The Escherichia coli tryptophan repressor
protein (TR) represses the transcription of several genes
in response to the concentration of tryptophan in the environment.
In the co-crystal structure of TR bound to a DNA fragment
containing its target very few direct contacts between
TR and the DNA were observed. In contrast, a number of
solvent mediated contacts were apparent. NMR solution structures,
however, did not resolve any solvent mediated bonds at
the complex interface. To probe for the role of water in
TR operator recognition, the effect of osmolytes on the
interactions between TR and a target oligonucleotide bearing
the operator site was examined. In the absence of specific
solvent mediated hydrogen bonding interactions between
the protein and the DNA, increasing osmolyte concentration
is expected to strongly stabilize the TR operator interaction
due to the large amount of macromolecular surface area
buried upon complexation. The results of our studies indicate
that xylose did not alter the binding affinity significantly,
while glycerol and PEG had a small stabilizing effect.
A study of binding as a function of betaine concentration
revealed that this osmolyte at low concentration results
in a stabilization of the 1:1 TR/operator complex, but
at higher concentrations leads to a switching between binding
modes to favor tandem binding. Analysis of the effects
of betaine on the 1:1 complex suggest that this osmolyte
has about 78% of the expected effect. If one accepts the
analysis in terms of the number of water molecules excluded
upon complexation, these results suggest that about 75
water molecules remain at the interface of the 1:1 dimer/DNA
complex. This value is consistent with the number of water
molecules found at the interface in the crystallographically
determined structure and supports the notion that interfacial
waters play an important thermodynamic role in the specific
complexation of one TR dimer with its target DNA. However,
the complexity of the effects of betaine and the small
or negligible effects of the other osmolytes could also
arise from osmolyte induced competition between antagonistic
coupled reactions.