Dynamical contribution into enzyme catalytic efficiency

TL;DR

This paper presents a physical model linking enzyme vibrational modes to catalytic efficiency, demonstrating how resonant vibrations can significantly accelerate reactions, aligning with observed enzyme behaviors.

Contribution

The study introduces a model connecting enzyme vibrational modes, specifically discrete breathers, to catalytic acceleration, highlighting the role of resonant activation in enzyme efficiency.

Findings

Resonant activation explains enzyme vibrational frequency selection.

Reaction acceleration varies from 10^3 to 10^8 depending on vibrational mode.

Model aligns with solvent viscosity effects on enzyme rates.

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 $100\div200 cm^{-1}$ 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 $10^3\div10^4$) in the case of three-site DB to enormous (up to $10^6\div10^8$) 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.