We have used the Smoldyn software to create spatially detailed models of the Escherichia coli chemotaxis
pathway. With it we can follow signalling reactions at high spatio-temporal resolution, observe the formation of gradients
of phospho-proteins as well as total protein and analyse the effects of macromolecular crowding on signalling. It has enabled
us to propose new regulatory elements of the signalling pathway, which are mediated through the dynamic localisation
and activity of the CheZ phosphatase. We used the Smoldyn software to model quantitative fluorescent microscopy
data and to determine diffusion coefficients and binding affinities. We can reliably gain information obtained under conditions
with high levels of experimental noise. Smoldyn can accommodate various cellular architectures, and we show that
cell shape becomes an integral part of the signalling process.
Keywords: Bacterial chemotaxis, cellular signalling, particle based simulation, protein gradients, review, smoldyn.
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