The alpha-galactosyl derivatives of ganglioside GD(1b) are essential for the organization of lipid rafts in RBL-2H3 mast cells

Gangliosides are complex glycosphingolipids that are important in many biological processes. The present study investigated the role of gangliosides in the organization of lipid rafts in RBL-2H3 mast cells and in the modulation of mast cell degranulation via FcRI. The role of gangliosides was examined using two ganglioside deficient cell lines (B6A4A2III-E5 and B6A4C1III-D1) as well as the parent cell line (RBL-2H3). All three cell lines examined express FcRI, Lyn, Syk and LAT. However, only in RBL-2H3 cells were FcRI, LAT and α-galactosyl derivatives of ganglioside GD_1b mobilized to lipid raft domains following FcRI stimulation. The inhibition of glycosphingolipid synthesis in RBL-2H3 cells also resulted in a decrease in the release of β-hexosaminidase activity after FcRI activation. The two mutant cell lines have a reduced release of β-hexosaminidase activity after FcRI stimulation, but not after exposure to calcium ionophore. These results indicate that the α-galactosyl derivatives of ganglioside GD_1b are important in the initial events of FcRI signaling upstream of Ca²⁺ influx. Since the initial signaling events occur in lipid rafts and in the mutant cell lines the rafts are disorganized, these results also suggest that these gangliosides contribute to the correct assembly of lipid rafts and are essential for mast cell activation via FcRI.     

Preparation of poly(-lysine) adsorbents and application to selective removal of lipopolysaccharides

To remove endotoxins (lipopolysaccharides; LPS) from cell products used as drugs, water-insoluble poly(-lysine) (PL) particles were prepared by cross-linking with PL originating from Streptomyces albulus and chloromethyloxirane (CMO). The apparent pK_a (pK_a,app) and the anion-exchange capacity of the particles were easily adjusted by changing the PL ratio and the CMO ratio. The higher the pK_a,app, the greater the LPS-adsorption capacity of the particles. On the other hand, when the PL ratio (in the particles) increased to 75 unit-mol% or higher, the adsorption of bovine serum albumin by the particles also increased, but decreased with increasing ionic strength of the buffer to μ=0.2 or higher. The adsorption of γ-globulin increased with decreasing PL ratio to 65 unit-mol% or lower. As a result, when the PL ratio was 70 unit-mol% and the pK_a,app was 6.7, the PL/CMO particles selectively removed LPS from various protein solutions that were naturally contaminated with LPS, at pH 6.0 and μ=0.05.     

Antigen-induced Ca mobilization in RBL-2H3 cells: Role of I(1,4,5)P3 and S1P and necessity of I(1,4,5)P3 production

Inositol 1,4,5-trisphosphate (IP3) has long been recognized as a second messenger for intracellular Ca2+ mobilization. Recently, sphingosine 1-phosphate (S1P) has been shown to be involved in Ca2+ release from the endoplasmic reticulum (ER). Here, we investigated the role of S1P and IP3 in antigen (Ag)-induced intracellular Ca2+ mobilization in RBL-2H3 mast cells. Antigen-induced intracellular Ca2+ mobilization was only partially inhibited by the sphingosine kinase inhibitor dl-threo-dihydrosphingosine (DHS) or the IP3 receptor inhibitor 2-aminoethoxydiphenyl borate (2-APB), whereas preincubation with both inhibitors led to complete inhibition. In contrast, stimulation of A3 adenosine receptors with N5-ethylcarboxamidoadenosine (NECA) caused intracellular Ca2+ mobilization that was completely abolished by 2-APB but not by DHS, suggesting that NECA required only the IP3 pathway, while antigen used both the IP3 and S1P pathways. Interestingly, however, inhibition of IP3 production with the phospholipase C inhibitor U73122 completely abolished Ca2+ release from the ER induced by either stimulant. This suggested that S1P alone, without concomitant production of IP3, would not cause intracellular Ca2+ mobilization. This was further demonstrated in some clones of RBL-2H3 cells excessively overexpressing a beta isoform of Class II phosphatidylinositol 3-kinase (PI3KC2beta). In such clones including clone 5A4C, PI3KC2beta was overexpressed throughout the cell, although endogenous PI3KC2beta was normally expressed only in the ER. Overexpression of PI3KC2beta in the cytosol and the PM led to depletion of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), resulting in a marked reduction in IP3 production. This could explain the abolishment of intracellular Ca2+ mobilization in clone 5A4C. Supporting this hypothesis, the Ca2+ mobilization was reconstituted by the addition of exogenous PI(4,5)P2 in these cells. Our results suggest that both IP3 and S1P contribute to FcvarepsilonRI-induced Ca2+ release from the ER and production of IP3 is necessary for S1P to cause Ca2+ mobilization from the ER.     

