DNA-binding proteins exert control by binding DNA at specific sequences. Describe how DNA and protein interact at the molecular level

Question

Are proteins able to identify specific DNA sequences, or do they bind to all regions with equal frequency? What motifs are commonly found in DNA-binding proteins?

Answer 1

DNA-protein interactions occur when the amino acid side chains of the proteins interact with the specific nucleotide bases and the sugar-phosphate backbone of DNA. The proteins make their contact with specific base pairs located in the major groove and the minor groove of the DNA helix using a unique pattern of hydrogen, nitrogen, and oxygen atoms that characterize each base pair. To achieve protein-DNA specificity in these interactions, the protein must simultaneously contact multiple nucleotides.
Protein secondary structures are a common motif in the structures of DNA-binding regulatory proteins, particularly α-helices.
Bacterial regulatory DNA sequences frequently contain inverted repeats or direct repeats, and proteins often interact with one of the inverted repeat segments. By far, the most common structural motif in these proteins in bacteria is the helix-turn-helix (HTH) motif. In the HTH motif, two α-helical regions in each of two polypeptides in a homodimer interact with inverted repeat regulatory sequences in DNA. In each of the polypeptides, one α-helical region forms the recognition helix that fits into the major groove of DNA and binds the inverted repeat sequences. This is connected to a short string of amino acids forming the "turn," which is connected to a second α-helical region known as the stabilizing helix. The stabilizing helix lies across the major groove and contacts the sugar-phosphate backbone, ensuring a strong DNA-protein interaction and properly orienting the recognition helix to sit in the major groove.