A three dimensional model of the basic Helix-Loop-Helix motif and its
sequence specific recognition of DNA is described. The basic-helix I is modeled
as a continuous ?-helix because no ?-helix breaking residue is found
between the basic region and the first helix. When the basic region of the two
peptide monomers are aligned in the successive major groove of the cognate
DNA, the hydrophobic side chains of the helix I-helix I come in van der Waals
proximity. In this way, the end residues of the helix I-helix I are placed far
from each other so that a "loop" is needed to bring the helix II-helix II close
together for hydrophobic interactions and therefore dimerization. The proposed
sequence specific recognition is by hydrogen bonding of the conserved Asn (or
Thr) and Glu side chains to the consensus guanine and adenine respectively.
The methyl group of Thr and the hydrophobic residue next to it also produce a
hydrophobic pocket for recognition of the methyl group of the consensus thymine.
The highly conserved Arg's interact with backbone phosphates and a direct
recognition of base pairs by Arg's is not likely