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Studying the structural properties of polyalanine and polyglutamine peptides

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Abstract

Poly-(Ala) and poly-(Gln) peptides have important biological effects, and can cause various human illnesses and neurodegenerative diseases. Conformational analysis of these homo-oligopeptides (HOPs) was carried out by simulated annealing in order to identify their structural properties regarding secondary structures and intramolecular H-bonding patterns. Poly-(Ala) and poly-(Gln) peptides composed of 7, 10, 14 or 20 amino acids were modelled in both charged and terminally blocked forms. In the case of conformers derived from simulated annealing calculations, the presence of various secondary structural elements (different types of β-turns, α-helix, 310-helix, poly-proline II helix, parallel and antiparallel β-strands) was investigated. Moreover, the intramolecular H-bonding patterns formed either between the backbone atoms for both HOPs or between the backbone and side-chain atoms for the poly-(Gln) peptides were examined. Our results showed that different secondary structural elements (type I and type III β-turns, α-helix, 310-helix, antiparallel β-strand) could be observed in both poly-(Ala) and poly-(Gln) peptides and, according to their presence, characteristic H-bonding patterns formed mainly by i←i+3 and i←i+4 H-bonds could be found.

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Acknowledgements

This research was supported by grants GVOP-3.1.1.-2004-05-0492/3.0 and RET 08/2004.

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Authors and Affiliations

  1. Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, 6726, Szeged, Hungary

    Balázs Leitgeb, Ádám Kerényi & Gábor Rákhely

  2. Supramolecular and Nanostructured Materials Research Group of the Hungarian Academy of Sciences, University of Szeged, Dóm tér 8, 6720, Szeged, Hungary

    Ferenc Bogár, Gábor Paragi & Botond Penke

  3. Department of Medical Chemistry, University of Szeged, Dóm tér 8, 6720, Szeged, Hungary

    Botond Penke

  4. Department of Biotechnology, University of Szeged, Temesvári krt. 62, 6726, Szeged, Hungary

    Gábor Rákhely

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  1. Balázs Leitgeb
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  2. Ádám Kerényi
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  3. Ferenc Bogár
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  4. Gábor Paragi
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  5. Botond Penke
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  6. Gábor Rákhely
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Correspondence to Balázs Leitgeb.

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Leitgeb, B., Kerényi, Á., Bogár, F. et al. Studying the structural properties of polyalanine and polyglutamine peptides. J Mol Model 13, 1141–1150 (2007). https://doi.org/10.1007/s00894-007-0241-4

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  • DOI: https://doi.org/10.1007/s00894-007-0241-4

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