Protein-Machine model of a single enzymatic reaction

TL;DR

This paper introduces a simplified Protein-Machine model that captures the conformational dynamics of enzymes, providing formulas for reaction times and enzyme activity, highlighting differences in kinetic mechanisms near and far from equilibrium.

Contribution

It presents a novel theoretical model of enzymatic reactions emphasizing conformational relaxation over chemical details, with analytical expressions for key kinetic parameters.

Findings

Derived formulas for chemical relaxation time and enzyme turnover number.

Showed that kinetic mechanisms vary depending on proximity to equilibrium.

Highlighted the importance of conformational dynamics in enzyme kinetics.

Abstract

The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual vibrational dynamics, a rich interconformational (activated) dynamics exists. The slowness of this dynamics makes any conventional theory of chemical reactions inapplicable for description of enzymatic reactions. It is presumably a rule that it is the process of conformational relaxation, and not the details of chemical mechanism, that affects their rate. In a simple model of Protein-Machine type, applied in constructing a novel theory of enzymatic reaction, conformational dynamics is treated as a realative quasi-continuous motion of solid-like structural elements of protein. Simple and tractable formulas for the chemical relaxation time and the enzyme turnover number in the steady state conditions are found. The important result obtained is that the kinetic mechanisms close to and far from the equilibrium can differ.