In particular, it is multi-scale with respect both to metabolite concentrations (because of the amplification) and reaction kinetics. We focused our interest on the simulation of a specific signaling pathway: the photoperception in Halobacterium salinarum, which belongs to Archæa and possesses four different rhodopsins, two of which have a sensory role (SR1 and SR2). These two pigments allow H. salinarum to react to light stimuli by altering its motile behavior. This photoresponse is very complex and depends on the duration, intensity and spectral composition of the stimulus; several models have been proposed in the literature to explain this puzzling behavior. Recently H. salinarum, independently of our work , has been suggested as a model system for Systems Biology in a international congress (CMSB 2008).