Exploring and characterizing the folding processes of Lys- and Arg-containing Ala-based peptides: A molecular dynamics study

Gábor Janzsó, F. Bogár, Liza Hudoba, B. Penke, G. Rákhely, Balázs Leitgeb

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

In this study, molecular dynamics simulations were carried out on Lys- and Arg-containing Ala-based peptides (i.e. Ace-(AAAAK) nA-NH 2 and Ace-(AAAAR) nA-NH 2, where n = 1-4), in order to explore and characterize their folding processes. For the oligopeptides, the evolution of α-helical structure with regard to the whole conformation, as well as to each residue was investigated, and the helix-forming propensities were characterized. On the basis of the helicity curves, representing the alteration of average helicity as a function of time, the typical time values describing the folding processes and subprocesses were identified. In the case of each peptide, the evolution and role of helix-stabilizing, non-local and side-chain-to-backbone H-bonds were examined. The appearing i ← i + 4 H-bonds pointed out the role of these interactions in the stabilization of α-helical conformations, while the occurring i ← i + 3 H-bonds indicated the presence of β-turn or 3 10-helical structures. Studying the formation and role of non-local and side-chain-to-backbone H-bonds led to the observation that these types of interactions produced an effect on the evolution of helical conformations, as well as on the folding processes.

Original languageEnglish
Pages (from-to)240-250
Number of pages11
JournalComputational Biology and Chemistry
Volume35
Issue number4
DOIs
Publication statusPublished - Aug 10 2011

Fingerprint

Molecular Dynamics Simulation
Folding
Conformation
Molecular Dynamics
Peptides
Conformations
Molecular dynamics
Helicity
Helix
Backbone
Oligopeptides
Interaction
Stabilization
Curve
Computer simulation
peptide A

Keywords

  • Ala-based peptide
  • Folding pathway
  • Folding process
  • Helical structure
  • Intramolecular H-bond
  • Molecular dynamics

ASJC Scopus subject areas

  • Biochemistry
  • Structural Biology
  • Organic Chemistry
  • Computational Mathematics

Cite this

Exploring and characterizing the folding processes of Lys- and Arg-containing Ala-based peptides : A molecular dynamics study. / Janzsó, Gábor; Bogár, F.; Hudoba, Liza; Penke, B.; Rákhely, G.; Leitgeb, Balázs.

In: Computational Biology and Chemistry, Vol. 35, No. 4, 10.08.2011, p. 240-250.

Research output: Contribution to journalArticle

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