The evolution of oxygenic photosynthesis and ensuing oxygenation of Earth's atmosphere represent a major transition in the history of life. Although many organisms retreated to anoxic environments, others evolved to use oxygen as a high-potential redox couple while concomitantly mitigating its toxicity. To understand the changes in biochemistry and enzymology that accompanied adaptation to O2, ...

Quantum chemical calculations are used to investigate the detailed reaction mechanism of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid (SEPHCHC) synthase (also known as MenD), a thiamin diphosphate-dependent decarboxylase that catalyzes formation SEPHCHC from 2-ketoglutarate and isochorismate. This enzyme is involved in menaquinone biosynthesis pathway M. tuberculosis thoug...

An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or 'invisible' states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the m...

Biochemical reactions in living organism usually take place inside cells. The characteristic feature of these reactions is their executability; the organism does not produce certain substances all the time, but only when they are needed. The reaction is usually triggered after receiving an extra(or intra-) cellular signal. Stimuli-responsiveness is mostly possible because of compartmentalizatio...

Aspartame is an artificial sweetener of low caloric value (approximately 200 times sweeter than sucrose). Aspartame is currently permitted for use in food and beverage production in more than 90 countries. The application of aspartame in food products requires development of rapid, inexpensive and accurate method for its determination. The new assay for determination of aspartame was based on s...

Cellular automata simulations for enzymatic reaction networks differ from other models for reaction-diffusion systems, since enzymes and metabolites have very different properties. This paper presents a model where each lattice site can can contain at most one enzyme molecule, but many metabolite molecules. The rules are constructed to conform to the Michaelis-Menten kinetics by modeling the un...

The scientific literature contains a tremendous amount of kinetic data describing the dynamic behaviour of biochemical reactions over time. These data are needed for computational modelling to create models of biochemical reaction networks and to obtain a better understanding of the processes in living cells. To extract the knowledge from the literature, biocurators are required to understand a...