Internal dynamics of biomolecules and statistical theory of biochemical processes

Abstract

Statistical theory of any physical process needs a formulation of possibly simple but adequate models of the phenomena underlying microscopic dynamics. Remarkable progress in studies of internal dynamics of biomolecules acomplished in the recent years has made it possible to formulate such models also for the basic biochemical processes. It is now clearly established that apart from the usual vibrations, the biomolecules, in particular proteins, reveal also a purely stochastic dynamics of transitions between a multitude of conformational substates. The slow character of this dynamics is the reason why neither steady-state kinetics nor the time course of biochemical processes involving protein enzymes can be described in terms of conventional chemical kinetics, i.e., reaction rate constants. A more sophisticated language of the mean first-passage times or the first-passage time distribution densities has to be used. These are to be determined within a definite model of conformational transition dynamics. A single and two coupled enzymatic reactions controlled and gated by the arbitrary type stochastic dynamics of conformational transitions are considered in more detail and an application to actomyosin molecular motor is discussed.