Launching of Davydov solitons in protein $α$-helix spines

Biological order provided by $α$-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 $α$-helix ends, whereas pinned solitons were produced in the $α$-helix interior. In this paper, we describe a general mechanism that launches moving solitons in the interior of the $α$-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 $α$-helices, and further support the plausibility of gradual optimization of quantum dynamics for achieving specialized protein functions through natural selection.

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