1.4.1 Motifs and supersecondary structures
Supersecondary structures or motifs are particular arrangements and combinations of two or three secondary structures, often with defined topology (or connectivity).describes some of the most common of these.
The term ‘motif’ is also used to describe a consensus sequence of amino acids, i.e. a partial sequence common to a number of different proteins, which may or may not adopt similar conformations in the different proteins.
The coiled-coil structure, in which α helices wrap around each other, is found in some structural proteins, such as myosin and α-keratin. The α helices have a strip of non-polar side-chains along one side, and formation of the coiled-coil is driven by interactions between these residues on the two α helices, causing them to twist around each other. In this way, the hydrophobic residues are buried and the hydrophilic groups extend into the aqueous environment. Although the specific amino acid sequences of myosin and α-keratin are quite different, in each case we can identify patterns of hydrophobic and hydrophilic residues in the linear sequence, which specify the coiled-coil conformation.
Table 3 describes two different motifs that have been identified in DNA or RNA binding proteins and which interact directly with the nucleic acid. The helix–turn–helix motif is one of the most common DNA-binding motifs. The C-terminal helix fits into the major groove of the DNA and its side-chains interact with the nucleotides in a sequence-specific manner. Thus different DNA-binding proteins will recognise different DNA sequences depending on the amino acid side-chains presented by this helix. The zinc finger motif is another motif commonly found in proteins that bind RNA and DNA. This finger-like structure consists of an α helix and two short antiparallel β strands all held together by a zinc ion, coordinated between two conserved cysteine and two histidine side-chains. Some forms of zinc finger have four cysteine residues bound to the zinc ion. This motif can be repeated many times in a DNA binding protein, with each finger folding independently. It is amino acids in the α helix that interact with the major groove of the DNA duplex. A third DNA-binding motif, not shown in Table 3, is the leucine zipper. In this motif, two identical subunits interact via α helices, forming a short stretch of coiled-coil. The interaction is mediated by hydrophobic interactions between side-chains, notably those of leucine residues.