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Dichotomous noise detected with the help of various single-molecule techniques convincingly reveals the actual occurrence of a multitude of conformational substates composing the native state of proteins. The nature of the stochastic dynamics of transitions between these substates is determined by the particular statistical properties of the noise observed. These involve nonexponential and possibly oscillatory time decay of the second order autocorrelation function, its relation to the third order autocorrelation function, and a relationship to dwell-time distribution densities and their correlations. Processes gated by specific conformational substates are distinguished from those with fluctuating barriers. This study throws light on the intriguing matter of the possibility of multiple stepping of the myosin motor along the actin filament per ATP molecule hydrolyzed.

An increasing body of experimental evidence indicates the slow character of internal dynamics of native proteins. The important consequence of this is that theories of chemical reactions, used hitherto, appear inadequate for description of most biochemical reactions. Construction of a contemporary, truly advanced statistical theory of biochemical processes will need simple but realistic models of microscopic dynamics of biomolecules. In this review, intended to be a contribution towards this direction, three topics are considered. First, an intentionally simplified picture of dynamics of native proteins which emerges from recent investigations is presented. Fast vibrational modes of motion, of periods varying from 10(-14) to 10(-11) s, are contrasted with purely stochastic conformational transitions. Significant evidence is adduced that the relaxation time spectrum of the latter spreads in the whole range from 10(-11) to 10(5) s or longer, and up to 10(-7) s it is practically quasi-continuous. Next, the essential ideas of the theory of reaction rates based on stochastic models of intramolecular dynamics are outlined. Special attention is paid to reactions involving molecules in the initial conformational substrates confirmed to the transition state, which is realized in actual experimental situations. And finally, the two best experimentally justified classes of models of conformational transition dynamics, symbolically referred to as "protein glass" and "protein machine", are described and applied to the interpretation of a few simple biochemical processes, perhaps the most important result reported is the demonstration of the possibility of predominance of the short initial condition-dependent stage of protein involved reactions over the main stage described by the standard kinetics. This initial stage, and not the latter, is expected to be responsible for the coupling of component reactions in the complete enzymatic cycles as well as more complex processes of biological free energy transduction.

Great progress in studies of protein dynamics in the past decade propels an essential alteration in our understanding of the enzymatic catalysis phenomenon. A careful analysis of assumptions made by the hitherto used conventional theory of chemical reactions shows that neither of them is in fact satisfied. One of the reasons is the presence of a slow interconformational dynamics within the protein native state. In consequence, the simple classical statement "enzymes accelerate reactions by decreasing the free energy of activation" represents only half of the truth. Enzymatic reactions actually proceed through 'gates' of relatively low free energy but it is not the process of activated gate crossing that limits the reaction rate, but the process of generally non-activated gate opening, controlled by the conformational relaxation. Possible consequences of this fact are pointed out.