Solitons on H bonds in proteins

A model for soliton dynamics on a hydrogen-bond network in helical proteins is proposed. It employs the formalism-of fully integrable Toda lattices in three dimensions which admit phonons as well as solitons along the hydrogen bonds of the helices. A simulation of the three-dimensional Toda lattice system shows that the solitons are spontaneously created and are stable and moving along the helix axis.

A perturbation on one of the three H-bond lines forms solitons on the other H bonds as well. The robust solitary wave may explain very long-lived modes in the frequency range of 100 cm(-1) which are found in recent x-ray laser experiments. The dynamics parameters of the Toda lattice are in accordance with the usual Lennard-Jones parameters used for realistic H-bond potentials in proteins.