Dynamical contribution into enzyme catalytic efficiency

Abstract

A realistic physical model for the so called rate promoting vibration (RPV) at enzyme action is constructed. The origin of the RPV is assumed to be an oscillating electric field produced by long-lived localized vibrational modes in protein dynamics, namely, by the so called discrete breather (DB) in secondary structure. The strength of interaction of the RPV with the reaction coordinate is evaluated and its effect on the reaction acceleration is assessed within the framework of modern theory for thermally activated escape rate at periodic driving. We reveal the phenomenon of resonant activation in our model elucidating why the frequency of the RPV in the range $100÷200c{m}^{-1}$ was chosen by the evolution of enzymes as an optimal one. The effect of the RPV on the reaction acceleration is shown to vary from moderate one (up to $10^3÷10^4$) in the case of three-site DB to enormous (up to $10^6÷10^8$) in the case of five-site DB and thus can significantly contribute into enzyme catalytic efficiency. Also the model is shown to be compatible with the known functional dependence of enzymatic reaction rates on solvent viscosity.

19 LaTex pages, 3 eps figures, final version, accepted for publication to Physica A

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Cited by in corpus (8)

• Discrete breathers in nonlinear network models of proteins
• Long-range energy transfer in proteins
• Solvent viscosity dependence for enzymatic reactions
• Discrete Breathers in a Realistic Coarse-Grained Model of Proteins
• Model for solvent viscosity effect on enzymatic reactions
• Model for vibrationally enhanced tunneling of proton transfer in hydrogen bond
• Schrödinger equation with Pauli-Fierz Hamiltonian and double well potential as model of vibrationally enhanced tunneling for proton transfer in hydrogen bond
• Low frequency limit for thermally activated escape with periodic driving