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In-Depth Information
2. Secondary structure
Secondary structures are stretches of the polypeptide where all the
ϕ
angles are similar so that successive residues have almost identical orientations relative to
each other. There are two highly populated regions of
φϕ
space, one near -60
o
, -40
o
, and
the other near -120
o
, +135
o
that correspond to the conformation of residues in
φ
angles and all the
α
-helices and
β
-strands respectively (the patterned areas in the Ramachandran map). These are the most
common secondary structures, usually forming the interior of the molecule and spanning its
diameter to be joined by turns and loops that are generally exposed at the surface.
2.1 Helices
A regular protein helix can be described by the rise per residue (d), the number of residues
per turn (n) and the radius
.
The helix is stabilized by hydrogen bonding between the amide
hydrogen of residue i and the carbonyl oxygen of residue i+n [7]. Table 1 describes the
parameters of the three main types of helix found in proteins.
Table 1. Parameters of protein helices
Structure
φ and ϕ angles
n
d
r
-60 -40
+3.6
1.5
2.3
α
-helix
3
10
helix
-60 -60
+3.0
2.0
1.9
Polyproline II
-75 145
-3.0
2.9
1.6
-helix, postulated by Pauling and Cory in 1951 [3],
was confirmed in the same year in the first crystal structure of haemoglobin [8]. The
Alpha-Helix The right-handed
α
-
helix, with 3.6 residues per turn and a hydrogen bond between the i and the i+4 residues
(figure 5b), is one of the most abundant secondary structure found in proteins, reflecting its
high stability due to well-aligned hydrogen bond dipoles and a radius small enough to allow
Van der Waals attraction across the helix axis. Alpha-helices in globular proteins can vary
in length from four to more than forty residues with an average length of 10 residues in
soluble proteins. They generally form straight rods although packing constraints and the
incorporation of proline will cause bends and kinks. Figure 5a illustrates the effect of
proline 37 on helix B in horse heart myoglobin. The ab-initio prediction of
α
-helices from
amino acid sequence is difficult since all the sidechains except proline have little effect on
the helix backbone. For L-amino acids, left-handed
α
-helices are energetically less
favourable than the right-handed variety due to packing constraints. However short sections
are found; for example there is one turn of left-handed
α
α
helix formed by residues 226-229
in thermolysin [9].
3
10
Helix The 3
10
helix has internal hydrogen bonds between residues i and i+3
which are not as well aligned as those in the
-helix. Moreover its smaller radius leads to
more strain due to unfavourable side chain packing and consequently the 3
10
helix is less
stable than the
α
-helix. Only short stretches of 1 or 2 turns are found in proteins, usually at
the C- or N- terminals of
α
α
-helices [7].
