Apr 15, 2020

Collective Excitations in α-helical Protein Structures Interacting with the Water Environment

BioRxiv : the Preprint Server for Biology
Vasiliy N Kadantsev, Alexey Goltsov


Low-frequency vibrational excitations of protein macromolecules in the terahertz frequency region are suggested to contribute to many biological processes such as enzymatic catalysis, intra-protein energy/charge transport, recognition, and allostery. To explain high effectiveness of these processes, two possible mechanisms of the long-lived excitation were proposed by H. Frohlich and A.S. Davydov which relate to either vibrational modes or solitary waves, respectively. In this paper, we developed a quantum dynamic model of vibrational excitation in -helical proteins interacting with the aqueous environment. In the model, we distinguished three coupled subsystems, i.e. (i) a chain of hydrogen-bonded peptide groups (PGs), interacting with (ii) the subsystem of the side-chain residuals which in turn interacts with (iii) the environment, surrounding water responsible for dissipation and fluctuation in the system. It was shown that the equation of motion for phonon variables of the PG chain can be transformed to nonlinear Schrodinger equation which admits bifurcation into the solution corresponding to the weak damped vibrational modes (Frohlich-type regime) and Davydov solitons. A bifurcation parameter is derived through the strengt...Continue Reading

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Mentioned in this Paper

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Nonlinear Dynamics
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