Chemistry Reference
In-Depth Information
, which would
avoid steric collisions either between atoms in different peptide groups or between a peptide unit and the side
chains attached to C
The Indian biophysicist G.N. Ramachandran made calculations of the allowed values of
f
and
j
in
Figure 3.7
b is called a Ram-
achandran plot, and it is clear that only a few regions of the diagram are sterically allowed. The areas corre-
sponding to right-handed
. The representation of the allowed values of
f
and
j
a
-helices are indicated, as are a number of other
secondary structures. Observed values for all amino acid residues, except glycine in well refined X-ray structures
of proteins which have been determined to high resolution and the observed values for Gly residues in these same
proteins, are shown in the two panels of
Figure 3.8
.
This underlines the remark made earlier that Gly plays a
a
-helices,
b
-strands, and left-handed
a
FIGURE 3.8
(a) Observed values for
f
and
j
angles in protein structures for all residues except Gly (b) observed values for Gly.
(From
Branden & Tooze, 1991
.
Reproduced with permission from Garland Publishing, Inc.)
structurally important role, by allowing unusual main chain conformations. This may explain why a high
proportion of Gly residues in homologous protein sequences are conserved.
The simplest way to create a local ordered structure within a polypeptide chain made up of amide linkages
would be to form hydrogen bonds between residues whichareclosetooneanotherintheaminoacid
sequence. As seen from
Figure 3.9
, this would involve either the second, third, fourth, or fifth NH group from
the C
O of the first amino acid residue. In the 2.2
7
ribbon description, 2.2 refers to the number of residues
per turn and the subscript 7 to the number of atoms between the main chain carbonyl oxygen and the amide
]
1
2
13
16
5
6
9
8
11
12
4
14
15
3
7
10
7
10
13
16
2.2
7
ribbon
3
10
helix
α
helix
π
helix
FIGURE 3.9
The hydrogen-bonding pattern of several polypeptide helices. The polypeptide chain is helically wound such that the N
e
H
group on residue n forms a hydrogen bond with the C
]
O bond on residues n
2, n
3, n
4orn
5.
