many DNA-binding proteins. It consists of three linked alpha helices, which are shown as cylinders in this figure. Most of the contacts with the DNA bases are made by helix number 3 (which is seen end-on in [B]). The asparagine (Asp) in this helix contacts an adenine in the manner shown in the previous figure. (C) The zinc finger motif is built from an alpha helix and a beta sheet (the latter shown as a twisted arrow) held together by a molecule of zinc (indicated by a sphere). Zinc fingers are often found in clusters covalently joined together to allow the alpha helix of each finger to contact the DNA bases in the major groove. The illustration here shows a cluster of three zinc fingers. (D) A leucine zipper motif. This DNA-binding motif is formed by two alpha helices, each contributed by a different protein molecule. Leucine zipper proteins thus bind to DNA as dimers, gripping the double helix like a clothes pin on a clothes line. These three motifs are found in gene regulatory proteins in virtually all eukaryotic organisms, where they are responsible for controlling the expression of thousands of different genes. Each motif makes many contacts with DNA. For simplicity, only the hydrogen-bond contacts are shown in (B), and none of the individual protein-DNA contacts are shown in (C) and (D). The names "homeodomain," "zinc finger," and "leucine zipper" all derive from historical terminology and are not meant to be accurate descriptions of these structures.
