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.

Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase.

Abstract: The enzymatic hydrolysis of O-glycosidic linkages is one of the most diverse and widespread reactions in nature and involves a classic “textbook” enzyme mechanism. A multidisciplinary analysis of a β-glycoside hydrolase, the Cel5A from Bacillus agaradhaerens, is presented in which the structures of each of the native, substrate, covalent-intermediate, and product complexes have been determined and their interconversions analyzed kinetically, providing unprecedented insights into the mechanism of this enzyme class. Substrate is bound in a distorted 1S3 skew-boat conformation, thereby presenting the anomeric carbon appropriately for nucleophilic attack as well as satisfying the stereoelectronic requirements for an incipient oxocarbenium ion. Leaving group departure results in the trapping of a covalent α-glycosyl-enzyme intermediate in which the sugar adopts an undistorted 4C1 conformation. Finally, hydrolysis of this intermediate yields a product complex in which the sugar is bound in a partially disordere...

Initiation of DNA-Dependent RNA Synthesis and the Effect of Heparin on RNA Polymerase

Abstract: The kinetics of RNA synthesis, catalyzed by DNA-dependent RNA polymerase from Escherichia coli, show a lag phase at high ionic strength or at low temperature when using a double-stranded DNA as template. This lag phase increases with decreasing temperature at constant ionic strength or with increasing ionic strength at constant temperature. With single-stranded DNA as template, no lag phase is observed. The length of the lag phase is greatly shortened by pre-incubation of the enzyme with DNA at low Mg++ concentration, independent of the presence of substrate. Heparin is a strong inhibitor of free and DNA-bound polymerase. Two heparin molecules are required for the inactivation of one enzyme molecule. Enzyme engaged in RNA synthesis is instantly inhibited on single-stranded DNA but not on double-stranded DNA. With the aid of this inhibitor it is shown that 10 minutes after the start of incubation, at 16°, all enzyme molecules have initiated RNA chains on double-stranded DNA.

Substrate specificity and kinetic mechanism of the Sir2 family of NAD+-dependent histone/protein deacetylases.

Abstract: The Silent information regulator 2 (Sir2) family of enzymes consists of NAD+-dependent histone/protein deacetylases that tightly couple the hydrolysis of NAD+ and the deacetylation of an acetylated substrate to form nicotinamide, the deacetylated product, and the novel metabolite O-acetyl-ADP-ribose (OAADPR). In this paper, we analyzed the substrate specificity of the yeast Sir2 (ySir2), the yeast HST2, and the human SIRT2 homologues toward various monoacetylated histone H3 and H4 peptides, determined the basic kinetic mechanism, and resolved individual chemical steps of the Sir2 reaction. Using steady-state kinetic analysis, we have shown that ySir2, HST2, and SIRT2 exhibit varying catalytic efficiencies and display a preference among the monoacetylated peptide substrates. Bisubstrate kinetic analysis indicates that Sir2 enzymes follow a sequential mechanism, where both the acetylated substrate and NAD+ must bind to form a ternary complex, prior to any catalytic step. Using rapid-kinetic analysis, we hav...

Micromotors Powered by Enzyme Catalysis

Abstract: Active biocompatible systems are of great current interest for their possible applications in drug or antidote delivery at specific locations. Herein, we report the synthesis and study of self-propelled microparticles powered by enzymatic reactions and their directed movement in substrate concentration gradient. Polystyrene microparticles were functionalized with the enzymes urease and catalase using a biotin-streptavidin linkage procedure. The motion of the enzyme-coated particles was studied in the presence of the respective substrates, using optical microscopy and dynamic light scattering analysis. The diffusion of the particles was found to increase in a substrate concentration dependent manner. The directed chemotactic movement of these enzyme-powered motors up the substrate gradient was studied using three-inlet microfluidic channel architecture.