In order to understand the overall structure of proteins it is necessary to go beyond the amino acid sequence or primary structure of the polypeptide chain and consider the higher degrees of order that lead to the final functional (or disfunctional) structure.
Polypeptide chains can in principle become folded into a huge number of structures, however most commonly a few structural motifs are repeated more or less the same way in all proteins. When looking at most protein structures it is possible to distinguish these motifs as sections of the polypeptide chain with a common arrangement that extends over a number of residues (sometimes tens to hundreds of residues can be involved in one secondary structural element).
These sections of polypeptide chain display no obvious ordering and therefore have the appearance of being truly random sequences. However, loops such as these (which may contain large numbers of residues and be quite long) usually form functional structures within proteins where they are commonly found connecting two sections of polypeptide chain that display more permanent structures with higher degrees of order such as the α-helix and β-sheet, below. As 'simple' linkers these loops can permit the more rigid orderly structures that are connected to them to more relative to one another which can be key in controlling the activity of functional proteins such as enzymes. This ability to rearrange the relative positions of protein subunits may be important in structural proteins where recognition of and binding to other proteins or macromolecular structures is required. Similarly, flexible loops can themselves move so as to open or close the entrance to a functional site on a protein in response to external stimuli and so make the protein only active under certain conditions.
Often, the flexibility of these loops means that they are poorly resolved (if at all) in X-ray crystallography studies and so may be missing in protein crystal structures.
The first of the more highly ordered structural features to be discovered was a right-handed helical arrangement of residues similar in appearance to a telephone cable. The α-helix is particularly stable since it contains a large number of hydrogen bonds between the turns of the helical structure (thin blue lines in the figure below). The α-helix is defined by a repeat distance of 540 pm and each turn contains 3.6 residues.
A common protein that is composed solely of α-helical structures is α-keratin which is the structural protein that impart strength to hair, nails, wool and feathers. A section of α-keratin is shown below minus its side chains and hydrogen atoms for clarity.
The second main structural element found in the secondary structure of proteins is the β-sheet. This type of structure involves hydrogen bonding between residues from two or more polypeptide units that may or may not be part of the same polypeptide chain. Rather than the helical arrangement seen above, these sections of polypeptide chain are fully extended so that if the two sections are part of the same chain then the polypeptide has to fold back on itself in order to create this structure.
Less common than the α-helix, the β-sheet is still an important structural motif and is found in many fibrous proteins such as fibroin (obtained from silk fibres). The individual strands of the β-sheet may be arranged parallel or antiparallel. The latter is most common when two strands on either side of a short fold in the protein chain come together to form a β-sheet structure which acts to stabilise the fold.
A backbone diagram of a β-sheet from fibroin is shown below, again with hydrogen bonds indicated by blue lines.