The combination between hemolysins and red cells or ghosts,as studied with a radioactive lysin and with new color reactions

The quantity of a radioactive hemolysin, sodium dodecyl sulfonate-S³⁵, taken up by red cells from concentrations too small to produce hemolysis varies with the lysin concentration, and does so in a way which can be described by an adsorption isotherm. Attempts to use color reactions or surface tension measurements to determine the quantity of digitonin, saponin, and the bile salts taken up by red cells from hypolytic concentrations have failed, principally because chromogenic, and also surface-active, substances are liberated from the cells when the lysin is added. Color reactions with the anthrone reagent show that digitonin and saponin are both taken up by or fixed to red cell ghosts; the extent of the uptake, however, is uncertain, again because of the liberation of chromogenic substances. Comparison of the results of the various methods which measure the apparent amount of lysin fixed, or utilized in reactions between lysins and red cells or ghosts show discrepancies between results given by direct methods (measurement of radioactivity or of color) and indirect methods (addition of a second population after lysis of a first, and dependence of the position of the asymptote of the time-dilution curve on the number of red cells). The discrepancies are traceable to the inhibitory effects of substances liberated from the red cells or ghosts. The ease with which a lysin, once taken up by red cells, can be detached by diluting the system determines the extent to which the hemolytic reaction is "progressive," but has no observed connection with the quantity taken up in the first place. There is now ample evidence that lysis in systems containing simple hemolysins is a process involving two stages in time and two phases, and that it is usually complicated by reactions between the hemolysin and liberated inhibitory material.     

Trypsin inhibition by Ligupurpuroside B as studied using spectroscopic,CD, and molecular docking techniques

It is well known that Ligupurpuroside B is a water-soluble polyphenolic compound and used to brew bitter tea with antioxidant activities. It acted as a stimulant to the central nervous system and a diuretic (increase the excretion of urine), was used to treat painful throat and high blood pressure, and also exerted weight-loss function. In this regard, a detailed investigation on the mechanism of interaction between Ligupurpuroside B and trypsin could be of great interest to know the pharmacokinetic behavior of Ligupurpuroside B and for the design of new analogues with effective pharmacological properties. Ligupurpuroside B successfully quenched the intrinsic fluorescence of trypsin via static quenching mechanism. The binding constants (K_a) at three temperatures (288, 298, and 308 K) were 1.7841?×?10⁴, 1.6251?×?10⁴ and 1.5483?×?10⁴ L mol^?1, respectively. Binding constants revealed the stronger binding interaction between Ligupurpuroside B and trypsin. The number of binding sites approximated to one, indicating a single class of binding for Ligupurpuroside B in trypsin. The enzyme activity result suggested that Ligupurpuroside B can inhibit trypsin activity. Thermodynamic results revealed that both hydrogen bonds and hydrophobic interactions play main roles in stabilization of Ligupurpuroside B-trypsin complex. Circular dichroism (CD) results showed that the conformation of trypsin changed after bound to ligupurpuroside B. Molecular docking indicated that Ligupurpuroside B can enter the hydrophobic cavity of trypsin and was located near Trp215 and Tyr228 of trypsin.

Communicated by Ramaswamy H. Sarma     

The nature of the substrate inhibition in lactate dehydrogenases as studied by a spin-labeled derivative of NAD.

The formation of the ternary complex of lactate dehydrogenase (L-lactate:NAD+ oxidoreductase, EC 1.1.1.27) from pig heart and skeletal muscle with the adduct of pyruvate to NAD", spin-labeled at N6 was studied by ultraviolet spectroscopy and ESR techniques. According to ultraviolet measurements we found identical binding characteristics for the natural coenzyme and its spin-labeled analog. The rate by which the ESR signal of free spin-labeled NAD+ decreased upon addition of pyruvate to the binary complexes was substantially different in the two isozymes. With the heart type an initial drop followed by a further linear decrease, zero order in the enzyme and coenzyme concentration was observed. In case of the skeletal muscle isozyme no immediate reaction and a first order process occurred. The initial reaction can be attributed to a non-covalent enzyme/spin-labeled NAD+/pyruvate complex with a dissociation constant for pyruvate of 11 +/- 1 mM, thus explaining the well-known substrate inhibition in the heart isozyme above 2 mM pyruvate. The further reaction is then determined by the buffer dependent enolization of pyruvate. In the muscle isozyme formation of the covalent adduct is not assisted by prior binding of pyruvate in a non-covalent ternary complex and therefore the rate depends on the binary complex concentration.     

