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Enzyme functioning: Along the lines of nonequilibrium phase transitions

In recent decades the mechanisms of regulation of enzyme activity attract growing attention. Even the cornerstone schemes and notions of enzymology, such as the Michaelis-Menten scheme or cooperativity, undergo permanent refinements and revisions. Theoretical interpretations of new data, however, remain within the standard chemical kinetics framework. Although this admits qualitative explanations of some significant regulation phenomena like performance of ‘hysteretic’ enzymes, many characteristic features of enzymatic reactions (essentially nonexponential kinetics, dependence of rate constants on substrate concentration, and others) can hardly be accommodated. On the other hand, the inherent factors of enzyme functioning – flux conditions, slow structural changeability, nonlinear feedback between fast reaction acts and slow conformational rearrangements – provide a natural basis for self-organization phenomena. While their typical manifestations are related to macroscopic systems, the enzyme functioning can serve as an example of self-organization on the lowest possible level, down to single molecules. We put forward this concept of dynamical molecular self-organization in early 90’s and then developed its theoretical and experimental substantiations with the example of primary reactions of photosynthesis. In this work, I apply it to the Michaelis-Menten scheme. Within this paradigm, suitable for either ensemble or single molecule conditions, the stable functional regimes of enzyme operation emerge and interchange/coexist due to analogues of nonequilibrium phase transitions determined by the strength of substrate-conformation interaction and controlled by substrate concentration. In particular, the phenomena like ‘monomeric cooperativity’ or self-inhibition naturally follow from even the simplest two-state model of an enzyme with an only binding site.