54
chapter
4 Three-Dimensional Structure of Proteins
mostly a-helix and
fi
-pleated sheet, respectively), or a
protein may have more than one kind (hemoglobin has
both a-helical and non-hydrogen-bonded regions).
Glob-
ular proteins
usually have mixed and fibrous proteins have
predominantly one kind of secondary structure.
«-Helix
The rod-shaped right-handed a-helix, one of the most
common secondary structures found in naturally occur-
ring proteins, consists of
L-a
-amino acids (Figure 4-4). In
the right-handed a-helix the helix turns counterclockwise
(C-terminal to N-terminal) and in the left-handed it turns
clockwise. The left-handed a-helix is less stable than a
right-handed a-helix because its carbonyl groups and the
R-groups are sterically hindered. The helical structure is
stabilized by intrachain hydrogen bonds involving each
-NH and -CO group of every peptide bond. These hydro-
gen bonds are parallel to the axis of the helix and form
between the amido proton of the first residue and the car-
bonyl oxygen of the fourth residue, and so on, producing
3.6 amino acid residues per turn of the helix. The rise per
residue is 0.15 nm and the length of one turn is 0.54 nm
(Figure 4-5).
In some proteins, a-helices contribute significantly to
the secondary structure (e.g., a-keratin, myoglobin, and
hemoglobin), whereas in others, their contribution may
FIGURE 4-4
Hydrogen bonds in the a-helix. (a) Each peptide group forms a hydrogen
bond with the fourth peptide group in each direction along the amino acid
chain, (b) Coiling of an amino acid chain brings peptide groups into
juxtaposition so that the hydrogen bonds shown in (a) can form. The
multiple hydrogen bonds (indicated by the three dots) stabilize the helical
configuration.
Rise per amino
acid residue
FIGURE 4-5
Average dimensions of an a-helix. Only the atoms of the a-carbon, the
carbonyl carbon and the nitrogen of the peptide bonds are shown. The rise
per residue and the length of one turn are 0.15 and 0.54 nm corresponding
to minor and major periodicity, respectively.
be small (e.g., chymotrypsin and cytochrome c) or absent
(e.g., collagen and elastin). Whether a polypeptide seg-
ment forms an a-helix depends on the particular R-groups
of the amino acid residues. Destabilization of an a-helix
may occur for a variety of reasons: electrostatic repul-
sion between similarly charged R-groups (Asp, Glu, His,
Lys, Arg); steric interactions due to bulky substitutions
on the /3-carbons of neighboring residues (lie, Thr); and
formation of side-chain hydrogen or ionic bonds. Glycine
residues can be arranged in an a-helix; however, the pre-
ferred and more stable conformation for a glycine-rich
polypeptide is the /3-pleated sheet because the R-group of
glycine (-H) is small and gives rise to a large degree of ro-
tational freedom around the a-carbon of this amino acid.
Prolyl and hydroxyprolyl residues usually create a bend
in an a-helix because their a-nitrogen atoms are located
in rigid ring structures that cannot accommodate the heli-
cal bonding angles. Moreover, they do not have an amido
hydrogen and therefore can form neither the necessary
hydrogen bond nor the usual planar peptide bond. How-
ever, some proteins such as rhodopsin do contain proline
residues embedded in a-helical segments.
In some proteins, the a-helices twist around each other
to form rope-like structures (coiled coils) to give rise to
a
supersecondary structure.
Examples of such proteins
are the a-keratins, which are major protein components of