The effect of anaesthetics on protein conformation in membranes as studied by the spin-labelling technique

The effect of general and local anaesthetics was studied on the membrane components (proteins and lipids) of frog sciatic nerve using the spin-labelling technique. A rapid and effective method was developed to incorporate fatty acid labels into the lipid regions and to attach the maleimide spin labels to the thiol sites of the proteins of the membrane. On the basis of the rotational correlation time of the attached maleimide spin labels, at least three different protein domains were identified. One part of the labels has a preferred orientation with respect to the axis of the nerve fibre. The effect of halothane and of local anaesthetics such as lidocaine and tetracaine, which influence primarily the lipid regions of the membrane, is efficiently transferred to the spin-labelled membrane proteins via strong lipid-protein interaction. The results support the concept that the architecture and the physiological activity of the membrane-bound proteins are sensitive to changes in the physical state of membrane lipids.     

siRNA as a tool for investigating organogenesis: The pitfalls and the promises

Removing the function of a specific gene from a developing organ, by making a ‘knockout’ mouse, is a powerful method for analyzing the molecular pathways that control organogenesis. The technique is expensive, though, in terms of time and money, and complex strategies for producing conditional knockouts are needed for genes that are essential for early development of the embryo, for which an unconditional knockout would be lethal before the organ of interest begins to form. Small interfering RNAs (siRNAs) offer a method of knocking down the expression of specific genes with no need for genomic manipulation. Almost as soon as they had been discovered, siRNAs began to be used to explore the molecular biology of mammalian cells in conventional, two-dimensional culture. They have now also been applied successfully, by several groups, to knock down specific genes in various organ rudiments developing in organ culture. This article reviews the basic technique of siRNA-mediated gene knockdown and how it is being applied to organ culture. It also reviews some of the current problems and challenges in the field, and the ways in which these problems are likely to be overcome.Key words: siRNA, RNAi, organ culture, organogenesis, organ development, 3D culture     

The mutagenic effect of benzene, toluene and xylene studied by the SCE technique.

In experiments in vitro, neither benzene, toluene nor xylene changed the number of sister-chromatid exchanges (SCEs) or the number of chromosomal aberrations in human lymphocytes. Toluene and xylene caused a significant cell growth inhibition which was not observed with benzene in the same concentrations.     

The EcoRI-DNA complex as a model for investigating protein-DNA interactions by atomic force microscopy

Atomic force microscopy (AFM) is a technique widely used to image protein-DNA complexes, and its application has now been extended to the measurements of protein-DNA binding constants and specificities. However, the spreading of the protein-DNA complexes on a flat substrate, generally mica, is required prior to AFM imaging. The influence of the surface on protein-DNA interactions is therefore an issue which needs to be addressed. For that purpose, the extensively studied EcoRI-DNA complex was investigated with the aim of providing quantitative information about the surface influence. The equilibrium binding constant of the complex was determined by AFM at both low and high ionic strengths and compared to electrophoretic mobility shift assay measurements (EMSA). In addition, the effect of the DNA length on dissociation of the protein from its specific site was analyzed. It turned out that the AFM measurements are similar to those obtained by EMSA at high ionic strengths. We then advance the idea that this effect is due to the high counterion concentration near the highly negatively charged mica surface. In addition, a dissociation of the complexes once they are adsorbed onto the surface was observed, which is weakly dependent on the ionic strength contrary to what occurs in solution. Finally, a two-step mechanism, which describes the adsorption of the EcoRI-DNA complexes on the surface, is proposed. This model could also be extended to other protein-DNA complexes.     

Mixed trehalose/sucrose glasses used for protein incorporation as studied by infrared and optical spectroscopy

Evaporation of water from a 1/1 mixture of trehalose and sucrose gives rise to optically clear glasses that are transparent in the UV and visible ranges and do not crystallize when they are prepared at ambient temperatures. Two proteins, liver alcohol dehydrogenase and parvalbumin, and the tryptophan derivative N-acetyl-tryptophanamide were incorporated into the glasses. Infrared spectroscopy of the amide I band reveals that the proteins retain secondary structure in the glass over a temperature range of 20-300K. The amide II band of the protein and the HOH bending band of residual water in the glass shift with temperature changes, consistent with increased H-bonding strength as temperature is lowered. Phosphorescence of tryptophan can be seen from the proteins at room temperature, which shows the immobilization of the protein by the glass and the curbing of oxygen diffusion. It is suggested that using mixed sugars to form glasses is a way to immobilize proteins over a wide temperature range without distortions from solvent crystals.     

Orientation of platelets on the surfaces of glass and Teflon plates as studied by a spin label technique

Platelets were found by a spin label technique to orient on flat surfaces of glass as well as of Teflon. This kind of platelet orientation was not caused by centrifugation or partial dehydration of the membrane preparation as employed usually to make oriented planar multilayers of biological membranes on the surface of a supporting plate (1-8), but was considered to be closely related to the adhesion or the aggregation properties of platelets. The amount of oriented platelets varied depending on the platelet treatment and was estimated from a computer simulation of the observed ESR spectra to be about one-half of that of the non-oriented ones in the case of thrombin-treated platelets. This technique may be useful as a new tool to explore the adhesion or aggregation properties of platelets.     

