The interaction of the trp repressor from Escherichia coli with the trp operator

We have examined the interaction of the trp repressor from Escherichia coli with a 20 base-pair synthetic operator. Nonspecific binding was relatively strong (K_d=2 μM), but only weakly sensitive to the concentration of added salt ( (d log K_d) (d log [Na])= -1). ¹H-NMR studies indicate that the structure of the repressor is not greatly altered on forming the complex, and that few if any of the lysine and arginine residues make direct contact with the DNA. However, the mobility of one of the two tyrosine residues is significantly decreased in the complex. The repressor makes close contact with the major grooves of the operator such that the base protons are broadened much more than expected on the basis of increased correlation time. There are large, differential changes in chemical shifts of the imino protons on forming the complex, as well as changes in the rate constants for exchange. The fraying of the ends is greatly diminished, consistent with a target size of about 20 base-pairs. The effects of the repressor on the NMR spectra and relaxation rate constants can be interpreted as a change in the conformation of the operator, possibly a kinking in the centre of the molecule.