Molecular dynamics simulation of antimicrobial peptide arenicin-2: beta-hairpin stabilization by noncovalent interactions.
Arenicin-2 is a 21 residue antimicrobial cyclic peptide, possessing one disulphide bond between residues Cys(3) and Cys(20). NMR and CD studies suggested that the structure of arenicin-2 in water represented a well formed, but highly twisted beta-hairpin. To investigate the spatial arrangement of the peptide side chains and to get a clear view of its possible amphipathic properties we performed molecular dynamics in explicit water. Four independent trajectories, 50 ns in length, were produced, starting from various initial conformations or by applying different simulation conditions. Arenicin-2 retained its beta-hairpin structure during simulations, although the residues close to strand ends were found to escape from the ideal hairpin conformation. The type I' beta-turn connecting the two strands fluctuated between type IV and II' beta-turn. Conversely, the right-handed twist of the beta-hairpin was well conserved with average twist value 203 degrees +/- 19 degrees per eight residues. Several nonbonded interactions, like hydrophobic interactions between aliphatic side chains, cation/pi-aromatic interactions, CH...pi aromatic bond and water bridges, contributed to the hairpin stabilization.
Stavrakoudis
Athanassios
A
Department of Economics, University of Ioannina, GR-45110, Ioannina, Greece. astavrak@cc.uoi.gr
Tsoulos
Ioannis G
IG
Shenkarev
Zakhar O
ZO
Ovchinnikova
Tatiana V
TV
D000595:Amino Acid Sequence; D000818:Animals; D000890:Anti-Infective Agents / Q000737:chemistry*; D023181:Antimicrobial Cationic Peptides; D003198:Computer Simulation; D015801:Helminth Proteins; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D014867:Water / Q000737:chemistry
D000890:Anti-Infective Agents; D023181:Antimicrobial Cationic Peptides; D015801:Helminth Proteins; D010455:Peptides; C496888:arenicin-1, Arenicola marina; D014867:Water