Novel application of surface plasmon resonance biosensor chips for measurement of advanced glycation end products in serum of Zucker diabetic fatty rats

Advanced glycation end products (AGEs) have been implicated in diabetic complications. To measure AGEs, especially N-(carboxymethyl)lysine (CML), in sera from Zucker diabetic fatty rats (ZDF) and Zucker lean rats (ZL), we used a novel method of protein chip and surface plasmon resonance imaging (SPRI). Serum samples were obtained from male ZDF and ZL rats at 20 weeks of age. Antibodies to AGEs or CML were immobilized on a gold surface, which was modified by cysteine-tagged, protein-G constructs. The gold chip upon which the serum was spotted was optically coupled with a prism coupler. The reflected images from the gold chip were obtained using a charge-coupled device (CCD) camera. The direct analysis of the glycated proteins and products using SPRI showed that AGEs and CML levels were elevated in ZDF serum, compared with ZL serum. The lowest detection limit of AGEs was 10 ng/ml, with a working range covering the physiological range. These results indicate that the protein chip and SPRI system is very suitable for the measurement of glycated proteins and end products in serum samples. This system offers high sensitivity without any fluorescent or other labeling of the components and saves a substantial amount of time, resources, and labor. Our results suggest that SPRI systems can be used as a tool to diagnose diabetic complications.     

Serine recombinases as tools for genome engineering

The serine recombinases differ mechanistically from the tyrosine recombinases and include proteins such as ?C31 integrase which, unlike Cre and Flp, promote unidirectional reactions. The serine recombinase family is large and includes many other proteins besides ?C31 integrase with the potential to be widely used in genome engineering. Here we review the details of the mechanism of the reactions promoted by the serine recombinases and discuss how these not only limit the utility of this class of recombinase but also creates opportunities for the engineering of new enzymes. We discuss the unanswered questions posed by genome engineering experiments in a variety of systems in which the serine recombinases have been used and finally describe more recently discovered serine recombinases that have the potential to be used in genome engineering.     

Synthesis and molecular structure of 14,15-pyrrolidino-and 14,16-ethano derivatives of estrone

Hydrolysis of 3-methoxy-16alpha-nitro-14,17-ethenoestra-1,3,5(10)-trien-17beta-yl acetate under weakly basic conditions leads to formation of 3-methoxy-2'-oxopyrrolidino-[4',5':14beta,15beta]-estra-1,3,5 (10)-trien-17-one, the structure of which has been confirmed by X-ray analysis and some chemical transformations. The reactivity of 3-methoxy-16alpha-nitro-14,17-ethanoestra-1,3,5(10)-trien-17beta-yl acetate under various conditions of basic hydrolysis has been investigated. The derived compounds have been identified by means of NMR spectroscopy and X-ray analysis.     

Purification and some properties of -poly-l-lysine-degrading enzyme from Kitasatospora sp. CCTCC M205012

An -poly-l-lysine-degrading enzyme (PLD) from Kitasatospora sp. CCTCC M205012 has been purified to homogeneity by three steps of anion-exchange chromatography including DEAE-Sepharose, Source 15Q and Mono Q, with a 500-fold increase in specific activity and 40.9% yield. The PLD has a molecular mass of approximately 87.0 kDa and consists of two identical subunits with a molecular mass of 43.6 kDa. Electrophoretic shows that the PLD isoelectric point was about 7.2. The optimum temperature and pH for the PLD was 30 °C and 7.0, respectively. The PLD was deactivated by EDTA, which was indicated that the enzyme was a metallo enzyme. The activity of PLD was stimulated by Co²⁺ and inhibited by Ca²⁺ remarkably. The apparent K_m with l-lysyl-p-nitroanilide as substrate was 0.216 mM and the V_max was 0.112 mmol/min mg. The PLD was an exo-type enzyme and monomers of l-lysine were detected during the enzymatic degradation of -PL.     

