Protein-Machine model of a single enzymatic reaction

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.