A variety of helical structures can be identified in proteins using X-ray diffraction. A helix can be described by the number of units (amino acid residues) per turn (n) and by its pitch (p), which is the distance that the helix rises along its axis per turn. These parameters are indicated in Figure 8 for a number of helices. In proteins, n is rarely a whole number.
An important point to note is that a helix has a ‘handedness’; that is, if viewed along its axis, the chain turns either in a clockwise direction (right-handed helix) or in an anticlockwise direction (left-handed helix). For example, helices (b) and (d) in Figure 8 are, respectively, right- and left-handed. By convention, the number of repeating units (n) is positive for right-handed helices and negative for lefthanded helices. A number of different helical structures have been identified in proteins. The most common is the α helix, depicted in Figure 9a with details of its conformational parameters.
The α helix was discovered by Linus Pauling in 1951, using a model-building approach. It was later identified experimentally in α-keratin, a protein component of skin, hair and nails. The α helix structure is stabilised by hydrogen bonds between peptide carbonyl groups (C=O) and the peptide amino (N–H) groups that are four residues along (Figure 9b). In this way, the full hydrogen bonding capacity of the polypeptide backbone is utilised. Note that the side-chains (R) all project outwards and backwards from the helix as it rises; thus steric interference with the backbone or with other side-chains is avoided. The helix core is tightly packed and stabilised by van der Waals interactions.
In globular proteins, a helical stretch will, on average, include 12 residues although some proteins include α helices that contain up to 50 residues.
If a 12-residue stretch of polypeptide adopts an α helix structure, how many turns will it contain and how long will it be? You can answer this question using the values for n and p for the right-handed α helix in Figure 9a.
It will contain 3.3 turns and will be 18 Å long.
Since the hydrophilic polypeptide backbone is optimally hydrogen-bonded to itself and hidden away at the core of the α helix, such regions of secondary structure are commonly seen in proteins that traverse the cell membrane, such as transmembrane receptors and transport proteins. In such cases, the side-chains, which project into the lipid environment, are typically non-polar.