NMR studies on the Myb-DNA system

Abstract

NMR structural studies on a bacterially produced DNA binding domain of Drosophila c-Myb protein as well as its cognate DNA sequence carried out in our laboratory have been surveyed. The structure of a self-complementary dodecamer DNA containing the Myb responsive element (TAACGG) has been determined to atomic resolution by the combined use of two-dimensional NMR, spectral simulations, restrained energy minimization and distance geometry calculations. The structure is seen to possess novel features which may play important roles during its interaction with the Myb protein, The DNA binding domain of c-Myb protein was seen to have a hydrophobic core and we have identified the types of residues contributing to its formation. Residues contributing to the hydrophobic core formation are seen to be well spread out over the whole length of the 160 residues in the protein and include isoleucines, valines, leuclnes, alanines threonines, aromatic residues, glutamines and possibly aspartates. Our experimental data in combination with those of others indicate that some of the amino acid residues which form the helical motifs that directly interact with DNA may also be a part of the hydrophobic core.