Solitons in alpha-helical proteins

TL;DR

This paper explores the formation, stability, and dynamics of solitons in alpha-helical proteins, emphasizing the role of helical symmetry and revealing that symmetry-breaking solitons are more stable and robust.

Contribution

It demonstrates analytically and numerically that symmetry-breaking solitons are more stable and introduces the concept of hybrid solitons with complex internal structures in alpha-helices.

Findings

Symmetry-breaking solitons are dynamically stable and low-energy.

Symmetry-preserving solitons decay rapidly during propagation.

Interspine oscillation frequency is proportional to soliton velocity.

Abstract

We investigate some aspects of the soliton dynamics in an alpha-helical protein macromolecule within the steric Davydov-Scott model. Our main objective is to elucidate the important role of the helical symmetry in the formation, stability and dynamical properties of Davydov's solitons in an alpha-helix. We show, analytically and numerically, that the corresponding system of nonlinear equations admits several types of stationary soliton solutions and that solitons which preserve helical symmetry are dynamically unstable: once formed, they decay rapidly when they propagate. On the other hand, the soliton which spontaneously breaks the local translational and helical symmetries possess the lowest energy and is a robust localized entity. We also demonstrate that this soliton is the result of an hybridization of the quasiparticle states from the two lowest degenerate bands and has an inner structure which can be described as a modulated multi-hump amplitude distribution of excitations on individual spines. The complex and composite structure of the soliton manifests itself distinctly when the soliton is moving and some interspine oscillations take place. Such a soliton structure and the interspine oscillations have previosly been observed numerically in [A.C. Scott, Phys.Rev. A 26 578 (1982)]. Here we argue that the solitons studied by A. Scott, are hybrid solitons and that the oscillations arise due to the helical symmetry of the system and result from the motion of the soliton along the $\alpha$-helix. The frequency of the interspine oscillations is shown to be proportional to the soliton velocity.