7 Combinatories and Topology of theβ-Sandwich andβ-Barrel Proteins 1417.4.8 Characterizing the Place of Distortion of Barrel Structures
The place of distortion of the beta sheet is where the two orthogonal subsheets
meet. It is largely defines the characteristic shape of the barrel proteins. It
is reasonable to assume that the essential structural and sequence invariant
features of barrels will be found at or near the place of distortion. We focus
our attention, therefore, on the two “edge strands,” a (or a′) and k (or k′)
that bind the subsheets and their immediate strand neighbors (Fig. 7.3a–c).
In one subsheet, strand a (ora′) is H-bonded with strand b, while in the other
subsheet strand k (or k′) forms H-bonds with strand m. Table 7.2 illustrates
strand arrangements in various barrel folds; the four strands that make up
the place of distortion are referenced by enlarged numerals in bold font.
The definition of the place of distortion as a part of the barrel structure
containing two edge strands and their two neighbors requires a qualification.
When we analyze the four strands of the place of distortion we omit from
consideration the “double prime” portion of the barrel strand(s). It allows us
to make our consideration general for all barrel structures. The strands that
do not bend and the prime part of the link strand are the conserved elements
of the barrel structures, while double prime portions of the link strands were
found in the part of the barrel proteins.
7.4.9 The Rule of the Arrangement of the “Edge Strands”
in the Barrel Structures
In 15 protein folds, the pair of strands in each subsheet that makes up the
part of the distortion region are labeled by consecutive indices, such as the
strands 2 and 3 in one subsheet and the strands 3 and 4 in the other in the
structure 1bia (Fig. 7.2). Table 7.2 shows these constraints for the structures
of the folds ## 40, 44, 45, 46, 48, 54, 65, 66, 52, 54, 55, 56, 59, 60, 69, 70, 71,
74, and 75 (see the enlarged in bold numbers of the strands).
In all other barrel folds one of the two subsheets contains a pair of se-
quentially numbered strands at the point of distortion (see subsheet B in
Table 7.2). The exceptions of this rule are found only in structures of folds
55–57, where two subsheets are connected by three linking strands.
7.4.10 Arrangement of the Barrel and Sandwich Structures
is Different
As shown above we found a strict constraint for the arrangement of the strands
in the sandwich-like proteins. In almost all sandwich-like proteins there exists
the definite rule of two interlocked pairs of strands, which are located in
twoβ-subsheets. It is important to test this rule in the two subsheets of the
barrel structure. The analysis of the arrangement of the strands in A and
Bβ-sheets showed that interlocked arrangement does not exist in the barrel