1H and 13C NMR assignments and molecular modelling of a minor groove DNA-binding peptide from the HMG-I protein

The HMG-I subfamily of high mobility group (HMG) chromatin proteins consists of DNA-binding proteins that preferentially bind to stretches of A·T-rich sequence both in vitro and in vivo. Recently, members of the HMG-I family have been suggested to bind in vitro to the narrow minor groove of A·T-DNA by means of an 11 amino acid peptide binding domain (BD) which, because of its predicted structure, is called the‘A·T-hook motif [Reeves, R. & Nissen, M. (1990) J. Biol. Chem. 265 , 8573–8582], and would appear to be crescent-shaped. A BD peptide with 13 amino-acid residues was synthesized and examined by proton and carbon-13 nuclear magnetic resonance (NMR) spectroscopy. The peptide contains four proline residues, and on the basis of NOES and ¹³C chemical shifts was found to exist in an all-trans conformation. Molecular modelling based on this result provides evidence for a dynamic equilibrium between turn-like conformations in solution, the most populated of which is likely to be an S-shaped conformer, on the basis of amide exchange data. © Munksgaard 1995.