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Molecular Dynamics Simulation and Analysis of the Antimicrobial Peptide–Lipid Bilayer Interactions

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Antimicrobial Peptides

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1548))

Abstract

A great deal of research has been undertaken in order to discover antimicrobial peptides (AMPs) with unexploited mechanisms of action to counteract the health-threatening issues associated with bacterial resistance. The intrinsic effectiveness of AMPs is strongly influenced by their initial interactions with the bacterial cell membrane. Understanding these interactions in the atomistic details is important for the design of the less prone bacteria-resistant peptides. However, these studies always require labor-intensive and difficult steps. With this regard, modeling studies of the AMPs binding to simple lipid membrane systems, e.g., lipid bilayers, is of great advantage. In this chapter, we present an applicable step-by-step protocol to run the molecular dynamics (MD) simulation of the interaction between cyclo-RRWFWR (c-WFW) (a small cyclic AMP) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer using the Groningen machine for chemical simulations (GROMACS) package. The protocol as described here may simply be optimized for other peptide–lipid systems of interest.

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Acknowledgments

The financial supports to MB from the Iran National Science Foundation (reference No. 94012757), the Iran’s National Elites Foundation (reference No. 15/45362-1392) and University of Tehran are gratefully acknowledged.

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Authors and Affiliations

  1. Department of Chemistry, Center for Biophysics and Computational Biology, Institute for Computational Molecular Science, Temple University, Philadelphia, PA, USA

    Shima Arasteh

  2. Peptide Chemistry Laboratory, Institute of Biochemistry and Biophysics, University of Tehran, 16 Azar Street, 14176-14335, Tehran, Iran

    Mojtaba Bagheri

Authors
  1. Shima Arasteh
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  2. Mojtaba Bagheri
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Correspondence to Mojtaba Bagheri .

Editor information

Editors and Affiliations

  1. Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Paul R. Hansen

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Arasteh, S., Bagheri, M. (2017). Molecular Dynamics Simulation and Analysis of the Antimicrobial Peptide–Lipid Bilayer Interactions. In: Hansen, P. (eds) Antimicrobial Peptides. Methods in Molecular Biology, vol 1548. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6737-7_8

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  • DOI: https://doi.org/10.1007/978-1-4939-6737-7_8

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6735-3

  • Online ISBN: 978-1-4939-6737-7

  • eBook Packages: Springer Protocols

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