Excitations in three-dimensional models of α-helix structures in proteins

In order to examine dynamic aspects, including excitations, in α-helix structures in proteins, models in three spatial dimensions of α helices have been set up and their dynamic behavior examined by numerical computations. The potential-energy function describing the system is based on empirical data and implemented in the molecular-dynamics computer program charmm. Two types of excitations have been examined: lattice vibrations and intramolecular vibrations. The former disperse rapidly while the latter (being essentially amide-I-type vibrations) evolve regularly. A simple model based on a system of coupled linear oscillators can reproduce the time evolution of the intramolecular vibrations.