Launching of Davydov solitons in proteins

Biological order provided by protein α-helices could be exploited to increase the efficiency of energy transport. Self-trapping of amide I excitons by the induced phonon deformation of the hydrogen-bonded lattice of peptide groups generates either pinned or moving solitons following the Davydov model. The effect of in-phase Gaussian pulses of amide I energy, however, is strongly dependent on the site of application. Moving solitons are only launched when the amide I energy is applied at one of the α-helix ends, whereas pinned solitons are produced in the α-helix interior.

In our recent article published in Physica E: Low-dimensional Systems and Nanostructures, 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. In particular, we have shown that moving solitons can be launched at any site in the protein for nonzero phase modulation (0 < |∆ω| < π/2) of the applied amide I energy Gaussian pulse. Phase modulation should occur naturally since the ATP hydrolysis sites would have different distances to different locations in nearby protein α-helices and quantum paths with different lengths would accumulate different phases according to Feynman's path integral formalism. Therefore, the relative orientation and distance between an ATP hydrolysis site and a receptive protein α-helix, should be sufficient for proteins to be able to control the direction and velocity of generated solitons. We have also demonstrated that low values of the nonlinear exciton-phonon coupling, which are otherwise below the threshold for soliton formation, could be compensated by an increased number of amide I quanta in the energy pulses. Thus, at early stages of natural evolution in environments that destabilize the α-helical secondary structure, protein functionality through soliton transport could have been achieved at the expense of higher energy fluxes.