Chemistry Reference
In-Depth Information
structure of the protein consists of local regular structures stabilised by hydrogen bonds involving the amide
backbone of the polypeptide chain, such as
a
-helices,
b
-pleated sheets, and reverse turns. The tertiary
structureisformedbythepackingofsuchstructuralelements into one or more compact globular units, often
referred to as either supersecondary structures or domains. This compact structure is described by the three-
dimensional localisation of all atoms of the protein's amino acid sequence, both main chain and side
chains. This often brings together amino acid residues which are far apart in the primary structure to form
a functional region, known as the active site. Some proteins, like haemoglobin, illustrated in
Figure 3.6
,
contain several polypeptide chains, each with their individual
tertiary structure, arranged together in
a quaternary structure.
When Linus Pauling and Robert Corey carried out their pioneering X-ray crystallographic studies on a number
of amino acids and dipeptides in the 1930s and 40s, they arrived at three very important conclusions and
constraints: (i) the most important constraint was that all six atoms of the amide (or peptide) group lie in the same
plane. Pauling had predicted planar peptide bonds because of resonance of electrons between the double bond of
the carbonyl group and the amide C
e
N bond of the peptide bond, which results in partial double bond character in
the C
O bond, (ii) the peptide bond is usually trans, and
(iii) the maximum amount of hydrogen bonding potential is realised between amide functions. Since the peptide
units are essentially rigid structures, linked by covalent bonds at the
e
N bond and partial single-bond character of the C
]
a
-carbons, the only degree of freedom that
they have are the rotations around these bonds
e
defined by the angles phi (
f
) around the N
e
C
a
bond and psi (
j
)
around the C
a
e
f
and
j
for each amino acid, we can describe the
conformation of the main chain of the protein.
FIGURE 3.7
(a) Diagram of a polypeptide chain with the peptide units represented as rigid structures showing the conformational angles
f
and
j
(Adapted from
Voet & Voet, 2004.)
by conventional mathematical signs for parallel and antiparallel as in
Figure 3.7
b
. (b) a Ramachandran plot,
showing the sterically allowed angles for
f
and
j
. The regular conformations of polypeptides are
a
R
, right-handed
a
-helix;
a
L
,left-handed
a
-helix;
B
, antiparallel
b
-sheet;
C
,parallel
b
-sheet; R, right-handed 3
10
helix;
p
, right-handed
p
-helix;
D
, polyPro.
