5.0 Helix supersecondary structures

These structures are formed from combinations of two or more helices and the strands connecting them. Structures 5.1 to 5.4 may all be considered to be subclasses of a 'helix-loop-helix' supersecondary structure. The distinction between a 'loop' and a 'turn' may not always be clear, and the length of the connecting strand between helices may not always make a good discriminator. Consequently, the structures are usually defined more by the orientation of the helices to each other and their biological roles. The 'helix-loop-helix' supersecondary structures are found frequently in proteins and some have important biological functions.

5.1 Helix hairpins

• As the name suggests this is 'looks like' a hairpin and is similar to a beta hairpin except that the hairpin is delimited by antiparallel helices and not beta strands as shown in Figure 5.0

• The helices in the hairpin can be connected by two or more residues. The more residues connecting the helices the more conformations allowed.

• If short strands connect helices then the individual helices will pack together through their hydrophobic residues (remember the amphilicity of helices earlier).

• The function of a helix hairpin is unknown but two helix hairpins can contribute to a four helix bundle (see below) and these have important ligand binding sites.

5.2 Helix Corner

• Figure 5.1 shows that the helices almost at right angles to each other and connected by a short 'loop'. Also known as alpha-alpha corner

• The corner in the 'loop' is formed from a hydrophobic residue sandwiched between the two helices

• No known function

5.3 Helix-loop-helix

• This secondary structure is seen frequently and the 'loop' term is usually reserved for those structures which are seen to bind ligands such as calcium. An example of this structure is seen in parvalbumin (Figure 5.2), a muscle protein which contains three helix-loop-helix motifs - two of which bind calcium.

• Figure 5.3 shows (if you manipulate the image) the motif in parvalbumin.

• Calcium binds with the carboxyl groups of the side chains within the loop region and between the two helices.

• Parvalbumin has six helices labeled A to F and the helix-loop-helix motif is also known as the 'E-F Hand', because these were the helices first used to show this motif.

5.4 Helix-turn-helix

• The helix-turn-helix has an important biological role in binding DNA. Consequently, this motif is often seen in many DNA binding proteins Figure 5.4

• Figure 5.5 shows the motif complexed with DNA.

• The method of protein binding to DNA is informative and you should take some time to study the interactions (refer to the references and your text).