Collective excitations in alpha-helical protein structures interacting with environment

Abstract

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 strength of phonon-phonon interaction between the side-chains and hydration-shell water molecules. As shown, the energy of these excited states is pumped through the interaction of the side-chains with fluctuating water environment of the proteins. The suggested mechanism of the collective vibrational mode excitation is discussed in connection with the recent experiments on the long-lived collective protein excitations in the terahertz frequency region and vibrational energy transport pathways in proteins.