Substrate (chemistry)

About: Substrate (chemistry) is a research topic. Over the lifetime, 35902 publications have been published within this topic receiving 740722 citations. The topic is also known as: enzyme substrate.

Mechanism-based enzyme inactivators.

Abstract: Publisher Summary An enzyme inactivator, in general, is a compound that produces irreversible inhibition of the enzyme— that is, it irreversibly prevents the enzyme from catalyzing its reaction. Irreversible in this context, however, does not necessarily mean that the enzyme activity never returns only that the enzyme becomes dysfunctional for an extended (but unspecified) period of time. A mechanism-based enzyme inactivator, by the definition used here, is a compound that is transformed by the catalytic machinery of the enzyme into a species that acts as an affinity labeling agent, a transition state analog, or a tight-binding inhibitor (either covalent or noncovalent) prior to release from the enzyme. Mechanism-based enzyme inactivation is a powerful tool for the studies of enzyme mechanisms and mechanisms of enzyme inactivation, by small molecules. Mechanistic hypotheses can be tested by appropriate molecular design, utilizing the isotopically labeled analogs, to permit the elucidation of the structures of metabolites produced and to determine the portions of the mechanism-based inactivators that become covalently attached to the target enzyme. This approach to the studies of enzyme mechanisms is well suited for those who are geared more to the organic chemistry of enzymecatalyzed reactions and who have insights into the chemical machinery of active sites of enzymes. The use of mechanism-based enzyme inactivators is yet another of the very important methods in enzymology.

Use of Fluorogenic Model Substrates for Extracellular Enzyme Activity (EEA) Measurement of Bacteria

Abstract: "ectoenzymes" and the latter "extracellular" enzymes. Substrates for hydrolysis are generally proteins, carbohydrates, fats and organic P- or S- compounds. Mechanisms of decomposition of individual compounds within these groups may be studied by in vitro experiments. However, aquatic microbial ecologists require, in many cases, a more general measurement of the in situ hydrolytic capacity of the prevailing bacterial community. This has led to the adaptation of biochemical methods for determination of overall bacterial extracellular enzyme activities (peptidases, a- and P-glucosidases, chi- tinases, etc.) in natural waters (Table 1). These methods enable us to study the impact of extracellular enzyme activity (EEA) on bacterial substrate uptake, bacterial growth, and water chemistry. The quantitative estimates of total bacterial extracellular enzyme activity are completed by rapid and sensitive tests for the detection of enzymatic properties of bacterial isolates. The methods used for these purposes are based on the application of fluorogenic model substrates. These substrates have some characteristics in common: (1) they contain an artificial fluorescent molecule and one or more natural molecules (e.g., glucose, amino acids), linked by a specific binding (e.g., peptide binding, ester binding); fluorescence is observed after enzymatic splitting of the complex molecule (Figure 1); (2) the hydrolysis of model substrates is competitively inhibited by a variety of natural compounds with the same structural characteristics; (3) hydrolysis of model substrates follows first order enzyme kinetics; and (4) application of those model substrates allows enzyme activity measurements under natural (in situ) conditions within short incubation periods. The latter is highly im- portant for microbial ecologists, because the process of enzymatic hydrolysis is fully

Enzyme Catalysis: Beyond Classical Paradigms†

Abstract: Despite many decades of intense study, a full description of enzyme catalysis at the molecular level remains to be achieved A number of aspects of biocatalysis are widely accepted, including (i) the conversion of a chemical reaction from an inter- to an intramolecular process with the concomitant decrease in the entropy of activation and (ii) the stabilization of the transition state (TS) by the precise orientation of multiple functional groups at the enzyme active site These functional groups perform the roles of general acid/base, electrophilic/nucleophilic catalysis and charge neutralization via electrostatic and H-bonding interactions The process of covalent bond breaking and forming in enzyme catalysis is accompanied by substrate binding, product release, and protein rearrangement steps, which are rate determining for many enzymes The resulting, multibarrier