ISSN:
0006-3525
Keywords:
protein structure
;
protein dynamics
;
protein-DNA complex
;
heteronuclear relaxation measurements
;
triple-resonance nmr
;
photo-CIDNP
;
Chemistry
;
Polymer and Materials Science
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
Notes:
The DNA-binding protein HU from Bacillus stearothermophilus (HUBst) is a dimer with a molecular weight of 19.5 kDa that is capable of bending DNA. An x-ray structure has been determined previously [Tanaka et al. (1984) Nature, Vol. 310, pp. 376-381], but no structure could be established for a large part of the supposed DNA-binding β-arms. Distance geometry and restrained molecular dynamics using nmr restraints were used to generate a set of 25 structures. These structures display a backbone rms deviation (RMSD) of 0.36 Å for the well-defined region (residues 2-54 and 75-90). The structure of the core is very similar to that observed in the x-ray structure, with a pairwise RMSD of 1.06 Å. The structure of the β-hairpin arm contains a double flip-over at the prolines in the two strands of the β-arm. Heteronuclear 15N relaxation measurements indicate that the β-arm and the tip of the β-arm is flexible. This explains the disorder observed in the solution and x-ray structures of the β-arm with respect to the core of the protein. Overlayed onto itself the β-arm is better defined, with an backbone RMSD of 1.0 Å calculated for residues 54-59 and 69-74. The tip of the arm adopts a well-defined 4 : 6 β-hairpin conformation. Changes in amide 15N and 1H chemical shifts upon titrating DNA are most pronounced for the residues in the β-hairpin arm and for the residues in the second half of the third α-helix. Heteronuclear 15N relaxation data for free and complexed HUBst show that the arms become structured upon DNA binding. Together with chemically induced nuclear polarization measurements on a mutant HUBst (M69Y; V76Y) this shows that the β-hairpin arm is involved in direct DNA interaction. © 1997 John Wiley & Sons, Inc. Biopoly 40: 553-559, 1996
Additional Material:
5 Ill.
Type of Medium:
Electronic Resource
