Principles of Gene Regulation:- Regulatory Proteins Also Have Protein-Protein Interaction Domains
Regulatory proteins contain domains not only for DNA binding but also for protein-protein interactions—with RNA polymerase, other regulatory proteins, or other sub units of the same regulatory protein. Examples include many eukaryotic transcription factors that function as gene activators, which often bind as dimers to the DNA, using DNA-binding domains that contain zinc fingers. Some structural domains are devoted to the interactions required for dimer formation, which is generally a pre requisite for DNA binding. Like DNA-binding motifs, the structural motifs that mediate protein-protein interactions tend to fall within one of a few common categories. Two important examples are the leucine zipper and the basic helix-loop-helix. Structural motifs such as these are the basis for classifying some regulatory proteins into structural families.
Leucine Zipper This motif is an amphipathic helix with a series of hydrophobic amino acid residues concentrated on one side (Fig. 1), with the hydrophobic surface forming the area of contact between the two polypeptides of a dimer. A striking feature of these α helices is the occurrence of Leu residues at every seventh position, forming a straight line along the hydrophobic surface. Although researchers initially thought the Leu residues interdigitated (hence the name “zipper”), we now know that they line up side by side as the interacting helices coil around each other (forming a coiled coil; Fig. 1b). Regulatory proteins with leucine zippers often have a separate DNA-binding domain with a high concentration of basic (Lys or Arg) residues that can interact with the negatively charged phosphates of the DNA backbone. Leucine zippers have been found in many eukaryotic and a few prokaryotic proteins Basic Helix-Loop-Helix Another common structural motif occurs in some eukaryotic regulatory proteins implicated in the control of gene expression during the develop ment of multicellular organisms. These proteins share a conserved region of about 50 amino acid residues important in both DNA binding and protein dimerization. This region can form two short amphipathic helices linked by a loop of variable length, the helix-loop-helix (distinct from the helix-turn-helix motif associated with DNA binding). The helix-loop-helix motifs of two polypeptides interact to form dimers (Fig. 2). In these proteins, DNA binding is mediated by an adjacent short amino acid sequence rich in basic residues, simi lar to the separate DNA-binding region in proteins containing leucine zippers.
Subunit Mixing in Eukaryotic Regulatory Proteins Several families of eukaryotic transcription factors have been defined based on close structural similarities. Within each family, dimers can sometimes form between two identical proteins (a homodimer) or between two different members of the family (a heterodimer). A hypo thetical family of four different leucine-zipper proteins could thus form up to ten different dimeric species. In many cases, the different combinations appear to have distinct regulatory and functional properties.
FIGURE 1 Leucine zippers. (a)Comparison of amino acid sequences of several leucine zipper proteins. Note the Leu (L) residues at every seventh position in the zipper region, and the number of Lys (K) and Arg (R) residues in the DNA-binding region. (b)Leucine zipper from the yeast activator protein GCN4 (PDB ID 1YSA). Only the “zippered” helices (gray and light blue), derived from different subunits of the dimeric protein, are shown. The two helices wrap around each other in a gently coiled coil. The inter acting Leu residues are shown in red.
FIGURE 2 Helix-loop-helix. The human transcription factor Max, bound to its DNA target site (PDB ID 1HLO). The protein is dimeric; one subunit is colored. The DNA-binding segment (pink) merges with the first helix of the helix-loop-helix (red). The second helix merges with the carboxyl-terminal end of the subunit (purple). Interaction of the carboxyl-terminal helices of the two subunits describes a coiled coil very similar to that of a leucine zipper , but with only one pair of interacting Leu residues (red side chains near the top) in this particular example. The overall structure is sometimes called a helix-loop-helix/leucine zipper motif.
