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Biochim Biophys Acta. 2012 May;1818(5):1402-9. doi: 10.1016/j.bbamem.2012.02.017. Epub 2012 Feb 23.

Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers.

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1
Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA. yiwang@ucsd.edu

Abstract

We report altogether 3-μs molecular dynamics (MD) simulations of the antimicrobial peptide CM15 to systematically investigate its interaction with two model lipid bilayers, pure POPC and mixed POPG:POPC (1:2). Starting with either an α-helical or a random-coil conformation, CM15 is found to insert into both bilayers. Peptide-lipid interaction is stronger with the anionic POPG:POPC than the zwitterionic POPC, which is largely attributed to the electrostatic attraction between CM15 and the negatively charged POPG. Simulations initiated with CM15 as a random coil allowed us to study peptide folding at the lipid-water interface. Interestingly, CM15 folding appears to be faster in POPC than POPG:POPC, which may be explained by a lower activation energy barrier of structural rearrangement in the former system. Our data also suggest that compared with the random-coil conformation, CM15 in a pre-folded α-helix has significantly reduced interactions with the lipids, indicating that peptide initial structures may bias the simulation results considerably on the 100-ns timescale. The implications of this result should be considered when preparing and interpreting future AMP simulations.

PMID:
22387432
PMCID:
PMC3329965
DOI:
10.1016/j.bbamem.2012.02.017
[Indexed for MEDLINE]
Free PMC Article
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