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-
a) b)
Figure 13. a) Erabutoxin , 1era, [41] A small protein formed from two β-hairpins
(Greek key) plus one β strand. b) Parvalbumin , 1b8c, [42] Example of an EF hand.
The sphere is a Ca
2+
ion.
4. Folds
Simple motifs combine to form folds or domains in which similarity is commonly defined
by the chain topology, allowing for insertions and deletions of secondary structure between
less closely related structures. Folds can also be defined according to their architecture,
which describes how secondary structures pack together irrespective of their connectivity.
For example, two
-sheets commonly pack one against the other so they are roughly
aligned in a configuration referred to as an aligned
β
-sandwich; the jellyroll and
immunoglobulin folds (figures 23 and 24) have
β
β
-sandwich architecture but different
topologies.
The prevalence of the two main secondary structures (
-sheets), means
that domains can be conveniently divided into four classes; mainly-
α
, mainly-
β
,
α
-helix and
β
α
/
β
in
which
structures are
segregated. The physical and chemical constraints on secondary packing gives rise to a
recurrence of the motifs illustrated in figure 12, which in turn generate groups of similar
folds within each class. Moreover, in many cases, an increase in fold size tends to be
accomplished by repeating or extending existing motifs suggesting that during evolution
the genes encoding the motifs are duplicated [43].
Although it is known that proteins with 30% sequence identity will very likely have
the same fold [44], convergent evolution can produce proteins with the same shape but little
sequence homology or conversely the sequences of closely related proteins may have
diverged over time so that only the structural similarity has remained [45]. Therefore it is
necessary to augment sequence alignment methods with automatic structure comparison
algorithms such as SSAP, VAST and DALI [46-48] to determine relationships and
categorise proteins into a structural hierarchy.
α
and
β
structures are interspersed and
α
+
β
in which
α
and
β
