Protein Structure and its Classification - Essays in Bioinformatics - page 105

Figure 12. Topology diagrams of common supersecondary structures described in
the text. a) β -hairpin. b) α-hairpin. c) βαβ-unit d) Greek-key e) αβ-Greek-Key

3.3 Greek Key

Two common extended supersecondary structures have been classified: the β 4 Greek key
[37] and the

αβ Greek key [38]. The classic β 4 Greek key motif illustrated in figure 12d

consists of four adjacent anti-parallel -hairpins that need not

belong to the same sheet. There are 24 ways in which to arrange a four stranded β -sheet
however only eight of these were found in a survey of known structures in 1991 [39], five
of which were arranged with all the strands anti-parallel. The Greek key motif is the
topological signature of

β -strands comprising two β

β -barrels and β sandwiches, which are the two most prevalent β -

folds (section 6). A variation is the -Greek Key (Figure 12e) in which strand 2 is

replaced by a α -helix and the three β -strands are part of the same β -sheet.

αβ

3.4 Larger Loops

Many supersecondary structures have specific functions for example a helix-loop-helix
motif specific for DNA binding is found in many prokaryotic and eukaryotic transcription
factors. A similar motif, the EF hand, is found in calcium-binding proteins such as
calmodulin, troponin C and parvalbumin (figure 13 b), [40]. The two -helices of the EF

hand are approximately perpendicular with a connecting loop containing 12 residues. Four
or five loop residues have oxygen containing side chains, preferably aspartate or glutamate
that coordinate with a calcium ion.

α