section
4.3
Secondary Structure
53
distance in this case is even greater (1 /r12). These repul-
sive forces operate when atoms not bonded to each other
approach more closely than the sum of their atomic radii
and are the underlying forces in steric hindrance between
atoms.
4.2 Primary Structure
Peptide Bond
Peptide bonds have a planar trans configuration and un-
dergo very little rotation or twisting around the amide bond
that links the a-amino nitrogen of one amino acid to the
carbonyl carbon of the next (Figure 4-2). This effect is due
to amido-imido tautomerization. The partial double-bond
character of the N-C bond in the transition state prob-
ably best represents what exists in nature. Electrons are
shared by the nitrogen and oxygen atoms, and the N-C and
C-O bonds are both (roughly) “one-and-one-half” bonds
(intermediate between single and double). The short car-
bonyl carbon-nitrogen bond length, 0.132 nm (the usual
carbon-nitrogen single bond length is 0.147 nm), is consis-
tent with the partial double-bond character of the peptide
linkage. The planarity and rigidity of the peptide bond are
accounted for by the fact that free rotation cannot occur
around double bonds.
Whereas most peptide bonds exist in the trans config-
uration to keep the side chains (R-groups) as far apart as
possible, the peptide bond that involves the -NH group
of the rigid pyrrolidone ring of proline can occur in both
trans and cis arrangements (Figure 4-3). However, x-ray
data suggest that the trans form occurs more frequently
in proteins than does the cis form. It has been further
postulated that some proline residues (known as “permis-
sive” proline residues) can exist in either the cis or trans
configuration. For example, of the four proline residues of
Peptide group in
a planar
trans
FIGURE 4-2
Geometry of a peptide (amide) linkage. For the peptide bond, bond angles
and bond lengths indicate that carbon-nitrogen bonds have a significant
amount of double-bond character and that the C, O, N, and H atoms all lie
in the same plane. The
<p
and
ijr
refer to rotations about the single bonds
connecting the «-carbon with the «-nitrogen and the «-carbonyl carbon,
respectively.
I'
'HN
CH
,CH — CH2
\
/
I
c —
n:
ah
o
CH— c o -
Proline
residue
trans
bond
involving proline
Ri
H-IN— CH
O
,C—N
/
\
CH—CO—
CH— CH2
Proline
residue
cis
bond
involving proline
FIGURE 4-3
The trans and cis configurations of peptide bonds involving proline.
ribonucléase A, at least two are thought to be in the trans
configuration in order to form a native structure, whereas
one or both of the other residues may be accommodated
in either the cis or trans configuration.
The bonds on either side of the «-carbon (i.e., between
the a-carbon and the nitrogen, and between the «-carbon
and the carbonyl carbon) are strictly single bonds.
Rotation is possible around these single bonds. The des-
ignation for the angle of rotation of the a-carbon-nitrogen
bond is
4>
,
whereas that of the a-carbon-carbonyl carbon
bond is
tfr.
Although theoretically an infinite number of
<
f>
and
1
// angles are possible around single bonds, only a
limited number of
<p
and
x[r
angles are actually possible in
proteins. A polypeptide has specific
rj>
and i// values for
each residue that determines its conformation.
4.3 Secondary Structure
The folding of polypeptide chains into ordered struc-
tures maintained by repetitive hydrogen bonding is called
secondary structure.
The chemical nature and structures of
proteins were first described by Linus Pauling and Robert
Corey who used both fundamental chemical principles
and experimental observations to elucidate the secondary
structures. The most common types of secondary struc-
ture are the right-handed
a-helix,
parallel and antiparallel
/
3-pleated sheets,
and
(3-turns.
The absence of repetitive
hydrogen-bonded regions (sometimes erroneously called
“random coil”) may also be part of secondary structure. A
protein may possess predominantly one kind of secondary
structure (a-keratin of hair and fibroin of silk contain
