title: Elongation of helix III of the NK-2 homeodomain upon binding to DNA: a secondary structure study by NMR.
abstract: The secondary structure of the homeodomain encoded by the NK-2 gene from Drosophila melanogaster, in both the free and DNA-bound states, was determined in solution using two- and three-dimensional (2D and 3D) NMR spectroscopy. Proton and 15N studies were carried out on a 77 amino acid residue protein that contains the homeodomain, which was synthesized in Escherichia coli. On the basis of NOE connectivities, vicinal coupling constants, and proton-deuterium exchange behavior, three helical segments were found that consist of homeodomain amino acid residues 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 shorter length of the third helix, also termed the recognition helix. Despite this shorter helix, NK-2 exhibits high-affinity binding to DNA compared to other homeodomains (kD = 2.0 x 10(-10) M; L.-H. Wang and M. Nirenberg, unpublished results). The formation of the complex of NK-2 with the duplex DNA (TGTGTCAAGTG-GCTGT) significantly increases the thermal stability of the protein. The Tm increases from 25 degrees C (free NK-2) to > 47 degrees C (DNA-bound NK-2). Also, a dramatic increase in the length of helix III is observed. In the absence of DNA, the DNA recognition helix is 11 amino acid residues long (residues 42-52), whereas in the presence of DNA, the length of this helix extends to 19 amino acids (residues 42-60).(ABSTRACT TRUNCATED AT 250 WORDS)
authors.affiliation: Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-0380.
authors.forename: D H
authors.initials: DH
authors.lastname: Tsao
authors.forename: J M
authors.initials: JM
authors.lastname: Gruschus
authors.forename: L H
authors.initials: LH
authors.lastname: Wang
authors.forename: M
authors.initials: M
authors.lastname: Nirenberg
authors.forename: J A
authors.initials: JA
authors.lastname: Ferretti
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000378:metabolism*; D003903:Deuterium; D004355:Drug Stability; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000378:metabolism*; D006358:Hot Temperature; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary
chemical_list: D018398:Homeodomain Proteins; D004247:DNA; D003903:Deuterium