Charged single α-helix: A versatile protein structural motif

Authors

  • Dániel Süveges,

    1. Department of Biochemistry, Eötvös Loránd University, Pázmány Péter s. 1/C, H1117 Budapest, Hungary
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    • Dániel Süveges and Zoltán Gáspári contributed equally to this work.

  • Zoltán Gáspári,

    1. Institute of Chemistry, Eötvös Loránd University, Pázmány Péter s. 1/C, H1117 Budapest, Hungary
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    • Dániel Süveges and Zoltán Gáspári contributed equally to this work.

  • Gábor Tóth,

    1. Bioinformatics Group, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, H2100 Gödöllő, Hungary
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  • László Nyitray

    Corresponding author
    1. Department of Biochemistry, Eötvös Loránd University, Pázmány Péter s. 1/C, H1117 Budapest, Hungary
    • Department of Biochemistry Eötvös Loránd University, Pázmány Péter s. 1/C, H1117 Budapest, Hungary
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Abstract

A few highly charged natural peptide sequences were recently suggested to form stable α-helical structures in water. In this article we show that these sequences represent a novel structural motif called “charged single α-helix” (CSAH). To obtain reliable candidate CSAH motifs, we developed two conceptually different computational methods capable of scanning large databases: SCAN4CSAH is based on sequence features characteristic for salt bridge stabilized single α-helices, whereas FT_CHARGE applies Fourier transformation to charges along sequences. Using the consensus of the two approaches, a remarkable number of proteins were found to contain putative CSAH domains. Recombinant fragments (50–60 residues) corresponding to selected hits obtained by both methods (myosin 6, Golgi resident protein GCP60, and M4K4 protein kinase) were produced and shown by circular dichroism spectroscopy to adopt largely α-helical structure in water. CSAH segments differ substantially both from coiled-coil and intrinsically disordered proteins, despite the fact that current prediction methods recognize them as either or both. Analysis of the proteins containing CSAH motif revealed possible functional roles of the corresponding segments. The suggested main functional features include the formation of relatively rigid spacer/connector segments between functional domains as in caldesmon, extension of the lever arm in myosin motors and mediation of transient interactions by promoting dimerization in a range of proteins. Proteins 2009. © 2008 Wiley-Liss, Inc.

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