Structural Chemistry

, Volume 22, Issue 6, pp 1287–1295 | Cite as

Helix and H-bond formations of alanine-based peptides containing basic amino acids

  • Balázs Leitgeb
  • Gábor Janzsó
  • Liza Hudoba
  • Botond Penke
  • Gábor Rákhely
  • Ferenc Bogár
Original Research

Abstract

We studied comprehensively the helicity and H-bonding evolutions during the folding processes of Lys- and Arg-containing alanine-based peptides. The evolution of α-helical conformation concerning the entire sequence and each amino acid residue was examined, as well as the helix-forming propensities were characterized. The formation of various types of the intramolecular H-bonds was also investigated, pointing out the helix-stabilizing role of local interactions and the destabilizing role of non-local interplays. Our study led to the observation that the non-local H-bonds affected the evolution of helical conformations, as well as the entire folding processes.

Keywords

Alanine-based peptide Molecular dynamics Folding Helical conformation Intramolecular H-bond 

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Balázs Leitgeb
    • 1
  • Gábor Janzsó
    • 1
  • Liza Hudoba
    • 1
  • Botond Penke
    • 2
    • 4
  • Gábor Rákhely
    • 1
    • 3
  • Ferenc Bogár
    • 2
    • 4
  1. 1.Institute of BiophysicsBiological Research Center of the Hungarian Academy of SciencesSzegedHungary
  2. 2.Department of Medical ChemistryUniversity of SzegedSzegedHungary
  3. 3.Department of BiotechnologyUniversity of SzegedSzegedHungary
  4. 4.Supramolecular and Nanostructured Materials Research Group of the Hungarian Academy of SciencesUniversity of SzegedSzegedHungary

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