Solitons on H-bonds in proteins
Abstract
A model for soliton dynamics on a hydrogen-bond network in helical proteins is proposed. It employs in three dimensions the formalism of fully integrable Toda lattices which admits 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 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.
Cite
@article{arxiv.cond-mat/0211626,
title = {Solitons on H-bonds in proteins},
author = {Francesco d'Ovidio and Henrik Bohr and Per-Anker Lindgaard},
journal= {arXiv preprint arXiv:cond-mat/0211626},
year = {2009}
}
Comments
6 pages, 7 figures