Reaction mechanism of non-allosteric phosphofructokinase.

The reaction mechanism of the non-allosteric phosphofructokinase from Lactobacillus plantarum was investigated by initial-rate bisubstrate kinetics and product inhibition kinetics adn by the measurement of equilibrium isotope exchange in the presence of various substrate and product concentrations. The reaction mechanism is clearly sequential. The product inhibition and equilibrium isotope-exchange patterns are consistent with an ordered bi-bi reaction sequence with fructose 6-phosphate as the leading substrate and ADP as the first product released from the enzyme.     

On the mechanism of alpha-amylase.

Two inhibitors, acarbose and cyclodextrins (CD), were used to investigate the active site structure and function of barley alpha-amylase isozymes, AMY1 and AMY2. The hydrolysis of DP 4900-amylose, reduced (r) DP18-maltodextrin and maltoheptaose (catalysed by AMY1 and AMY2) was followed in the absence and in the presence of inhibitor. Without inhibitor, the highest activity was obtained with amylose, kcat/Km decreased 103-fold using rDP18-maltodextrin and 10(5) to 10(6)-fold using maltoheptaose as substrate. Acarbose is an uncompetitive inhibitor with inhibition constant (L1i) for amylose and maltodextrin in the micromolar range. Acarbose did not bind to the active site of the enzyme, but to a secondary site to give an abortive ESI complex. Only AMY2 has a second secondary binding site corresponding to an ESI2 complex. In contrast, acarbose is a mixed noncompetitive inhibitor of maltoheptaose hydrolysis. Consequently, in the presence of this oligosaccharide substrate, acarbose bound both to the active site and to a secondary binding site. alpha-CD inhibited the AMY1 and AMY2 catalysed hydrolysis of amylose, but was a very weak inhibitor compared to acarbose.beta- and gamma-CD are not inhibitors. These results are different from those obtained previously with PPA. However in AMY1, as already shown for amylases of animal and bacterial origin, in addition to the active site, one secondary carbohydrate binding site (s1) was necessary for activity whereas two secondary sites (s1 and s2) were required for the AMY2 activity. The first secondary site in both AMY1 and AMY2 was only functional when substrate was bound in the active site. This appears to be a general feature of the alpha-amylase family.     

Kinetic mechanism of myofibril ATPase.

The kinetic mechanism of myofibril ATPase was investigated using psoas and mixed back muscle over a range of ionic strengths. Myofibrils were labeled with pyrene iodoacetamide to measure the rate constants for the binding of ATP and formation of the weakly attached state. The velocity of shortening was measured by stopping the contraction at various times by mixing with pH 4.5 buffer. The transient and steady-state rates of ATP hydrolysis were measured by the quench flow method. The results fitted the kinetic scheme [formula: see text] The rate constants (or equilibrium constants for steps 1 and 6) were obtained for the six steps. k5 was calculated from the KM for shortening velocity, K1, and k2. The rate constants were essentially equal for myofibrils and acto-S-1 at low ionic strength. Increasing the ionic strength up to 100 mM in NaCl increased the rate of the hydrolysis step and the size of the phosphate burst and the effective rate of product release became the rate-limiting step. The step calculated from the velocity of shortening, k5, and k2 is 15 nm, based on a model in which step 4 is the force-generating step.     

Reaction mechanism of erythrocyte phosphofructokinase.

The reaction mechanism of erythrocyte phosphofructokinase (PFK) was investigated by the initial velocity and the product inhibition. Intersecting lines obtained with initial velocity studies are consistent with a sequential mechanism and the formation of ternary complex as an intermediate. The product inhibition studies support an ordered Bi Bi mechanism in which fructose 6 phosphate (F6P) is the first substrate binding and adenosine diphosphate (ADP) is dissociated from the enzyme before fructose-1,6-P2 (FDP).     

Human glutamic-gamma-semialdehyde dehydrogenase. Kinetic mechanism.

The kinetic mechanism of homogeneous human glutamic-gamma-semialdehyde dehydrogenase (EC 1.5.1.12) with glutamic gamma-semialdehyde as substrate was determined by initial-velocity, product-inhibition and dead-end-inhibition studies to be compulsory ordered with rapid interconversion of the ternary complexes (Theorell-Chance). Product-inhibition studies with NADH gave a competitive pattern versus varied NAD+ concentrations and a non-competitive pattern versus varied glutamic gamma-semialdehyde concentrations, whereas those with glutamate gave a competitive pattern versus varied glutamic gamma-semialdehyde concentrations and a non-competitive pattern versus varied NAD+ concentrations. The order of substrate binding and release was determined by dead-end-inhibition studies with ADP-ribose and L-proline as the inhibitors and shown to be: NAD+ binds to the enzyme first, followed by glutamic gamma-semialdehyde, with glutamic acid being released before NADH. The Kia and Kib values were 15 +/- 7 microM and 12.5 microM respectively, and the Ka and Kb values were 374 +/- 40 microM and 316 +/- 36 microM respectively; the maximal velocity V was 70 +/- 5 mumol of NADH/min per mg of enzyme. Both NADH and glutamate were product inhibitors, with Ki values of 63 microM and 15,200 microM respectively. NADH release from the enzyme may be the rate-limiting step for the overall reaction.     

DNA fiber-FISH staining mechanism.

