Bacterial chemotaxis: using computers to represent biology
The set of biochemical reactions by which an E. coli bacterium detects and responds to distant sources of attractant or repellent molecules is probably the simplest and best understood example of a cell-signalling pathway. The pathway has been saturated genetically and all of its protein components have been isolated, measured biochemically and their atomic structures determined. We have used detailed computer simulations, tied to experimental data, to ask how the pathway works as an integrated unit. We found that the physical location of molecular components within the molecular jungle of the cell interior is crucial for an understanding of their function. Signal amplification, for example, appears to depend on the propagation of activity across clusters of receptors and associated molecules.
Because it is relatively simple and well documented, the E. coli chemotaxis pathway serves as a benchmark for our understanding of cells in general.How close are we to a complete understanding? Can we expect in the near future to build computer models that capture every essential aspect? Or are there features of living cells that are currently beyond our ability to resolve experimentally or reproduce on silicon chips? Questions such as these are increasingly pertinent in a world populated by intelligent machines.
Please see the comp-cell website for further information, downloadable programs, and list of publications.
Bray D, (2014), Intrinsic activity in cells and the brain, Mol. Biol. Cell, 25: 737-738
Alberts B, Bray D, Hopkin K, Johnson A, Lewis J, Roberts K, Walter P, (2014), Essential Cell Biology, 4th edition Garland Publishing, New York (726 pp)
Bray D, (2013), The propagation of allosteric states in large multiprotein complexes, J. Molecular Biology, 425: 1410-1414
Bray D, (2013), Brain versus Machine. in A.H. Eden et al (eds), Singularity Hypotheses, The Frontier Collection, Springer-Verlag, Berlin
Bray D, (2012), Is the brain a good model for machine intelligence?, Nature, 482: 7386:462-463
Bray D, (2011), The cell as a thermostat: How much does it know?, Advances in Experimental Medicine and Biology, 736: 193-198
Bray D, (2009), Wetware: a Computer in Every Living Cell, Yale University Press, New Haven (267 pp)
Goldman JP, Levin MD, Bray D, (2009), Signal amplification in lattice of coupled protein kinases, Molecular BioSystems, 5: 1853-1859.