1.3 Protein secondary structure
From our consideration of the steric constraints that apply to peptide bonds and amino acid residues in a polypeptide, we have already begun to discuss some of the factors that determine how the backbone of the polypeptide folds. The conformation adopted by the polypeptide backbone of a protein is referred to as secondary structure. Whilst it is true to say that all proteins have a unique three-dimensional structure or conformation, specified by the nature and sequence of their amino acids, there are certain structural elements, or types of secondary structure, that can be readily recognised in many different proteins. These secondary structural elements include helices, pleated sheets and turns.
Table 2 Torsion angles, ɸ and ψ, for some secondary structures.
| Secondary structure | ɸ / deg | ψ; / deg |
|---|---|---|
| right-handed α helix | –57 | –47 |
| parallel β sheet | –119 | 113 |
| antiparallel β sheet | –139 | 135 |
As well as conforming to allowed torsion angles for component residues, secondary structures are stabilised by non-covalent interactions between atoms and groups in the polypeptide, namely hydrogen bonds and van der Waals forces. The polypeptide may fold and turn many times, and such interactions are often between residues some distance apart in terms of the primary structure.
Roughly half of an average globular protein consists of regular repetitive secondary structures (helices and pleated sheet) whilst the remainder has an irregular so-called coil or loop conformation.