Kinetic mechanisms of rat polymerase beta-ssDNA interactions. Quantitative fluorescence stopped-flow analysis of the formation of the (Pol beta)(16) and (Pol beta)(5) ssDNA binding mode.

Kinetics of rat polymerase beta (pol beta) binding to the single-stranded DNA (ssDNA) in the (pol beta)(16) and (pol beta)(5) binding modes has been examined, using the fluorescence stopped-flow technique. Binding of the enzyme to the ssDNA containing fluorescein is characterized by a strong increase of the DNA fluorescence, which provides an excellent signal to quantitatively study the complex mechanism of the ssDNA recognition process. The experiments were performed with a 20-mer ssDNA, which can engage the enzyme in the (pol beta)(16) binding mode, i.e. it encompasses the entire, total DNA-binding site of rat pol beta, and with a 10-mer which binds the enzyme exclusively in the (pol beta)(5) binding mode where only the 8 kDa domain of the enzyme is engaged in interactions with the DNA. The data indicate that the formation of the (pol beta)(16) binding mode occurs by a minimum three-step mechanism with the bimolecular binding step followed by two isomerizations: [formula-see text] A similar mechanism is observed in the formation of the (pol beta)(5) binding mode, although at low salt concentrations there is an additional, slow step in the reaction. The data analysis was performed using the matrix projection operator technique, a powerful method to address stopped-flow kinetics, particularly, amplitudes. The binding modes differ in the free energy changes of the partial reactions and ion effects on transitions between intermediates that reflect different participation of the two structural domains. The formation of both binding modes is initiated by the fast association with the ssDNA through the 8 kDa domain, followed by transitions induced by interactions at the interface of the 8 kDa domain and the DNA. In the (pol beta)(16) binding mode, the subsequent intermediates are stabilized by the DNA binding to the DNA-binding subsite on the 31 kDa domain. The data indicate that interactions of the ssDNA-binding subsite of the 8 kDa domain with the ssDNA, controlled by the ion binding, induce conformational transitions of the formed complexes in both binding modes. The sequential nature of the determined mechanisms indicates a lack of kinetically significant conformational equilibrium of rat pol beta, prior to ssDNA binding.

Interactions of nucleotide cofactors with the Escherichia coli replication factor DnaC protein.

Quantitative analyses of the interactions of nucleotide cofactors with the Escherichia coli replicative factor DnaC protein have been performed using thermodynamically rigorous fluorescence titration techniques. This approach allowed us to obtain stoichiometries of the formed complexes and interaction parameters, without any assumptions about the relationship between the observed signal and the degree of binding. The stoichiometry of the DnaC-nucleotide complex has been determined in direct binding experiments with fluorescent nucleotide analogues, MANT-ATP and MANT-ADP. The stoichiometry of the DnaC complexes with unmodified ATP and ADP has been determined using the macromolecular competition titration method (MCT). The obtained results established that at saturation the DnaC protein binds a single nucleotide molecule per protein monomer. Analyses of the binding of fluorescent analogues and unmodified nucleotides to the DnaC protein show that ATP and ADP have the same affinities for the nucleotide-binding site, albeit the corresponding complexes have different structures, specifically affected by the presence of magnesium cations in solution. Although the presence of the gamma-phosphate does not affect the affinity, the structure of the triphosphate group is critical. While the affinity of ATP-gamma-S is the same as the affinity of ATP, the affinities of AMP-PNP and AMP-PCP are approximately 2 and approximately 4 orders lower than that of ATP, respectively. Moreover, the ribose plays a significant role in forming a stable complex. The binding constants of dATP and dADP are approximately 2 orders of magnitude lower than those for ribose nucleotides. The nucleotide-binding site of the DnaC protein is highly base specific. The intrinsic affinity of adenosine triphosphates and diphosphates is at least 3-4 orders of magnitude higher than for any of the other examined nucleotides. The obtained data indicate that the recognition mechanism of the nucleotide by the structural elements of the binding site is complex with the base providing the specificity and the ribose, as well as the second phosphate group contributing to the affinity. The significance of the results for the functioning of the DnaC protein is discussed.

