Solitons on H-bonds in proteins

TL;DR

This paper models soliton dynamics on hydrogen-bond networks in helical proteins using a 3D Toda lattice formalism, demonstrating stable, spontaneously created solitons that may explain long-lived vibrational modes observed experimentally.

Contribution

It introduces a 3D Toda lattice model for protein hydrogen-bond solitons, linking integrable systems to biological vibrational phenomena.

Findings

Solitons are spontaneously generated and stable in the model.

Perturbations on one H-bond induce solitons on others.

Model parameters align with realistic H-bond potentials.

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$^{-1}$ 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.