Question

Illustrate and describe the four different motifs used to bind proteins with DNA.

Answer 1

Question:

Illustrate and describe the four different motifs used to bind proteins with DNA.

Answer:

For any genomic action in cells, there needs interactions between DNA and proteins and not all proteins can interact with DNA, as the DNA binding proteins should DNA-binding region that could recognize specific sequences to bring genomic actions.

These could be Transcription factors, Polymerases, Nucleases or Nuclear receptors (Androgen, Estrogen or Progesterone receptors)

Binding of the above-said factors brings about conformational changes in the protein and DNA.

There are 4 major motifs

1. Helix-turn-helix (HTH) motif
2. Helix-loop-helix (HLH) motif
3. Zinc fingers (ZnFs) motif
4. Basic region-leucine zippers

1. Helix-turn-helix (HTH) motif

          It is an approximately 20 amino acid in length and is formed of 2 helices that are connected by a short turn. The first helix is involved in stabilization of the motif, and the second helix is responsible for sequence-specific recognition at the major groove of the DNA. On an average the DNA-protein interaction belonging to this motif can be 10-20 interactions involving different kinds of amino acid residues in that protein. Example: Homeobox domains

2. Helix-loop-helix (HLH) motif

          This motif bearing transcription factors contains two regions that include highly conserved basic DNA-binding region and two amphipathic helices connected by a loop, hence the name. The basic region with N-terminal region binds to the DNA at its major groove, and the C-terminal region helps in dimerization of the protein interacting with DNA that brings about genomics actions in cell. Example: MYC

3. Zinc fingers (ZnFs) motif

          This motif contains different types of domains and is usually seen in eukaryotic transcription factors. It is approximately 30 amino acid domains where the alpha-helix binds to the major groove of the DNA. Here the Zinc is involved in bringing structural functions and is coordinated by four or two cysteine and two histidine residues. Example: Nuclear receptors (Androgen, Estrogen or Progesterone receptors)

4. Basic region-leucine zippers

          Leucine zipper domain consists of a basic region that specifically recognizes DNA sequences and an alpha-helix which is a leucine zipper having a stretch of leucines that are spaced seven residues apart capable of dimerization. Dimers of leucine zipper bind to inverted repeat sequences. Examples: c-fos, jun and CREB