(Logo) Super Secondary Structure


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Secondary structure elements are observed to combine in specific geometric arrrangements known as motifs or supersecondary structures. In this section we will look at motifs consisting of no more than three secondary structure elements. Larger motifs such as the greek key will be examined in the sections on tertiary structure and protein folds.


Beta-hairpins are one of the simplest supersecondary structures and are widespread in globular proteins. They occur as the short loop regions between antiparallel hydrogen bonded beta-strands. In general a reverse turn (or beta-turn, as it they are sometimes called) is any region of a protein where there is a hydrogen bond involving the carbonyl of residue i and the NH group of residue i+3. An alternative definition states that the alpha-carbons of residues i and i+3 must be within 7.0 Angstroms. The structures of reverse turns are outlined in the section on peptide geometry. In this section we will concentrate on those turns which occur between consecutive beta-strands, known as beta-hairpins. Sibanda and Thornton have devised a system for classifying beta-hairpins which is based on two conventions for defining loop regions. In this section we will not go into such details as the objective is indicate the most commonly observed hairpin loop structures.

Beta-hairpin loops adopt specific conformations which depend on their lengths and sequences. Sibanda and Thornton have shown that 70% of beta-hairpins are less than 7 residues in length with the two-residue turns forming the most noticeable component. These two-residue beta-hairpins all adopt one of the classical reverse turn conformations with an obvious preference for types I' and II'. Type I 2-residue hairpins also occur but with lower abundance. This contrasts with reverse turns where types I and II tend to dominate. In beta-hairpins the type I' turn has the correct twist to match the twist of the beta-sheet and modelling studies indicated that if either type I or type II turns were to connect the antiparallel beta-strands, they would diverge within a short distance from the turn.

Two-residue beta-hairpins

  1. Type I'.The first residue in this turn adopts the left-handed alpha-helical conformation and therefore shows preference for glycine, asparagine or aspartate. These residues can adopt conformations with positive phi angles due to the absence of a side chain with glycine and because of hydrogen bonds between the side chain and main chain in the case of asparagine or aspartate. The second residue of a type I' turn is nearly always glycine as the required phi and psi angles are well outside the allowed regions of the Ramachandran plot for amino acids with side chains. Were another type of amino acid to occur here there would be steric hindrance between its side chain and the carbonyl oxygen of the preceding residue.

  2. Type II'. The first residue of these turns has a conformation which can only be adopted by glycine (see below Ramachandran plot). The second residue shows a preference for polar amino acids such as serine and threonine.

  3. Type I. Both residues of these turns adopt alpha-helical conformations.

j.cooper 26/1/95

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Last updated 31st May '96