Collective vibrations of an alpha-helix. A molecular dynamics study.

The internal dynamics of a 20-residue polyalanine helix was investigated by molecular dynamics simulations. Special attention was paid to the collective vibrations of the helix backbone. The stretch and bend vibrations could be assigned unambiguously to oscillations with periods of 1.4 and 4.3 ps, respectively. The influence of the environment on the dynamics of the collective vibrations was studied by coupling the helix to a heat bath and by adding water molecules. In the presence of water, the stretch vibration becomes more strongly dampened, but still exists as a vibration , while the bend vibration becomes overdamped and degenerates into a relaxation process. The results are compared with available experimental data.