What is Secondary structure? — Biology

Definition 12.5 University Biology — Year 1 · Chapter 12 — Amino Acids and Proteins

The secondary structure of a protein is the local, regular folding of its backbone, held by hydrogen bonds between backbone C=O and N–H groups. Two patterns dominate. The $\alpha$ helix: a right-handed coil of 3.6 residues per turn, rising $0.15\,\mathrm{nm}$ per residue ( $0.54\,\mathrm{nm}$ per turn), each C=O bonded to the N–H four residues ahead, with the side chains pointing outward. The $\beta$ sheet: chains stretched almost fully ( $0.35\,\mathrm{nm}$ per residue) and laid side by side, parallel or antiparallel, bonded between neighbouring strands, with side chains alternating above and below the sheet. Between them, turns and loops reverse the chain’s direction. Proline, whose ring locks $\phi$ , breaks helices; glycine, with no side chain, allows turns that no other residue can make.

The Ramachandran plot: the combinations of and that a residue can adopt. Two large allowed regions correspond to the sheet and the right-handed helix; most of the plane is forbidden by collisions between atoms. — The Ramachandran plot: the combinations of $\phi$ and $\psi$ that a residue can adopt. Two large allowed regions correspond to the $\beta$ sheet and the right-handed $\alpha$ helix; most of the plane is forbidden by collisions between atoms.

Linus Pauling (1901–1994), who deduced the helix and the sheet in 1951 from the planarity of the peptide bond and the geometry of hydrogen bonds, before either had been seen in a protein. Photograph: Nobel Foundation, 1962, public domain. — Linus Pauling (1901–1994), who deduced the $\alpha$ helix and the $\beta$ sheet in 1951 from the planarity of the peptide bond and the geometry of hydrogen bonds, before either had been seen in a protein. Photograph: Nobel Foundation, 1962, public domain.

Examples

Example 12.6 (Helix and sheet by the numbers)

A membrane-spanning $\alpha$ helix must cross $3\,\mathrm{nm}$ of hydrophobic core: $3/0.15 = 20$ residues, and indeed the transmembrane segments of Chapter 7 are runs of about twenty hydrophobic residues. A $\beta$ strand of the same length spans $7\,\mathrm{nm}$ : silk fibroin is stacked antiparallel sheets of glycine and alanine, and a silk thread is stronger than steel of the same weight because the covalent backbones lie along the fibre.

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Examples

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