ELONGATION OF HELIX-III OF THE NK-2 HOMEODOMAIN UPON BINDING TO DNA -A SECONDARY STRUCTURE STUDY BY NMR

The secondary structure of the homeodomain encoded by the NK-2 gene fr om Drosophila melanogaster, in both the free and DNA-bound states, was determined in solution using two- and three-dimensional (2D and 3D) N MR Spectroscopy. Proton and N-15 studies were carried out on a 77 amin o acid residue protein that contains the homeodomain, which was synthe sized in Escherichia coli. On the basis of NOE connectivities, vicinal coupling constants, and proton-deuterium exchange behavior, three hel ical segments were found that consist of homeodomain amino acid residu es 10-22, 28-38, and 42-52 for the protein in the absence of DNA. The major structural differences between free NK-2 and other homeodomains are the increased internal mobility of the second helix and the shorte r length of the third helix, also termed the recognition helix. Despit e this shorter helix, NK-2 exhibits high-affinity binding to DNA compa red to other homeodomains (k(D) = 2.0 x 10(-10) M; L.-H. Wang and M. N irenberg, unpublished results). The formation of the complex of NK-2 w ith the duplex DNA (TGTGTCAAGTGGCTGT) significantly increases the ther mal stability of the protein. The T-m increases from 25 degrees C (fre e NK-2) to >47 degrees C (DNA-bound NK-2). Also, a dramatic increase i n the length of helix m is observed. In the absence of DNA, the DNA re cognition helix is 11 amino acid residues long (residues 42-52), where as in the presence of DNA, the length of this helix extends to 19 amin o acids (residues 42-60). The exchange rates of the amide protons in t he proton-deuterium exchange experiments are slower in general for the DNA-bound protein than for the free NK-2 homeodomain, which is indica tive of a stable conformation for NK-2. A preliminary model of the unb ound NK-2 tertiary structure is presented.