Closed loops of nearly standard size: Common basic element of protein structure

Igor N. Berezovsky, Alexander Y. Grosberg, Edward N. Trifonov

    Research output: Contribution to journalArticle

    Abstract

    By screening the crystal protein structure database for close Cα-Cα contacts, a size distribution of the closed loops is generated. The distribution reveals a maximum at 27±5 residues, the same for eukaryotic and prokaryotic proteins. This is apparently a consequence of polymer statistic properties of protein chain trajectory. That is, closure into the loops depends on the flexibility (persistence length) of the chain. The observed preferential loop size is consistent with the theoretical optimal loop closure size. The mapping of the detected unit-size loops on the sequences of major typical folds reveals an almost regular compact consecutive arrangement of the loops. Thus, a novel basic element of protein architecture is discovered; structurally diverse closed loops of the particular size. (C) 2000 Federation of European Biochemical Societies.

    Original languageEnglish (US)
    Pages (from-to)283-286
    Number of pages4
    JournalFEBS Letters
    Volume466
    Issue number2-3
    DOIs
    StatePublished - Jan 28 2000

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    Keywords

    • Polymer statistic
    • Protein
    • Protein evolution
    • Protein folding
    • Typical fold
    • Unit loop contour length

    ASJC Scopus subject areas

    • Biophysics
    • Structural Biology
    • Biochemistry
    • Molecular Biology
    • Genetics
    • Cell Biology

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