Refined Solution Structure and Dynamics of the DNA-binding Domain of the Heat Shock Factor from Kluyveromyces lactis

Abstract

The solution structure of the 92 residue (11 kDa) winged helix-turn-helix DNA-binding domain from the kluyveromyces lactisheat shock factor was refined using a total of 932 NOE, 35 φ, 25 χ1, 5 χ2 and 44 hydrogen bond restraints. The overall root-mean-square deviation for structured regions was 0.75(±0.15) Å. The three-helix bundle and four-stranded β-sheet are well defined with rmsd of 0.53(±0.10) Å and 0.60(±0.17) Å, respectively. Helix H2 is underwound and bent near Pro45. The angle between helix H2 and the proposed recognition helix H3 is 96(±6)°. Detailed comparisons are made with the X-ray structure of this protein as well as other structural studies on HSF. Overall, the results are consistent with the earlier studies. Differences are related to protein – protein interactions in the crystal and dynamics in solution. Backbone dynamics was investigated via 15N relaxation. The average R 1, R 2and NOE values for residues in segments of secondary structure were 1.9(±0.9) s −1, 7.8(±0.9) s −1and 0.81(±0.05), respectively. The correlation time based on these data was 5.6(±0.4) ns. Motional order parameters were calculated by fitting the relaxation data to one of three models. Low-order parameters were found for residues that comprise the turn between helices H2 and H3 (residues Lys49 to Phe53), and most strikingly, the 16 residue wing (residues Val68 to Arg83). These data are consistent with the lack of long-range NOEs identified in these regions. The data provide a basis for comparison with results of the protein-DNA complex. The relationship between structure and function is discussed.