Uridine diphosphate release mechanism in O-N-acetylglucosamine (O-GlcNAc) transferase catalysis.

O-linked N-acetylglucosamine transferase (OGT) is an essential enzyme that catalyzes the covalent bonding of N-acetylglucosamine (GlcNAc) to the hydroxyl group of a serine or threonine in the target protein. It plays an important role in many important cellular physiological catalytic reactions. Here, we determine the binding mode and the binding free energy of the OGT product (uridine diphosphate, UDP) as well as the hydrogen-bond-dependent release mechanism using extensive molecular dynamic simulations. The Lys634, Asn838, Gln839, Lys842, His901, and Asp925 residues were identified to play a major role in the UDP stabilization in the active site of OGT, where hydrogen bonding and π-π interactions mainly occur. The calculations on the mutant forms support our results. Sixteen possible release channels were identified while the two most favorable channels were determined using random acceleration molecular dynamics (RAMD) simulations combined with the constant velocity pulling (PCV) method. The thermodynamic and dynamic properties as along with the corresponding mechanism were determined and discussed according to the umbrella sampling technique. For the most optimal channel, the main free energy barrier is 13 kcal/mol, which probably originates from the hydrogen bonds between UDP and the Ala896 and Asp925 residues. Moreover, the unstable hydrogen bonds and the rollback of the ligand likely cause the other two small obstacles. This work clarifies the ligand transport mechanism in the OGT enzymatic process and is a great resource for designing inhibitors based on UDP or UDP-GlcNAc.

Activación de la calcio calmodulina quinasa II, CaMKII, por el uridin nucleósido difosfato, UDP, en neuronas granulares de cerebelo / Calcium Calmoduline Kinase II, CaMKII, activation by the uridine nucleoside diphosphate, UPD, in cerebellar granule neurons

Las neuronas granulares de cerebelo en cultivo presentan receptores metabotrópicos de nucleótidos de tipo P2Y6, cuyo agonista fisiológico específico es el nucleótido, uridina difosfato, UDP. Estudios de PCR muestran la presencia de este receptor y el incremento de la expresión con el tiempo. Los estudios de respuesta en célula individual mediante microfluorimetría muestran un incremento del calcio citosólico al estimular con UDP, siendo los incrementos mas significativos en el soma. El incremento del calcio citosólico produce la activación de diversos enzimas dependientes de calcio y concretamente de la calcio-calmodulina quinasa II, CAMKII, enzima que se encuentra ampliamente distribuida en toda la topografía de la neurona granular. Este enzima al activarse se auto-fosforila y mediante anticuerpos contra la forma fosforilada se pueden detectar las zonas mas activas en la célula. Cuando se estimula con UDP, la CaMKII fosforilada aparece fundamentalmente asociada al soma neural, con mucha menor actividad en las prolongaciones axodendríticas, lo que se corresponde con la distribución de los receptores P2Y6 funcionales

Cultured granule cells from cerebellum exhibit nucleotide metabotropic receptors such as the P2Y6 subtype, which physiological agonist is the uridine diphosphate, UDP. The PCR analysis show the presence of P2Y6 messenger RNA, increasing with the days in culture. Single cell microfluorimetric studies show citosolic calcium increase in response to UDP, this being more significant at the soma level. The cytosolic calcium increase triggers cellular responses mediated by calcium dependent enzymes. This is the case for calcium-calmodulin kinase II, CaMKII, which is extensively distributed through the granule neuron, according the immunocytochemical studies. This enzyme once activated is able to autophosphorylate and by using antibodies against the phosphorylated form the active zones can be detected. After UDP stimulation, the location of the phosphorylated form of CaMKII appears to be mainly at the neural soma, with lower presence at the axodendritic prolongations, which correlates with the functional P2Y6 subtype receptor distribution

Glucose production, gluconeogenesis, and hepatic tricarboxylic acid cycle fluxes measured by nuclear magnetic resonance analysis of a single glucose derivative.

A triple-tracer method was developed to provide absolute fluxes contributing to endogenous glucose production and hepatic tricarboxylic acid (TCA) cycle fluxes in 24-h-fasted rats by (2)H and (13)C nuclear magnetic resonance (NMR) analysis of a single glucose derivative. A primed, intravenous [3,4-(13)C(2)]glucose infusion was used to measure endogenous glucose production; intraperitoneal (2)H(2)O (to enrich total body water) was used to quantify sources of glucose (TCA cycle, glycerol, and glycogen), and intraperitoneal [U-(13)C(3)] propionate was used to quantify hepatic anaplerosis, pyruvate cycling, and TCA cycle flux. Plasma glucose was converted to monoacetone glucose (MAG), and a single (2)H and (13)C NMR spectrum of MAG provided the following metabolic data (all in units of micromol/kg/min; n = 6): endogenous glucose production (40.4+/-2.9), gluconeogenesis from glycerol (11.5+/-3.5), gluconeogenesis from the TCA cycle (67.3+/-5.6), glycogenolysis (1.0+/-0.8), pyruvate cycling (154.4+/-43.4), PEPCK flux (221.7+/-47.6), and TCA cycle flux (49.1+/-16.8). In a separate group of rats, glucose production was not different in the absence of (2)H(2)O and [U-(13)C]propionate, demonstrating that these tracers do not alter the measurement of glucose turnover.

Inhibition of nucleoside diphosphate kinase in rat liver mitochondria by added 3'-azido-3'-deoxythymidine.

The effect of 3'-azido-3'-deoxythymidine on nucleoside diphosphate kinase of isolated rat liver mitochondria has been studied. This is done by monitoring the increase in the rate of oxygen uptake by nucleoside diphosphate (TDP, UDP, CDP or GDP) addition to mitochondria in state 4. It is shown that 3'-azido-3'-deoxythymidine inhibits the mitochondrial nucleoside diphosphate kinase in a competitive manner, with a Ki value of about 10 microM as measured for each tested nucleoside diphosphate. It is also shown that high concentrations of GDP prevent 3'-azido-3'-deoxythymidine inhibition of the nucleoside diphosphate kinase.