Combined administration of glucose precursors is more efficient than that of glucose itself in recovery from hypoglycemia.

The purpose of the present study was to investigate the effect of the combined administration of hepatic gluconeogenic substrates (glycerol + L-lactate + L-alanine + L-glutamine) on glucose recovery during insulin induced hypoglycemia (IIH), in rats. IIH was obtained by an ip injection of regular insulin (1 U/kg). Thus, 150 min after insulin administration the rats received an ip injection of glycerol + L-lactate + L-alanine + L-glutamine (each 100 mg/kg). In these experiments control groups, which received saline, glucose or isolated precursors (100 mg/kg), were employed. Glycemia was measured 30 min later, i.e., 180 min after insulin injection. The results showed that the combined administration of gluconeogenic precursors is more efficient than that of glucose itself to promote glycemia recovery. Since, the blood levels of hepatic glucose precursors were decreased (glycerol, L-lactate and L-alanine) or maintained (L-glutamine) during IIH, the ability of the liver to produce glucose from these gluconeogenic substrates was investigated. The results showed that the maximal capacity of the liver to produce glucose from glycerol (2 mM), L-lactate (2 mM), L-alanine (5 mM) and L-glutamine (5 mM) was increased. To L-alanine and L-glutamine, not only the glucose production was increased (P < 0.05) but also the production of L-lactate, pyruvate and urea. Therefore, the results suggest that the decreased availability of glucose precursors, promoted by insulin administration, limits the participation of hepatic gluconeogenesis to glycemia recovery. However, the administration of gluconeogenic precursors could overcome this limitation and promote better glycemia recovery than glucose itself.

Analytical titration curves of glycosyl hydrolase Cel45 by combined isoelectric focusing-electrophoresis.

The electrical charge of endocellulase Cel45-core has been determined by combined isoelectric focusing-electrophoresis in the range of pH 3-9. In order to transform electrophoretic mobility to absolute electrical charge value, several corrections were applied: the frictional coefficient theoretically calculated from the molecular dimensions depends on porous gel structure and on the ionic strength of the solution. By comparing the curve calculated according to the Linderstrom-Lang equation, the number of charged electrical groups exposed to the solvent and their apparent ionization constants, pK(o)i, can be determined. Furthermore, the macromolecule structure can be assumed not to change in this pH range. This finding is necessary to understand the structure and the electrical properties of the entire Cel45 molecule.

Hepatic gluconeogenesis in rats trained to eat a single meal daily. Role of eating periodicity and the amount of food ingested in the last meal.

Rats trained to eat a single daily meal (MF rats), from 8:00-10:00 a.m., increased food intake from the 1st to the 12th (125%) day of feeding training. In this work we compared the influence of the higher food ingestion in the last meal and feeding training on hepatic gluconeogenesis. Thus, rats at the 1st (MF(1st day-5g) group) and 13th day (MF(13th day-5g) group) of training, refed with a fixed amount of food (5g) were employed. In addition, a third group of MF rats, refed on day 12 with 75% (12g) of the food ingested by MF rats on the 13th day of the feeding training (MF(13th day-12g)) was included. The experiments were performed at 22 h after meal (8:00 a.m.). Our results demonstrated that feeding training had a crucial role in determining gluconeogenesis from pyruvate (5 mM). Additionally, gluconeogenesis from L-glutamine (5 mM) was influenced by periodicity of eating and the amount of food ingested in the last meal. In contrast, gluconeogenesis from L-alanine (5 mM) was not influenced by both factors. In conclusion, our findings suggested that the hepatic gluconeogenesis was influenced by food ingestion and/or feeding training depending of the substrate investigated. These effects on gluconeogenesis may have implications for use in diabetic regimens.