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

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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.

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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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Authors and Affiliations

  1. Department of Nuclear Physics and Biophysics, Comenius University, Mlynská dolina F1, 842 48, Bratislava, Slovak Republic

    Milan Melicherčík, Alžbeta Holúbeková, Tibor Hianik & Ján Urban

  2. Institute of Nanobiology and Structural Biology of GCRC, Academy of Sciences of the Czech Republic, Zámek 136, 37333, Nové Hrady, Czech Republic

    Milan Melicherčík

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  1. Milan Melicherčík
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  2. Alžbeta Holúbeková
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Correspondence to Milan Melicherčík.

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Melicherčík, M., Holúbeková, A., Hianik, T. et al. Effect of the aminoacid composition of model α-helical peptides on the physical properties of lipid bilayers and peptide conformation: a molecular dynamics simulation. J Mol Model 19, 4723–4730 (2013). https://doi.org/10.1007/s00894-012-1550-9

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  • DOI: https://doi.org/10.1007/s00894-012-1550-9

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