The turnover of skeletal muscle glycogen phosphorylase studied using the cofactor, pyridoxal phosphate, as a specific label

The turnover of glycogen phosphorylase has been measured using the cofactor, pyridoxal phosphate, as a label specific for this enzyme in skeletal muscle. Radiolabelled pyridoxine administered in vivo is incorporated into a protein-bound fraction in skeletal muscle, shown by several criteria to be equivalent to glycogen phosphorylase. This pool of radiolabel disapears slowly with a half-life of 11.9 days, taken to be a good estimate of the intracellular half-life of the enzyme. The use of the cofactor in this fashion minimises overestimation of half-life that results from reincorporation of the label. Further, premature dissociation of the cofactor from native enzyme, which would lead to underestimation of half-life, is unlikely. At the level of sensitivity given by this method there was little evidence for the appearance of pyridoxal phosphate-labelled degradation intermediates of the enzyme.     

Pressure and temperature as tools for investigating the role of individual non-covalent interactions in enzymatic reactions Sulfolobus solfataricus carboxypeptidase as a model enzyme

Sulfolobus solfataricus carboxypeptidase, (CPSso), is a heat- and pressure-resistant zinc-metalloprotease. Thanks to its properties, it is an ideal tool for investigating the role of non-covalent interactions in substrate binding. It has a broad substrate specificity as it can cleave any N-blocked amino acid (except for N-blocked proline). Its catalytic and kinetic mechanisms are well understood, and the hydrolytic reaction is easily detectable spectrophotometrically. Here, we report investigations on the pressure- and temperature-dependence of the kinetic parameters (turnover number and Michaelis constant) of CPSso using several benzoyl- and 3-(2-furyl)acryloyl-amino acids as substrates. This approach enabled us to study these parameters in terms of individual rate constants and establish that the release of the free amino acid is the rate-limiting step, making it possible to dissect the individual non-covalent interactions participating in substrate binding. In keeping with molecular docking experiments performed on the 3D model of CPSso available to date, our results show that both hydrophobic and energetic interactions (i.e., stacking and van der Waals) are mainly involved, but their contribution varies strongly, probably due to changes in the conformational state of the enzyme.     

Characterization of the cloned full-length and a truncated human target of rapamycin: activity, specificity, and enzyme inhibition as studied by a high capacity assay

The mammalian target of rapamycin (mTOR/TOR) is implicated in cancer and other human disorders and thus an important target for therapeutic intervention. To study human TOR in vitro, we have produced in large scale both the full-length TOR (289 kDa) and a truncated TOR (132 kDa) from HEK293 cells. Both enzymes demonstrated a robust and specific catalytic activity towards the physiological substrate proteins, p70 S6 ribosomal protein kinase 1 (p70S6K1) and eIF4E binding protein 1 (4EBP1), as measured by phosphor-specific antibodies in Western blotting. We developed a high capacity dissociation-enhanced lanthanide fluorescence immunoassay (DELFIA) for analysis of kinetic parameters. The Michaelis constant (Km) values of TOR for ATP and the His6-S6K substrate were shown to be 50 and 0.8 microM, respectively. Dose-response and inhibition mechanisms of several known inhibitors, the rapamycin-FKBP12 complex, wortmannin and LY294002, were also studied in DELFIA. Our data indicate that TOR exhibits kinetic features of those shared by traditional serine/threonine kinases and demonstrate the feasibility for TOR enzyme screen in searching for new inhibitors.     

Accessory cell requirements for the mixed-leukocyte reaction and polyclonal mitogens, as studied with a new technique for enriching blood dendritic cells

Human blood dendritic cells can be enriched to 40-80% purity by a new technique that is simpler, provides greater yields than prior methods, and resolves other populations that are enriched in monocytes and B and T lymphocytes. The procedure involves separation over two Percoll gradients after 0 and 2 days of culture, followed by removal of contaminating monocytes by panning on plates coated with human Ig. The resultant dendritic cell-enriched fraction is 10 times or more potent than the monocyte-enriched populations in stimulating T-cell proliferative responses to alloantigens and to Con A. Small B lymphocytes are inactive in both systems. Dendritic cells do not initiate mitogenesis to anti-CD3 monoclonal antibodies, a response for which the monocyte appears to be the critical accessory cell.     

The photophysics of nitrocarbazoles studied by using spectroscopic,photoacoustic and luminescence techniques

The photophysical behaviour of 1-nitrocarbazol and 3-nitrocarbazol in different organic solvents has been studied by using spectroscopic, luminescence and photoacoustic techniques. Absorption spectra and triplet state transient spectra were recorded and formation quantum yields and lifetimes determined. Phosphorescence emission at 77 K and laser induced luminescence in acetonitrile solution at 298 K for the nitrocarbazoles were studied. Results are discussed in terms of the optimized structure of 1-nitrocarbazole and 3-nitrocarbazole and compared with that of carbazole. The nitro group attached to the carbazole moiety induces important changes in the photophysical behavior of those compounds.