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and is unsatisfactory for deciding where a section of secondary structure ends. For example,
in
-helices, the last 3 residues of the carboxyl terminus only contribute NH groups to
hydrogen bonding and the N terminus contributes only CO groups. It is also difficult to
identify short and irregular sections of secondary structure.
Since the late 1970's a number of pattern recognition algorithms have been
developed to determine secondary structure from crystallographic data. These include
DEFINE_S, which derives secondary and first level supersecondary structure from the C α
trace [30], Define Secondary Structure of Proteins (DSSP) [31], which uses hydrogen-
bonding patterns, STRIDE, which assigns structure from atomic coordinates based on
hydrogen-bond patterns and main chain dihedral angles [32], and XTLSSTR [33], uses the
same criteria that are used visually.
α
3. Supersecondary Structure (Motifs)
Secondary structures combine to form energetically stable arrangements called motifs, the
smallest containing two secondary structural elements connected by a specific turn. In a
comparative analysis of 240 proteins, Sun and Jiang [34] were able to classify thirty-four
supersecondary motifs of the types: αα , αβ , βα , and ββ in which the connecting peptide
consisted of 5 or fewer residues. The classification is based on the hydrogen-bonding
pattern and the conformation of the residues in the connecting loop, which in turn
determines the relative orientation of the main secondary structure elements. Since the
demarcation between secondary structure and simple motifs is somewhat arbitrary, some of
the motifs have already been described in section 3.
3.1 Hairpins
The most common basic motifs include,
-Hairpins
consist of two α -helices packed anti-parallel to each other and joined by a δ or χ turn. More
abundant are
α
and
β
-hairpins (figures 12b and 12a).
α
β
-hairpins in which two adjacent strands forming part of an anti-parallel
β
-
sheet are connected by either
-turns [35].
Figure 13a shows a Raswin diagram of the snake venom erabutoxin (PDB code1era), which
consists of two
δ
or
χ
turns but most commonly by types I
or II
′β
β
-hairpins plus one
β
-strand.
3.2 Mixed
αβ
motifs
The segment of peptide chain connecting two parallel β -strands often forms a α -helix
giving rise to the
motif (figure 12c). The helix is packed anti-parallel to the sheet and
in the most common configuration it lays above the plane of the
βαβ
-sheet forming a right-
handed loop between the β -strands. Other recurrent themes include ααβ , and ββα motifs
[36].
β
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