Opening Image: λ repressor-operator complex. The operator site is 17 base pairs of double-stranded DNA. The repressor is a dimeric protein. Each chain contains an N-terminal domain (residues 1 through 92) that binds to the DNA, and a C-terminal domain. The C-terminal domains interact with each other to hold the dimer together. The isolated N-terminal domains retain their ability to bind specifically to the operator subsites.
cartoon model of one subunit. Notice how one of the α-helices fits into the major groove of the double helix.
Small, single domain proteins in the all-α class are the fastest folding proteins. The speed record is currently held by the N-terminal domain of the λ repressor. The wild-type fragment folds with a half-life of 240 μs. Randall Burton et al. have engineered a double mutant, G46A/G48A, in which two glycines in the third α-helix have been replaced with alanines. The G46A/G48A variant unfolds with the same rate as the wild-type protein but it folds with a half-life of less than 10 μs, making it the fastest folding protein known.
Now let's turn our attention to a single monomer. Each monomer contains six glycines, shown in CPK colors.
all atoms. How many many glycines are exposed?
The third α-helix (cyan) fits neatly into the major groove of the DNA. Altogether, eight side chains contact the DNA.
the third helix. Specific recognition between the third helix and DNA arises from hydrogen bonds between the side chains of Gln44 and Ser45 and exposed edges of the base pairs in the major groove.
The third α-helix is the only helix in the λ repressor that contains glycines. The residues are at positions 46 and 48.
The Gly α-carbons are colored dark gray. Which α-hydrogens are replaced with methyl groups in the G46A/G48A variant?
wild-type vs. double mutant. The β-carbons of Ala46 and Ala48 are shown in green.
The differences in folding rates for the wild-type λ repressor N-terminal domain and the G46A/G48A variant arise primarily from increased conformational freedom for glycine in the unfolded protein. The presence of the methyl group in alanine reduces the number of allowed conformations in the peptide backbone by a factor of three.