NH2-terminal arm of phage lambda repressor contributes energy and specificity to repressor binding and determines the effects of operator mutations.

Several lines of evidence indicate that the phage lambda repressor recognizes its operator by using, in part, an alpha helix (the "recognition helix"), which it inserts into the major groove of DNA. In addition to its recognition helix, lambda repressor has an "arm," consisting of the first six amino acids, that wraps around the DNA helix. We constructed plasmids that, in Escherichia coli, direct the expression of derivatives of lambda repressor that lack the NH2-terminal one, three, six, or seven amino acids. We studied these modified proteins in vivo and in vitro, and from our results we argue that the arm: contributes a large portion of the binding energy; helps to determine sequence specificity of binding and, in particular, the relative affinities for two wild-type binding sites; determines entirely repressor's response to one operator mutation (a "back-side" mutation); magnifies repressor's response to other operator mutations ("front-side" mutations); and increases the sensitivity of repressor binding to salt concentration and temperature.