  Conformational fluctuations are believed to play an important role in the
process by which transcription factor proteins locate and bind their target
site on the genome of a bacterium. Using a simple model, we show that the
binding time can be minimized, under selective pressure, by adjusting the
spectrum of conformational states so that the fraction of time spent in more
mobile conformations is matched with the target recognition rate. The
associated optimal binding time is then within an order of magnitude of the
limiting binding time imposed by thermodynamics, corresponding to an idealized
protein with instant target recognition. Numerical estimates suggest that
typical bacteria operate in this regime of optimized conformational
fluctuations.
