Levels of protein structure – secondary

Protein structures are also classified by their secondary structure. Secondary structure refers to regular, local structure of the protein backbone, stabilised by intramolecular and sometimes intermolecular hydrogen bonding of amide groups.

There are two common types of secondary structure (Figure 11). The most prevalent is the alpha helix. 

The alpha helix (α-helix) has a right-handed spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues before it in the sequence.

The other common type of secondary structure is the beta strand. A Beta strand (β-strand) is a stretch of polypeptide chain, typically 3 to 10 amino acids long, with its backbone in an almost fully extended conformation. Two or more parallel or anti-parallel adjacent polypeptide chains of beta strand stabilised by hydrogen bonds form a beta sheet. For example, the proteins in silk have a beta sheet structure. Those local structures are stabilised by hydrogen bonds and connected by tight turns and loose, flexible loops.

The two common types of secondary structures
Figure 11 Alpha helix (blue) and anti-parallel beta sheet composed of three beta strands (yellow and red).

A common way for researchers to look at the conformations of amino acids in proteins is to use a Ramachandran plot (Figure 12). If successive amino acids are found in particular so-called “favourable” regions of the plot, these tend to form particular secondary structures (sheets, strands and helices). However, it should be noted that loop and turn residues are also found in these areas and it is possible to find individual amino acids in “unfavourable” regions.

A Ramachandran plot
Figure 12: Ramachandran plot generated with coordinates from the human DNA clamp PCNA, showing two regions containing the most favorable combinations of ψ and φ and contain the greatest number of data points (blue) and four allowed regions (green).

The Ramachandran plot  is a plot of the torsional angles (angles between two planes) – psi (ψ) and phi (φ) – of amino acids contained in a peptide. It is used to show the ranges of angles that are permissible and the main types of structure adopted by a polypeptide chain (for example, α helix, β sheet). By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides.