[Relationship between structure and amino acid sequence of strongly twisted and coiled β-hairpins in globular proteins].
β-Hairpins are widespread in proteins, and it is possible to find them both within β-sheets and separately. In this work, a comparative analysis of amino acid sequences of β-strands within strongly twisted β-hairpins from different structural protein subclasses has been conducted. Strongly twisted and coiled β-hairpin generates in the space a right double helix out of β-strands that are connected by a loop region (connections). The frequencies of amino acid residues on the internal (concave) and external (convex) surfaces of strongly twisted β-hairpins have been determined (220 β-hairpins from nonhomologous proteins were studied). The concave surface of these β-hairpins is mainly generated by hydrophobic residues, while the convex surface by hydrophilic residues; accordingly, the alternation of hydrophobic internal and hydrophilic external residues is observed in their amino acid sequences. Amino acid residues of glycine and alanine (especially in places of the largest twisting of the strands) were anomalously frequently found in internal positions of strongly twisted and coiled β-hairpins. It was established that internal positions never contain the proline residues, while external positions in the twisting region contain them in a relatively large amount. It was demonstrated that at least one amino acid residue in αL- or ε-conformation is required for generation of relatively short (up to 7 amino acid residues) connection. As a rule, these positions are occupied by glycines. Thus, not only the alternation of hydrophobic and hydrophilic amino acid residues, but also the presence of one or two glycine residues in the connection region and the excess of glycines and alanines in the places of the largest strand twisting on the concave surface, as well as the presence of prolines on the convex surface, are required to generate a strongly twisted and coiled β-hairpin.
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.
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Boshkova
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.
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Brazhnikov
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.|efimov@protres.ru.
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Efimov
D000595:Amino Acid Sequence; D030562:Databases, Protein; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics
D011506:Proteins
alignment; amino acid sequence; conformation; stereochemical analysis; twisted β-hairpin; β-turn