From 2010.igem.org

Modeling of the light switch

Schematical overview of the devices and change upon light pulse induction. LSP refers to light switch protein, AP to anchor protein, anchor to the plasmid anchor and Che to the attacked protein of the chemotaxis pathway.

Background

In our biological setup, the relocation of one of the chemotaxis pathway proteins (either CheR, CheB, CheY or CheZ) is achieved by fusing them to a light-sensitive protein LSP1 (either to PhyB or to PIF3), which dimerizes by red light induction with the corresponding LSP2 (PIF3 or PhyB), fused to a spatially dislocated anchor. Since we decided to implement two different models of the chemotaxis pathway (see Sektion Chemotaxis Pathway), modeling all setups implemented in the wet-lab would have resulted in 16 different models:

|{CheR, CheB, CheY, CheZ} × {PhyB, PIF3} × {Model 1, Model 2}|=16.

Inspired by the modular approach used as the Cloning Strategy in the wet-lab, we decided to decrease the combinatorial explosion by also applying a novel modular approach. Not only did this approach reduce the amount of models by a factor of four, it also allowed to widely separate the differential equations of the chemotaxis pathway from those of the light-induced localization system by simultaneously decreasing redundancies and thus decreasing the danger of slip of the pens. The underlying mathematical model for the light-induced relocation was completely developed by us (for a short discussion of the recently by Sorokina et al. published light-induced relocation system and why we did not use it, see here) as well as - to our knowledge - the approach to couple this model to models of the chemotaxis pathway.

Facing the Combinatorical Explosion