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Characterization of Antimicrobial Peptide–Membrane Interaction Using All-Atom Molecular Dynamic Simulation

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Immunity in Insects

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

The investigation of peptides interaction with cell membranes is essential for understanding the basic functions such as membrane transport, fusion, and signaling processes, which may elucidate the potential applications of peptides in biomedicine. Antimicrobial peptides (AMPs) are now widely explored as an alternative to antibiotics owing to their superior ability to disrupt cell membrane both alone and with cargo molecules. Understanding the interaction mechanism of AMP is significant for many therapeutic purposes, including targeted microbial cell death. Cell membranes are mostly characterized by a membrane bilayer, which presents a complex and heterogeneous association of molecules flexible for an external agent. Hence, studies of protein–membrane interactions constitute a challenge in the structural biology field. Molecular dynamics (MD) is one of the useful methods to investigate membrane-associated processes. An extensive set of model bilayers and micelles differing in lipid composition are used to study different classes of membrane-active proteins and peptides like toxins, antimicrobial, Trojan, and fusion peptides. Regardless of the limitations of the MD timescale, membrane simulation results are capable of giving a balanced picture for the mechanism of action.

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Authors and Affiliations

  1. Department of Biophysics, Bose Institute, Kolkata, India

    Shruti Mukherjee, Rajiv K. Kar & Anirban Bhunia

Authors
  1. Shruti Mukherjee
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  2. Rajiv K. Kar
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  3. Anirban Bhunia
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Corresponding author

Correspondence to Anirban Bhunia .

Editor information

Editors and Affiliations

  1. Department of Biology, University of Padova, Padova, Italy

    Federica Sandrelli

  2. Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy

    Gianluca Tettamanti

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Mukherjee, S., Kar, R.K., Bhunia, A. (2020). Characterization of Antimicrobial Peptide–Membrane Interaction Using All-Atom Molecular Dynamic Simulation. In: Sandrelli, F., Tettamanti, G. (eds) Immunity in Insects. Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0259-1_10

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  • DOI: https://doi.org/10.1007/978-1-0716-0259-1_10

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0258-4

  • Online ISBN: 978-1-0716-0259-1

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