Despite the flexibility of the peptide chain, most proteins do not
assume random conformations in solution. Contrariwise, the conformation
mostly is highly ordered, and some higher levels of structural organization
are distinguished, i.e., secondary, tertiary, and quaternary structures.
7.1.3 Secondary Structure
This concerns fairly regular arrangements of adjacent amino acid residues.
Several types exist, but the most common ones area-helices andb-strands.
In the right-handeda-helix, the peptide chain forms a helix (like a cork
screw) with the side groups on the outside, where each turn takes 3.6
residues (18 residues making 5 turns); the translation of the helix is 0.15 nm
per residue (i.e., a pitch of 0.54 nm per turn), compared to 0.36 nm per
residue for a stretched chain (Figure 7.2). The helical conformation is
stabilized by H-bonds, between the O of peptide bondiand the NH of
peptide bond iþ4. Moreover, enhanced van der Waals attraction is
involved. The possibility for the latter to occur varies among amino acid
residues, which means that not all of them readily partake in ana-helix. Ala,
Glu, Phe, His, Ile, Leu, Met, Gln, Val, and Trp have strong tendencies to
form helices, whereas Pro, owing to its cyclic structure, is a ‘‘helix breaker.’’
The formation of an a-helix is a clear example of acooperative
transition. Although each of the bonds involved is weak, at most a few times
kBT, the collective bond energy of the whole structure may be sufficient to
FIGURE7.2 Bond angles and lengths (A ̊) and rotational freedom in the peptide
unit.