Molecular dynamics simulation of the interactions of antimicrobial peptides with phospholipids of the inner membrane of gram-negative bacteria
by Yury Lisnyak; Artur Martynov; Boris Farber
International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 16, No. 1, 2024

Abstract: Antimicrobial peptides (AMP), positively charged polypeptides, are now extensively studied in the world to develop efficient drugs against extremely resistant bacterial strains. By molecular dynamics (MD) simulations, there were studied the ligand-receptor interactions of polymyxin B with two model systems in the water-salt solution: an anionic sodium dodecyl sulphate (SDS) micelle and explicit lipid bilayer of zwitterionic phosphatidylethanolamine (PEA), which mimics the gram-negative bacteria membrane. As a result, the polymyxin binding to PEA is stronger. The polymyxin B molecule interacts differently with these two types of membrane mimetics. The interaction of the peptide with SDS micelle occurs mainly due to electrostatic interactions and/or hydrogen bonding interactions of protonated Dab groups and polar groups of polymyxin with charged and polar groups of SDS micelles. The interaction of the peptide with the DPC micelle occurs mainly by the hydrophobic interactions of its Phe, Leu, and methyloctanoyl.

Online publication date: Tue, 02-Jul-2024

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