  Antimicrobial peptides are a class of small, usually positively charged
amphiphilic peptides that are used by the innate immune system to combat
bacterial infection in multicellular eukaryotes. Antimicrobial peptides are
known for their broad-spectrum antimicrobial activity and thus can be used as a
basis for a development of new antibiotics against multidrug-resistant
bacteria. The most challengeous task on the way to a therapeutic use of
antimicrobial peptides is a rational design of new peptides with enhanced
activity and reduced toxicity. Here we report a molecular dynamics and circular
dichroism study of a novel synthetic antimicrobial peptide D51. This peptide
was earlier designed by Loose et al. using a linguistic model of natural
antimicrobial peptides. Molecular dynamics simulation of the peptide folding in
explicit solvent shows fast formation of two antiparallel beta strands
connected by a beta-turn that is confirmed by circular dichroism measurements.
Obtained from simulation amphipatic conformation of the peptide is analysed and
possible mechanism of its interaction with bacterial membranes together with
ways to enhance its antibacterial activity are suggested.
