7 Combinatories and Topology of theβ-Sandwich andβ-Barrel Proteins 1357.4 Common Structural and Sequence Features
of Barrel-Like Proteins
7.4.1 Search for Sequence and Structural Invariants in Barrel
Proteins: An Outline of the Approach
In this work we analyze two barrel characteristics crucial for sequence/
structure relationship, which are not still consider in detail. They are the
arrangement of strands in theβ-sheet and a characteristic of a “place of a
distortion” in theβ-sheet, i.e., a place where strands curve to form a bar-
rel structure. These features distinguish “oneβ-sheet geometry” of the barrel
proteins.
Our approach is based on a comparison of elements of secondary structures
with analogous structural role in their respective barrel proteins. The first step
is to define precisely the strands that make up the main sheet and determine
the arrangements of the strands in space. Special attention is devoted to the
key region of the barrel proteins, the right-angle “turn” in supersecondary
structure. Examination of the strands that make up this crucial region allows
us to identify invariant substructure present in all barrel structures. Analysis
of amino acid sequences of the substructure led to discovery of conserved
positions: sequence invariants of the barrel proteins.
7.4.2 Overview of theβ-Barrel Structures
In general, the mainβ-sheet of the barrel proteins is folded to form a closed
structure. However, some proteins, though structurally very similar to “closed
barrels” and possessing a characteristically bent main sheet, have their edge
strands too far from each other in space to form hydrogen bonds. These pro-
teins are referred to as “partly open barrels” in SCOP database nomenclature
and are grouped together with closed barrels [2]. Each of the strands of the
mainβ-sheet forms hydrogen bonds with two or three adjacent strands.
McLachlan [9] has shown that the main structural parameters of the barrel
structures are the number of strands that form theβ-sheet,n, and the measure
of its stagger, “the shear number,” S [17]. Later it was shown that these
parameters define the geometry of barrel structures ([19, 20], see, as well, [27]).
According to the SCOP database, release 1.61 [2], one or more domains in
2311 protein structures form barrel-like structure. For example, RNA-binding
(SM-like) protein, listed as structure 1i4k in PDB, contains 28 barrel-like do-
mains. Barrel-like structures make up 114 protein families, 66 superfamilies,
and 36 protein folds (##40–75 of “All beta” proteins in the SCOP data-
base). Proteins in different barrel superfamilies do not share either functional
homology or sequence similarity.