Question

• Describe in molecular detail DNA-Protein interactions including the various protein motifs observed in both Eukaryotes and Prokaryotes
• DNA-binding helix (helix-turn-helix motif)
• Trp and met repressor binding
• Zinc fingers
• Leucine Zippers

Answer 1

Molecular recognition in biology generally relies on an exact fit between the surfaces of two molecules, and the study of gene regulatory proteins has provided some of the clearest examples of this principle.

A gene regulatory protein recognizes a specific DNA sequence because the surface of the protein is extensively complementary to the special surface features of the double helix in that region. In most cases the protein makes a large number of contacts with the DNA, involving hydrogen bonds, ionic bonds, and hydrophobic interactions.

Although each individual contact is weak, the 20 or so contacts that are typically formed at the protein-DNA interface add together to ensure that the interaction is both highly specific and very strong.

Although each example of protein-DNA recognition is unique in detail, x-ray crystallographic and NMR spectroscopic studies of several hundred gene regulatory proteins have revealed that many of the proteins contain one or another of a small set of DNA-binding structural motifs.

These motifs generally use either α helices or β sheets to bind to the major groove of DNA; this groove, as we have seen, contains sufficient information to distinguish one DNA sequence from any other. The fit is so good that it has been suggested that the dimensions of the basic structural units of nucleic acids and proteins evolved together to permit these molecules to interlock.

The first DNA-binding protein motif to be recognized was the helix-turn-helix. Originally identified in bacterial proteins, this motif has since been found in hundreds of DNA-binding proteins from both eucaryotes and procaryotes. It is constructed from two α helices connected by a short extended chain of amino acids, which constitutes the “turn”.

. The two helices are held at a fixed angle, primarily through interactions between the two helices. The more C-terminal helix is called the recognition helix because it fits into the major groove of DNA; its amino acid side chains, which differ from protein to protein, play an important part in recognizing the specific DNA sequence to which the protein binds.