Bacterial Chemotaxis

Project Title

Bacterial Chemotaxis Project

Summary

The chemotaxis pathway of Eschelichia coli is among the most thoroughly studied cell signaling pathways to date. A number of models have been proposed in the past to explain the mechanisms by which this pathway controls the swimming behavior of this bacterium.

But each modeling study employs different formalisms and simulation algorithms, making comparisons of their performance a non-trivial problem. To study the characteristics of each of these models and to compare their behaviour, it would be very helpful to be able to execute simulations on a single platform.

The E-Cell Simulation Environment (E-Cell SE) provides a flexible framework in which both deterministic and stochastic algorithms can be used to simulate models with either continuous or discrete variables. To demonstrate the utility of this framework, we are constructing a model library of E. coli chemotaxis that allows comparative analysis of previously published models.

(Yuri Matsuzaki)

Background

• Bacterial chemotaxis
• Assumptions for robust perfect adaptation
• Models
  • Canonical adaptation model

    A "minimal" deterministic model for near perfect adaptation, loosely based on Bray et. al. 1993[1]

  • Mello2003a

    Detailed deterministic model based on Mello and Tu 2003[2]

  • Mello2003b

    based on Mello2003b[3]

  • Morton-Firth1998

    Detailed stochastic model based on Morton-Firth et. al. 1998[4]

[1] Bray, D., Bourret, R.B. and Simon, M.I., Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis. Mol. Biol. Cell (1993) 4:469-482.

[2] Mello, B.A. and Tu, Y. Perfect and near perfect adaptation in a model of bacterial chemotaxis. Biophys. J. (2003) 84:2943-2956.

[3] Mello, B.A.

[4] Morton-Firth, C.J., Shimizu, T.S. and Bray D. A free-energy-based stochastic simulation of the Tar receptor complex. J Mol Biol (1999) 286:1059-1074.

Developer info

• Yuri Matsuzaki

Development status (scrach, stable, obsolete, etc..)

running

Environment

E-Cell SE version 3.1.103 or later

License

UNKNOWN

Tracker

• mada

Workgroup

• mada

CVS

• mada
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