Diffusion models of internal dynamics of proteins

Abstract

Formulation of a truly advanced statistical theory of biochemical processes needs simple but adequate models of phenomena underlying microscopic dynamics of biomolecules, in particular enzymatic proteins. A synthetic picture of microscopic dynamics of proteins emerging from the recent studies is outlined and two classes of theoretical models of slow conformational (activated) dynamics within protein native state, both of diffusion type, are described. In the first class, referred symbolically to as Protein-Glass, the dynamics is represented by diffusion of structural deflects in liquid-like region of protein of an effective dimension between 1 and 2, to be be approximated by various fractal lattices. In the second, Protein-Machine class of models the conformational dynamics is treated as a relative motion of solid-like fragments of secondary structure, also of the nature of quasicontinuous diffusion. It is presumably a rule that it is the process of conformational relaxation, and not the details of chemical mechanism, that affects the rate of biochemical processes. Under this assumption a particular Protein-Machine model is applied for constructing a theory of single enzymatic reaction. The important result obtained is that the reaction pathways close to and far from the chemical equilibrium can differ. A possibility is indicated of direct coupling among several reactions taking place at the same multienzyme complex.