Simple combinations of a few secondary structure elements with a specific geometric arrangement are called supersecondary structures or motifs. Motif has functional and structural specificity. The simplest motif is helix-loop-helix motif. This motif has a specific function and consists of two alpha helices that joined by a short loop region. Two such motifs are: DNA-binding motif and the calcium-binding motif.
Two alpha helices that are joined by a short loop region in a specific
geometric arrangement constitute a helix-turn-helix motif.
Proteins that regulate transcription of DNA recognize specific DNA sequences through discrete DNA-binding domains within their polypeptide chains. This picture represents lambda repressor DNA binding domains contain a helix-turn-helix motif that recognizes and binds specific regulatory regions of DNA.
This helix-loop-helix motif is called the EF-hand motif (a). "EF HAND" motif
is specific for calcium binding and is present in parvalbumin, calmodulin,
troponin-C, and other proteins that bind calcium and thereby regulate cellular
activities. The middle picture (b) shows the calcium atom is bound to one of
the motifs in the muscle protein troponin-C through six oxygen atoms: one
each from the side chains of Asp (D) 9, Asn (N) 11, and Asp (D) 13; one from
the main chain of residue 15; and two from the side chain of Glu (E) 20. In
addition, a water molecule (W) is bound to the calcium atom. (c): Schematic
diagram illustrating that the structure of troponin-C is built up from four
Motif-based database search