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Antimicrobial Peptides

Volume 618 of the series Methods in Molecular Biology pp 267-285

Date:

Molecular Simulations of Antimicrobial Peptides

  • Allison LanghamAffiliated withDepartment of Chemical Engineering and Materials Science, University of Minnesota
  • , Yiannis N. KaznessisAffiliated withDepartment of Chemical Engineering and Materials Science, University of Minnesota

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Abstract

Recent advances in molecular dynamics (MD) simulation methods and in available computational resources have allowed for more reliable simulations of biological phenomena. From all-atom MD simulations, we are now able to visualize in detail the interactions between antimicrobial peptides (AMPs) and a variety of membrane mimics. This helps us to understand the molecular mechanisms of antimicrobial activity and toxicity. This chapter describes how to set up and conduct molecular dynamics simulations of AMPs and membrane mimics. Details are given for the construction of systems of interest for studying AMPs, which can include simulations of peptides in water, micelles, or lipid bilayers. Explanations of the parameters needed for running a simulation are provided as well.

Key words

Molecular dynamics CHARMM NAMD, micelles, lipid bilayers