Paper Citing NAMD - Abstract
Stavrakoudis, Athanassios; Tsoulos, Ioannis G.; Shenkarev, Zakhar O.; Ovchinnikova, Tatiana V.
Molecular Dynamics Simulation of Antimicrobial Peptide Arenicin-2: beta-Hairpin Stabilization by Noncovalent Interactions
BIOPOLYMERS, 92:143-155, 2009
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-harpin. 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 center dot center dot center dot pi aromatic bond and water bridges, contributed to the hairpin stabilization. (C) 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 143-155, 2009.
