Protein
Secondary structure in proteins consists of local inter-residue interactions mediated by hydrogen bonds, or not. The most common secondary structures are alpha helices and beta sheets. Other helices, such as the 310 helix and π helix, are calculated to have energetically favorable hydrogen-bonding patterns but are rarely if ever observed in natural proteins except at the ends of α helices due to unfavorable backbone packing in the center of the helix. Other extended structures such as the polyproline helix and alpha sheet are rare in native state proteins but are often hypothesized as important protein folding intermediates. Tight turns and loose, flexible loops link the more "regular" secondary structure elements. The random coil is not a true secondary structure, but is the class of conformations that indicate an absence of regular secondary structure.
Amino acids vary in their ability to form the various secondary structure elements. Proline and glycine are sometimes known as "helix breakers" because they disrupt the regularity of the α helical backbone conformation; however, both have unusual conformational abilities and are commonly found in turns. Amino acids that prefer to adopt helical conformations in proteins include methionine, alanine, leucine, glutamate and lysine ("MALEK" in amino-acid 1-letter codes); by contrast, the large aromatic residues (tryptophan, tyrosine and phenylalanine) and -branched amino acids (isoleucine, valine, and threonine) prefer to adopt β-strand conformations. However, these preferences are not strong enough to produce a reliable method of predicting secondary structure from sequence alone.
There are several methods for defining protein secondary structure (e.g. DEFINE, DSSP, STRIDE (protein), SST).
| Geometry attribute | α-helix | 310 helix | π-helix |
|---|---|---|---|
| Residues per turn | 3.6 | 3.0 | 4.4 |
| Translation per residue | 1.5 Å (0.15 nm) | 2.0 Å (0.20 nm) | 1.1 Å (0.11 nm) |
| Radius of helix | 2.3 Å (0.23 nm) | 1.9 Å (0.19 nm) | 2.8 Å (0.28 nm) |
| Pitch | 5.4 Å (0.54 nm) | 6.0 Å (0.60 nm) | 4.8 Å (0.48 nm) |
Read more about this topic: Protein Secondary Structure
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