130 A.E. Kister et al.
adopted in the SCOP and CATH databases [3, 14]. Proteins grouped together
based on their common architectural properties often do not have share any
functional homology or significant sequence homology.
Systematic theoretical analysis has revealed certain structural features
common for theβ-sheet as for example, Greek key and jellyrolls patterns
and specific characteristics of the edge strands [15, 16]. In many works the
geometric parameters of theβ-proteins such as distance or angle matrices
between strands, the number of strands and shear number of proteins and the
analysis of bifurcation ofβ-sheets, and the spatial organizations of secondary
structures [17–27] are investigated.
Analysis of arrangement of strands of the sandwich and barrel proteins re-
vealed that only a limited number of possible strand arrangements are realized
in existing structures. We found that each fold structural classification of the
barrel and the sandwich structures can be described by a unique arrangement
of strands. This finding has implications for protein classification. Since strand
arrangement of a protein can be deduced from its matrix of hydrogen bonds,
it follows that one can in most cases assign a query protein to its proper fold
given sufficient information about its hydrogen bonds.
7.3 Common Features in Structures and Sequences
of Sandwich-Like Proteins
7.3.1 General Features of the Sandwich-Like Proteins
Proteins of 69 superfamilies in 38 protein folds have been described as
“sandwich-like proteins” (SPs) (see folds 1.2.1 – 1.2.38 in SCOP (3), release
1.59). Spatial structures of SPs are composed ofβ-strands, which form two
mainβ-sheets that pack face to face. Although the general architecture of
SP is relatively uniform, the number of strands and the arrangement of the
strands vary widely [28–30]. Some SPs, in addition to two “main” sandwich
sheets, contain “auxiliary” beta sheets. Comparison of proteins in different
superfamilies does not show either functional homology or significant sequence
homology.
7.3.2 Supersecondary Patterns in the Sandwich-Like Proteins
The determination of H-bonds between the main chain atoms allowed us to
determine the arrangements of the strands and identify those strands that
make up the two main sandwich sheets. Analysis of the arrangements of
strands in all known sandwich-like known protein structures revealed the def-
inite rules that are valid for almost all sandwich proteins.
At first, this rule can be stated as follows: in any given sandwich-like
protein structure there exist two pairs of strands (i, i+ 1) and (k,k+ 1),
such that: (1) strands of each pair are adjacent to each other in sequence
(Fig. 7.1a); (2) strandiis located in one main sheet andi+ 1 – in the other