Protein structure - Pharmaceutical Biotechnology: Concepts and Aapplications - page 25

if the polypeptide has a commercial application. In some cases a polypeptide can be ob-
tained in suffi cient quantities by direct extraction from its natural producer source. However,
polypeptides may also be produced by direct chemical synthesis, as long as their amino acid
sequence (and any PTMs) has been elucidated. Synthesis can be undertaken via a biologi-
cal route (recombinant DNA technology), as is the case for virtually all modern therapeutic
proteins.

2.3 Higher level structure

Thus far we have concentrated on the primary structure (amino acid sequence) of a polypeptide.
Higher level protein structure can be described at various levels, i.e. secondary, tertiary and qua-
ternary:

• Secondary structure can be described as the local spatial conformation of a polypeptide's back-

bone, excluding the constituent amino acid's side chains. The major elements of secondary
structure are the α-helix and β-strands, as described below.

• Tertiary structure refers to the three-dimensional arrangement of all the atoms that contribute

to the polypeptide.

• Quaternary structure refers to the overall spatial arrangement of polypeptide subunits within a

protein composed of two or more polypeptides.

2.3.1 Secondary structure

By studying the backbone of most proteins, stretches of amino acids that adopt a regular, recur-
ring shape usually become evident. The most commonly observed secondary structural elements
are termed the

-strands, which are usually separated by stretches largely devoid of
regular, recurring conformation. The α-helix and β-sheets are commonly formed because they
maximize formation of stabilizing intramolecular hydrogen bonds and minimize steric repulsion
between adjacent side chain groups, while also being compatible with the rigid planar nature of
the peptide bonds.
The α-helix contains 3.6 amino acid residues in a full turn ( Figure 2.5). This approximates
to a length of 0.56 nm along the long axis of the helix. The participating amino acid side chains
protrude outward from the helical backbone. Amino acids most conducive with α-helix formation
include alanine, leucine, methionine and glutamate. Proline, as well as the occurrence in close
proximity of multiple residues with either bulky side groups or side groups of the same charge,
tends to disrupt

α -helix and β

-helical formation. The helical structure is stabilized by hydrogen bonding, with
every backbone C= O group forming a hydrogen bond with the N—H group four residues ahead of
it in the helix. Stretches of

α

-helix found in globular (i.e. tightly folded, approximately spherical)
polypeptides can vary in length from a single helical turn to greater than 10 consecutive helical
turns. The average length is about three turns.

α