Fluorescence in situ hybridization to DNA fibers (Fiber-FISH) is a high-resolution, wide-ranging physical DNA mapping method that finds increasing application in the study of pathological gene rearrangements. Here we present experiments designed to understand the nature of the discontinuous FISH signal patterns seen after Fiber-FISH. Use of a novel cisplatin-based chemical labeling method enabled us to produce intact biotin-labeled cosmid target DNA molecules. We monitored by immunofluorescence the fate of such cosmid targets during denaturation and hybridization. The same cosmid DNA labeled with digoxigenin by nick-translation was used to analyze the FISH probe signal distribution in a different color. The probe signals proved to be a subset of the target signals remaining after denaturation and hybridization. We argue that the discontinuity of probe signals in Fiber-FISH is mainly caused by loss of target DNA and limited accessibility due to in situ renaturation and attachment. Furthermore, we conclude that FISH sensitivity is determined by hybridization efficiency and not the ability to generate sufficient signal from small probes. (J Histochem Cytochem 48:743-745, 2000)     

The mechanism of skeletal muscle myosin ATPase. The mechanism of ADP interaction

The mechanism of interaction between ADP and the myosin active center has been studied using a transient kinetic technique. The results show that the interaction of ADP with the myosin active center is a homogeneous process independent of the association state of the active centers; namely, whether ADP interacts with the monomeric myosin subfragment-1, or with the dimeric forms heavy meromyosin and myosin. The kinetics of the interaction conforms to a simple two-step reaction mechanism for ADP binding. The kinetic and thermodynamic constants for this mechanism have been determined. In addition, analysis of the binding isotherm indicates that the two active sites in heavy meromyosin and myosin function as identical and independent sites.     

Analysis of the mechanism of chloramphenicol acetyltransferase by steady-state kinetics. Evidence for a ternary-complex mechanism.

The mechanism of the enzymic reaction responsible for chloramphenicol resistance in bacteria was examined by steady-state kinetic methods. The forward reaction catalysed by chloramphenicol acetyltransferase leads to inactivation of the antibiotic. Use of alternative acyl donors and acceptors, as well as the natural substrates, has yielded data that favour the view that the reaction proceeds to the formation of a ternary complex by a rapid-equilibrium mechanism wherein the addition of substrates may be random but a preference for acetyl-CoA as the leading substrate can be detected. Chloramphenicol and acetyl-CoA bind independently, but the correlation between directly determined and kinetically derived dissociation constants is imperfect because of an unreliable slope term in the rate equation. The reverse reaction, yielding acetyl-CoA and chloramphenicol, was studied in a coupled assay involving citrate synthase and malate dehydrogenase, and is best described by a rapid-equilibrium mechanism with random addition of substrates. The directly determined dissociation constant for CoA is in agreement with that derived from kinetic measurements under the assumption of an independent-sites model.     

The mechanism of action of glycosidases.

The factors that may contribute to the rate enhancement observed with enzymatic versus non-enzymatic hydrolysis of glycosides are discussed. The nature of the active site as deduced from labelling studies with beta-glucosidases is described. A two-step mechanism involving either an enzyme stabilized glycosyl ion or a covalent glycosyl-enzyme intermediate is proposed. Experiments with a beta-glucosidase from almonds show that even with 2-deoxy glucosides with good leaving groups as aglycon which are hydrolyzed 1000 times more slowly than the corresponding glucosides, the deglucosylation step is faster than the cleavage of the glycosidic bond.     

Kinetic mechanism of pulmonary carbonyl reductase.

An IgG1 monoclonal antibody, Sulph I, reacting with sulphatide (3'-sulphogalactosylceramide), was produced by immunizing Balb/c mice with that glycolipid coated on Salmonella minnesota bacterial membrane. Radioimmunodetection of the binding of the monoclonal antibody to structurally related glycolipids adsorbed to microtitre plates or chromatographed on thin-layer plates was used to determine its binding epitope. The antibody showed similar binding avidity to three sulphated glycolipids: sulphatide, sulpholactosylceramide and seminolipid. Lysosulphatide did bind the antibody, but, compared with sulphatide, 30 times more antigen was needed for half-maximal binding. Bis(sulphogangliotriosyl)ceramide and bis-sulphogangliotetraosylceramide did not bind the antibody. These results suggest that terminal galactose-3-O-sulphate and part of the hydrophobic region of the glycolipid are recognized by the Sulph I antibody.     

Substrate recognition mechanism of carboxypeptidase Y.

To clarify the substrate-recognition mechanism of carboxypeptidase Y, Fmoc-(Glu)n Ala-OH (n = 1 to 6), Fmoc-(Glu)n Ala-NH2 (1 to 5), and Fmoc-Lys(Glu)3Ala-NH2 were synthesized, and kinetic parameters for these substrates were measured. Km for Fmoc-peptides significantly decreased as peptide length increased from n = 1 to n = 5 with only slight changes in kcat. Km for Fmoc-(Glu)(5,6)Ala-OH were almost the same as one for protein substrates described previously (Nakase et al., Bull. Chem. Soc. Jpn., 73, 2587-2590). These results show that the enzyme has six subsites (S1' and S1-S5). Each subsite affinity calculated from the Km revealed subsite properties, and from the differences of subsite affinity between pH 6.5 and 5.0, the residues in each subsite were predicted. For Fmoc-peptide amide substrates, the priorities of amidase and carboxamide peptidase activities were dependent on the substrate. It is likely that the interactions between side chains of peptide and subsites compensate for the lack of P1'-S1' interaction, so the amidase activity prevailed for Fmoc-(Glu)(3,5)Ala-NH2. These results suggest that these subsites contribute extensively to substrate recognition rather than a hydrogen bond network.