Launching of Davydov solitons in protein $\alpha$-helix spines

TL;DR

This study demonstrates a mechanism to generate and control Davydov solitons within protein alpha-helices using phase-modulated pulses, advancing understanding of energy transport in biological structures.

Contribution

It introduces a phase modulation technique to launch moving solitons inside alpha-helices, expanding the control over energy transport models in proteins.

Findings

Phase-modulated pulses can generate moving solitons in protein alpha-helices.

Soliton velocity can be explicitly controlled through pulse parameters.

Results support the role of quantum dynamics in protein function optimization.

Abstract

Biological order provided by $\alpha$-helical secondary protein structures is an important resource exploitable by living organisms for increasing the efficiency of energy transport. In particular, self-trapping of amide I energy quanta by the induced phonon deformation of the hydrogen-bonded lattice of peptide groups is capable of generating either pinned or moving solitary waves following the Davydov quasiparticle/soliton model. The effect of applied in-phase Gaussian pulses of amide I energy, however, was found to be strongly dependent on the site of application. Moving solitons were only launched when the amide I energy was applied at one of the $\alpha$-helix ends, whereas pinned solitons were produced in the $\alpha$-helix interior. In this paper, we describe a general mechanism that launches moving solitons in the interior of the $\alpha$-helix through phase-modulated Gaussian pulses of amide I energy. We also compare the predicted soliton velocity based on effective soliton mass and the observed soliton velocity in computer simulations for different parameter values of the isotropy of the exciton-phonon interaction. The presented results demonstrate the capacity for explicit control of soliton velocity in protein $\alpha$-helices, and further support the plausibility of gradual optimization of quantum dynamics for achieving specialized protein functions through natural selection.