A free-energy-based stochastic simulation of the Tar receptor complex

We recently developed a stochastic-based program that allows individual mol ecules in a cell signalling pathway to be simulated. This program has now b een used to model the Tar complex, a multimeric signalling complex employed by coliform bacteria. This complex acts as a solid-state computational cas sette, integrating and disseminating information on the presence of attract ants and repellents in the environment of the bacterium. In our model, the Tar complex exists in one of two conformations which differ in the rate at which they generate labile phosphate groups and hence signal to the flagell ar motor. Individual inputs to the complex (aspartate binding, methylation at different sites, binding of CheB, CheR and CheY) are represented as bina ry flags, and each combination of nags confers a different free energy to t he two conformations. Binding and catalysis by the complex are performed st ochastically according to the complete set of known reactions allowing the swimming performance of the bacterium to be predicted. The assumption of two conformational states together with the use of free e nergy values allows us to bring together seemingly unrelated experimental p arameters. Because of thermodynamic constraints, we find that the binding a ffinity for aspartate is linked to changes in phosphorylation activity. We estimate the pattern of Tar methylation and effective affinity constant of receptors over a range of aspartate levels. We also obtain evidence that bo th the methylating and demethylating enzymes must operate exclusively on on e or other of the two conformations, and that sites of methylation of the c omplex are occupied in sequential order rather than independently. Detailed analysis of the response to aspartate reveals several quantitative discrep ancies between simulated and experimental data which indicate areas for fut ure research. (C) 1999 Academic Press.