3.0 Types of Secondary Structure

3.4 Other

Approximately 80-90% of residues in globular proteins can be classified as participating in an alpha helix, beta sheet, or reverse turn. Exact numbers are difficult since defining the secondary structures themselves is a bit of a problem and will differ from survey to survey. However, a number of other secondary structures have been proposed and will be briefly mentioned below. Even though structural characterization of these non-regular polypeptide segments is difficult, remember that most (>90%) potential backbone hydrogen bond donors and acceptors are involved in hydrogen bonds in solution (46% of C=O and 68% of NH groups are involved in backbone-backbone hydrogen bonds and 15% and 10%, respectively involve sidechain atoms; Baker & Hubbard, 1984).

Loops

Leszczynski & Rose (1986) found a type of loop structure in what was previously classified as "random" conformation. In their survey of 67 proteins, they tabulated 26% Helix, 19% sheet, 26% turns and 21% in loops. These loop structures contain between 6 and 16 residues and are compact and globular in structure. Like turns, they generally contain polar residues and hence are predominantly at the protein surface.

Paperclips

Milner-White (1988) has extended the classification of helical C-terminal "caps" (see also Figure 3.1.4.1 ) in his identification of "paperclips". These paperclips occur frequently (in over half the proteins in the presented study), but not exclusively at helix C-termini and can be grouped into two classes based on the number of residues at the loop end. The type shown in Figure 18 A is by far the most common. Glycine occurs very often in position 5 in the paperclip presented in Figure 18 A since a residue at this position must adopt a left-handed helical conformation.

Figure 18. Hydrogen bond patterns in "paperclips". The dotted lines indicate hydrogen bonds between donor and acceptor atoms (e.g., in A, the carbonyl oxygen of residue 1 and the amide nitrogen of residue 6). This figure is redrawn from Milner-White (1988).

Loops
Paperclips

No Title - 31 MAY 96

written by Kurt D. Berndt

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