A strained N-capping motif in α-helices of βαβ-units

A novel helical N-capping motif has been considered. It occurs in the βα-arches of right-handed βαβ-units and contains an N-cap residue in a sterically strained conformation. Moreover, this amino acid position contains almost no glycines, that could relieve strain. It was shown that the N-cap adopts this conformation as a result of the unusual convergence between the second and third amino acid positions of the α-helix (counting from the N-cap) and the second position of the preceding β-strand. This is achieved by the presence of glycines in the specified positions (i.e. positions i - 2, i + 2 and i + 3, if N-cap is i). The N-cap conformation is stabilized by a hydrogen bond between the backbone amide group in the second position of the α-helix and the carbonyl group in the first position of the β-strand. The occurrence of similar N-capping motifs in different types of βαβ-units was compared and their structural differences caused by the influence of the environment were described. Study results may be useful for protein design and ab initio prediction of the 3D protein structure.

Structural features of split and unsplit βαβ-units

In this study, 1064 nonhomologous "unsplit", "one-strand split" and "two-strand split" right-handed βαβ-units having standard α-helices and loops up to seven residues in length have been analyzed. It was found that the α-helices in these kinds of βαβ-units have different distributions of the hydrophobic and hydrophilic amino acid residues along the chain. In the unsplit βαβ-units, most α-helices have hydrophobic residues in positions N4-N7-N8-N11 or N6-N7-N10, where N1 is the first N-terminal residue. In the one-strand split βαβ-units, most α-helices have hydrophobic residues in positions N4-N7-N8-N11 and those in two-strand split βαβ-units in positions N4-N5-N8-N12. On the other hand, in all kinds of βαβ-units, there are commonly occurring hydrophobic stripes of type C4-C7-C8 at the C-terminal parts of the α-helices. As a rule, the C- and N-terminal hydrophobic stripes overlap and the extent of their overlapping determine the length of α-helices.

Structural motifs in which β-strands are clipped together with the П-like module

In this study, the structural motifs that can be represented as combinations of small motifs such as β-hairpins, S-, and Z-like β-sheets and βαβ-units, and the П-like module are described and analyzed. The П-module consists of connected elements of the β-strand-loop-β-strand type arranged in space so that its overall fold resembles a clip or the Greek letter П. In proteins, the П-module itself and the structural motifs containing it exhibit unique overall folds and have specific sequence patterns of the key hydrophobic, hydrophilic and glycine residues. All this together enables us to conclude that these structural motifs can fold independently of the remaining part of the molecule and can act as nuclei and/or "ready-made" building blocks in protein folding.

Super-secondary structures and modeling of protein folds

A characteristic feature of the polypeptide chain is its ability to form a restricted set of commonly occurring folding units composed of two or more elements of secondary structure that are adjacent along the chain. Some of these super-secondary structures exhibit a unique handedness and a unique overall fold irrespective of whether they occur in homologous or nonhomologous proteins. Such super-secondary structures are of particular value since they can be used as starting structures in protein modeling. The larger protein folds can be obtained by stepwise addition of other secondary structural elements to the starting structures taking into account a set of simple rules inferred from known principles of protein structure.

Structures closed into cycles in globular proteins

Different types of structures closed into cycles are widespread at all the levels of structural organization of proteins. β-Hairpins, triple-stranded β-sheets, and βαβ-units represent simple structural motifs closed into cycles by systems of hydrogen bonds. Secondary closing of these simple motifs into larger cycles by means of different superhelices, split β-hairpins, or SS-bridges results in formation of complex structural motifs such as abcd-units, φ-motifs, five- and seven-segment α/β-motifs, etc. At the level of tertiary structure many proteins and domains fold into structures closed into cylinders. Apparently, closing the motifs and domains into cycles and cylinders results in formation of more cooperative and stable structures as compared with open ones, and this may be the reason for high frequencies of occurrence of the motifs in proteins.

PCBOST: Protein classification based on structural trees

In this paper, we present the protein classification based on structural trees (PCBOST). This is a novel hierarchical classification of proteins that is primarily based on similarity of overall folds of proteins as well as on the modeled folding pathways of proteins. Amino acid sequences, functions of proteins and their evolutionary relationship are not taken into account in this classification. To date the database includes 3847 proteins and domains grouped into six categories having structural similarity and forming six structural trees (total 10,547 PDB-entries). The work on extension of the database and construction of novel structural trees is in progress. The service is free for all users and available at the URL <http://strees.protres.ru/>.