title: Molecular Dynamics Simulation and Analysis of the Antimicrobial Peptide-Lipid Bilayer Interactions.
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.
authors.affiliation: Department of Chemistry, Center for Biophysics and Computational Biology, Institute for Computational Molecular Science, Temple University, Philadelphia, PA, USA.
authors.forename: Shima
authors.initials: S
authors.lastname: Arasteh
authors.affiliation: Peptide Chemistry Laboratory, Institute of Biochemistry and Biophysics, University of Tehran, 16 Azar Street, 14176-14335, Tehran, Iran. mojtabagheri@ut.ac.ir.
authors.forename: Mojtaba
authors.initials: M
authors.lastname: Bagheri
mesh_terms: D000890:Anti-Infective Agents / Q000737:chemistry* / Q000378:metabolism; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D008051:Lipid Bilayers / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D010456:Peptides, Cyclic / Q000737:chemistry / Q000378:metabolism; D012984:Software; D012997:Solvents; D064878:Web Browser
chemical_list: D000890:Anti-Infective Agents; D023181:Antimicrobial Cationic Peptides; D008051:Lipid Bilayers; D010456:Peptides, Cyclic; D012997:Solvents
keywords: Cyclic antimicrobial peptides; Force fields; Lipid bilayers; Molecular dynamics simulation; Peptide structure