Protein structure - Pharmaceutical Biotechnology: Concepts and Aapplications - page 29

2.4 Protein stability and folding

Upon biosynthesis, a polypeptide folds into its native conformation, which is structurally s ta-
ble and functionally active. The conformation adopted ultimately depends upon the polypep-
tide's amino acid sequence, explaining why different polypeptide types have different char-
acteristic conformations. We have previously noted that stretches of secondary structure are
stabilized by short-range interactions between adjacent amino acid residues. Tertiary struc-
ture, on the other hand, is stabilized by interactions between amino acid residues that may
be far apart from each other in terms of amino acid sequence, but which are brought into
close proximity by protein folding. The major stabilizing forces of a polypeptide's overall
conformation are:

• hydrophobic interactions

• electrostatic attractions

• covalent linkages.

Hydrophobic interactions are the single most important stabilizing infl uence of protein native
structure. The 'hydrophobic effect' refers to the tendency of non-polar substances to minimize
contact with a polar solvent such as water. Non-polar amino acid residues constitute a signifi cant
proportion of the primary sequence of virtually all polypeptides. These polypeptides will fold
in such a way as to maximize the number of such non-polar residue side chains buried in the
polypeptide's interior, i.e. away from the surrounding aqueous environment. This situation is most
energetically favourable.
Stabilizing electrostatic interactions include van der Waals forces (which are relatively weak),
hydrogen bonds and ionic interactions. Although nowhere near as strong as covalent linkages
( Table 2.5), the large number of such interactions existing within a polypeptide renders them col-
lectively quite strong.
Although polypeptides display extensive networks of intramolecular hydrogen bonds, such
bonds do not contribute very signifi cantly to overall conformational stability. This is because
atoms hydrogen bonding with each other in a folded polypeptide can form energetically equivalent
hydrogen bonds with water molecules if the polypeptide is in the unfolded state. Ionic attractions
between (oppositely) charged amino acid side chains also contribute modestly to overall protein
conformational stability. Such linkages are termed salt bridges, and, as one would expect, they are
located primarily on the polypeptide surface.

Table 2.5 Approximate bond energies associated with various (non-covalent)
electrostatic interactions, compared with a carbon-carbon single bond

Bond type Bond strength (kJ mol 1 )

Van der Waals forces 10

Hydrogen bond 20

Ionic interactions 86

Carbon-carbon bond 350