Synthetic biology aims at rationally implementing biological systems from scratch. Given the complexity of living systems and our current lack of understanding of many aspects of living cells, this is a major undertaking. The design of in vitro systems can be considerably easier, because they can consist of fewer constituents, are quasi time invariant, their parameter space can be better access...

Conformational dynamics in bilobed enzymes can be used to regulate their activity. One such enzyme, the eukaryotic decapping enzyme Dcp2, controls the half-life of mRNA by cleaving the 5' cap structure, which exposes a monophosphate that is efficiently degraded by exonucleases. Decapping by Dcp2 is thought to be controlled by an open-to-closed transition involving formation of a composite activ...

The advent of molecular techniques has improved our understanding of the microbial communities responsible for denitrification and is beginning to address their role in controlling denitrification processes. There is a large diversity of bacteria, archaea, and fungi capable of denitrification, and their community composition is structured by long-term environmental drivers. The range of tempera...

We have determined the kinetic parameters of the individual steps of the threonine pathway from aspartate in Escherichia coli under a single set of experimental conditions chosen to be physiologically relevant. Our aim was to summarize the kinetic behaviour of each enzyme in a single tractable equation that takes into account the effect of the products as competitive inhibitors of the substrate...

Gibbsian equilibrium statistical thermodynamics is the theoretical foundation for isothermal, closed chemical, and biochemical reaction systems. This theory, however, is not applicable to most biochemical reactions in living cells, which exhibit a range of interesting phenomena such as free energy transduction, temporal and spatial complexity, and kinetic proofreading. In this article, a nonequ...

A number of enzyme digestion assays show apparent first-order kinetics of reactant depletion. There are four possible explanations of this phenomenon: (i) the reaction is dominated by a first-order limiting step, (ii) the digestion follows a pseudo-first-order kinetics under the excess of a reactant species, (iii) the first-order kinetics is only applicable to the slow transient of the reaction...

An analysis of complex kinetic mechanisms is proposed that consists of two steps, (i) building of an kinetic scheme from experimental data other than steady-state kinetics and (ii) numerical simulation and analysis of the kinetics of the proposed scheme in relation to the experimental kinetics. Procedures are introduced to deal with large numbers of enzymatic states and rate constants, and nume...

Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. Œis procedure provides stoichiometries, reaction ƒuxes (rate laws), and reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicabilit...

Abbreviated expressions for enzyme kinetic expressions, such as the Michaelis-Menten (M-M) equations, are based on the premise that enzyme concentrations are low compared with those of the substrate and product. When one does progress experiments, where the solute is consumed during conversion to form a series of products, the idealized conditions are violated. Here, we analyzed data of xanthin...

This article sketches the road from the establishment of the principles of enzyme kinetics, at the beginning of the 20th century, to the discovery of regulatory mechanisms and the models to explain them, from the middle of the century onwards. A long gap in time separates the two periods, in which technological advances were made that allowed the discovery of feedback inhibition and cooperativi...