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Analysis of the flexibility and stability of the structure of magainin in a bilayer, and in aqueous and nonaqueous solutions using molecular dynamics simulations

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Abstract

The precise mode of the antimicrobial activity of Magainin (Mag)—an antimicrobial peptide (AMP)—is still unclear. In this study, the conformation of Mag was characterized in water, and in a methanol and lipid bilayer [palmitoyl-oleoylphosphatidylcholine (POPC)] using a molecular dynamics (MD) simulation technique. To describe the role conformation plays in Mag function, the global conformational differences within three systems were studied. Through analysis of the resulting configuration ensembles, the differences in the three systems, such as overall flexibility and average secondary structure, were studied. It is suggested that these differences may be important enough to influence interactions with lipid biomembranes, thereby influencing key properties such as penetration into cell membrane and stability.

Snapshot of the simulation system for a Magainin (Mag) monomer (peptide is in surfacerepresentation colored by residue). Lipids are shown in gray licorice representation with wateratoms colored green on either side

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Acknowledgments

We would like to thank the two anonymous reviewers for their very useful comments and suggestions, which help us improve the quality of our paper.

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Authors and Affiliations

  1. Department of Biochemistry, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran

    Elham Esmaili

  2. Medical Biology Research Center, Kermanshah University of Medical Sciences, 67346-67149, Kermanshah, Iran

    Mohsen Shahlaei

  3. Medicinal Chemistry department, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran

    Mohsen Shahlaei

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Correspondence to Mohsen Shahlaei.

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Esmaili, E., Shahlaei, M. Analysis of the flexibility and stability of the structure of magainin in a bilayer, and in aqueous and nonaqueous solutions using molecular dynamics simulations. J Mol Model 21, 73 (2015). https://doi.org/10.1007/s00894-015-2622-4

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