Super Secondary Structure
Beta-strands have a slight right-handed twist such that when they pack side-by-side to form a beta-sheet, the sheet has an overall left-handed curvature. Antiparallel beta-strands forming a beta-hairpin can accommodate a 90 degree change in direction known as a beta-corner. The strand on the inside of the bend often has a glycine at this position while the other strand can have a beta-bulge. The latter involves a single residue in the right-handed alpha-helical conformation which breaks the hydrogen bonding pattern of the beta-sheet. This residue can also be in the left-handed helical or bridging regions of the Ramachandran plot. Take a look at this example structure file from penicillopepsin (3APP) to examine with RasMol.
Beta-corners are observed to have a right-handed twist when viewed from the concave side.
A helix hairpin or alphaalpha-hairpin refers to the loop connecting two antiparallel alpha-helical segments. Clearly, the longer the length of the loop the greater the number of possible conformations. However, for short connections there are a limited number of conformations and for the shortest loops of two or three residues, there is only one allowed conformation. Antiparallel alpha-helices will interact generally by hydrophobic interactions between side chains at the interface. Therefore, hydrophobic amino acids have to be appropriately positioned in the amino acid sequence (one per turn of each helix) to generate a hydrophobic core. Efimov has analysed the conformations of alpha-alpha-hairpins and some of his results are summarised below.
The shortest alpha-helical connections involve two residues which are oriented approximately perpendicular to the axes of the helices. Analysis of known structures reveals that the first of these two residues adopts phi and psi angles in the bridging or alpha-helical regions of the Ramachandran plot. The second residue is always glycine and is in a region of the Ramachandran plot with positive phi which is not available to other amino acids. Here is an example structure file to look at with RasMol.
Three residue loops are also observed to have conformational preferences. The first residue occupies the bridging region of the Ramachandran plot, the second adopts the left-handed helical conformation and the last residue is in a beta-strand conformation.
Four-residue loops adopt one of two possible conformations. One is similar
to the three residue loop conformation described above except that there
is an additional residue in the beta-strand conformation at the fourth position.
The other conformation involves the four residues adopting bridging, beta,
bridging, and beta conformations, respectively.
Last updated 7th April '97