trp repressor arms contribute binding energy without occupying unique locations on DNA

The amino-terminal arms of dimeric Escherichia coli trp repressor were removed by chymotryptic cleavage of the first 6 residues from each subunit. The role of the arms in structure and function of the repressor was probed by comparing the properties of intact and proteolyzed forms. The armless protein retains the ability to form stable dimers and to bind the corepressor L-tryptophan, but its affinity for both operator and nonoperator DNA is reduced by about 50-fold. Footprinting analysis shows that the intact repressor makes contacts with nucleotides on only one face of operator DNA. Thus, the arms do not wrap around the DNA as is the case for several other DNA binding proteins. All the contact sites identified by footprinting using the intact repressor are preserved in the complex formed with the armless repressor. This result indicates that the arms do not occupy a unique position on the DNA although they contribute substantially to the energy of DNA binding.