Journal of Molecular Modeling

, Volume 19, Issue 11, pp 4723–4730 | Cite as

Effect of the aminoacid composition of model α-helical peptides on the physical properties of lipid bilayers and peptide conformation: a molecular dynamics simulation

  • Milan Melicherčík
  • Alžbeta Holúbeková
  • Tibor Hianik
  • Ján Urban
Original Paper
First Online:
Received:
Accepted:

Abstract

The interaction of a model Lys flanked α-helical peptides K2-X24-K2, (X = A,I,L,L+A,V) with lipid bilayers composed of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) both, in a gel and in a liquid-crystalline state, has been studied by molecular dynamics simulations. It has been shown that these peptides cause disordering of the lipid bilayer in the gel state but only small changes have been monitored in a liquid-crystalline state. The peptides affect ordering of the surrounding lipids depending on the helix stability which is determined by amino acid side chains – their volume, shape, etc. We have shown that the helix does not keep the linear shape in all simulations but often bends or breaks. During some simulations with a very small difference between hydrophobic length of peptide and membrane thickness the peptide exhibits negligible tilt. At the same time changes in peptide conformations during simulations resulted in appearance of superhelix.

Keywords

Bilayer lipid membranes Helical peptides Molecular dynamics simulations Phase transitions 
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Notes

Acknowledgments

This publication is the result of the project implementation: “The development of the center of excellence for utilization of information on bio-macromolecules in disease prevention and in improvement of quality of life” (ITMS 26240120027) supported by the Research and Development Operational Programme funded by the European Regional Development Fund. The access to the METACentrum computing facilities provided under the research intent MSM6383917201 is highly appreciated. This work was also supported by the Slovak Research and Development Agency (Project No. APVV – 0410-10 and LPP-0341-09).

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Milan Melicherčík
    • 1
    • 2
  • Alžbeta Holúbeková
    • 1
  • Tibor Hianik
    • 1
  • Ján Urban
    • 1
  1. 1.Department of Nuclear Physics and BiophysicsComenius UniversityBratislavaSlovak Republic
  2. 2.Institute of Nanobiology and Structural Biology of GCRCAcademy of Sciences of the Czech RepublicNové HradyCzech Republic

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