Evidence for increased proton dissociation in low-activity forms of dephosphorylated squash-leaf nitrate reductase

Functional roles of slow enzyme conformational changes in network dynamics

Extensive studies from different fields reveal that many macromolecules, especially enzymes, show slow transitions among different conformations. This phenomenon is named such things as dynamic disorder, heterogeneity, hysteretic or mnemonic enzymes across these different fields, and has been directly demonstrated by single molecule enzymology and NMR studies recently. We analyzed enzyme slow conformational changes in the context of regulatory networks. A single enzymatic reaction with slow conformational changes can filter upstream network noises, and can either resonantly respond to the system stimulus at certain frequencies or respond adaptively for sustained input signals of the network fluctuations. It thus can serve as a basic functional motif with properties that are normally for larger intermolecular networks in the field of systems biology. We further analyzed examples including enzymes functioning against pH fluctuations, metabolic state change of Artemia embryos, and kinetic insulation of fluctuations in metabolic networks. The study also suggests that hysteretic enzymes may be building blocks of synthetic networks with various properties such as narrow-banded filtering. The work fills the missing gap between studies on enzyme biophysics and network level dynamics, and reveals that the coupling between the two is functionally important; it also suggests that the conformational dynamics of some enzymes may be evolutionally selected.

Hysteretic enzyme adaptation to environmental pH: change in storage pH of alkaline phosphatase leads to a pH-optimum in the opposite direction to the applied change

The activity of alkaline phosphatase (AP) shows a change in optimum pH in the opposite direction to the applied change in storage pH. Typically, a change in storage pH from 9.8 to 8.5 results in a (reversible) change of the pH-optimum from 10.0 to 10.8. Protein fluorescence analysis shows that this response is probably due to conformational changes induced by the different storage conditions. As storage pH increases, a more 'open' or less 'compact' conformation is attained. Analysis of the diprotic model (a model which describes possible pH-responses of enzymes) indicates, that, as the AP conformation is getting more 'open' an increase in the dissociation of activity-regulating protons of AP occurs. This leads to a decrease in pH-optimum, precisely as found in the experiment. The prerequisite for such a response, however, is that the conformational adaptation to environmental assay pH is slow (hysteretic) when compared with assay time (400 s). The relaxation time of this adaptation was found to be in the order of 2 h.