Exploring the cupin-type metal-coordinating signature of acetylacetone dioxygenase Dke1 with site-directed mutagenesis: Catalytic reaction profile and Fe binding stability of Glu-69 → Gln mutant

Glu-69 belongs to a proposed active-site consensus motif His⁶²-X-His⁶⁴-X₄-Glu⁶⁹ (where X is any amino acid) that acetylacetone dioxygenase Dke1 from Acinetobacter johnsonii shares with structurally related non-heme metal enzymes of the cupin protein superfamily. We report functional consequences of the site-directed replacement Glu-69 → Gln based on a detailed biochemical and kinetic characterization of the purified Dke1 mutant. Perturbations of the free energy profile of the wild-type caused by the mutation were surprisingly small, with key points of the reaction pathway such as β-diketone substrate binding, the rate-limiting reduction of dioxygen, and CC bond cleavage essentially left unaltered. Release of Fe²⁺ from the mutant active site occurred at twice the wild-type rate, and the thermal stability of β-sheet secondary structure in Fe²⁺-depleted apo-proteins was lower in the mutant. The substitution Glu-69 → Gln is thus remarkably silent regarding Dke1 function. These results do not support a unified catalytic or metal-coordinating role of Glu-69 (and its positional homologues) in O₂-dependent cupin-fold enzymes.     

Polyphenol-enriched fractions from Sicilian grape pomace: HPLC-DAD analysis and antioxidant activity

On the basis of a preliminary screening of seven different samples of Sicilian grape pomace, the 'Nerello Mascalese' sample NM2 was selected for an ethanol preparative extraction. The defatted NM2 EtOH extract was subjected to DPPH() and GAE assays, showing good radical scavenging activity (SC(50)=9.9 microg/mL) and a GAE value of 397.7 mg/g extract. HPLC-DAD analysis of NM2 extract allowed a quantitative determination of the main anthocyanins (AN) and flavonols/flavonol glycosides (FL/FG). Aliquots of the NM2 extract were subjected to three different fractionation protocols (FP1, FP2 and FP3). The fractions were examined by DPPH() and GAE assays, and subjected to HPLC-DAD analysis for the quantitative determination of the main AN and FL/FG. FP3 allowed obtaining a polyphenol-enriched fraction with SC(50)=14.8 microg/mL and GAE=184.1mg/g of fraction, accounting for only 1.3% in weight of the EtOH extract. Some considerations about the relationship between antioxidant activity and AN/FL/FG HPLC-DAD profiles are also reported.     

Geometry of nonbonded interactions involving planar groups in proteins

Although hydrophobic interaction is the main contributing factor to the stability of the protein fold, the specificity of the folding process depends on many directional interactions. An analysis has been carried out on the geometry of interaction between planar moieties of ten side chains (Phe, Tyr, Trp, His, Arg, Pro, Asp, Glu, Asn and Gln), the aromatic residues and the sulfide planes (of Met and cystine), and the aromatic residues and the peptide planes within the protein tertiary structures available in the Protein Data Bank. The occurrence of hydrogen bonds and other nonconventional interactions such as C-H...pi, C-H...O, electrophile-nucleophile interactions involving the planar moieties has been elucidated. The specific nature of the interactions constraints many of the residue pairs to occur with a fixed sequence difference, maintaining a sequential order, when located in secondary structural elements, such as alpha-helices and beta-turns. The importance of many of these interactions (for example, aromatic residues interacting with Pro or cystine sulfur atom) is revealed by the higher degree of conservation observed for them in protein structures and binding regions. The planar residues are well represented in the active sites, and the geometry of their interactions does not deviate from the general distribution. The geometrical relationship between interacting residues provides valuable insights into the process of protein folding and would be useful for the design of protein molecules and modulation of their binding properties.     

Mechanism and stoichiometry of 2,2-diphenyl-1-picrylhydrazyl radical scavenging by glutathione and its novel α-glutamyl derivative

Kinetic mechanism and stoichiometry of scavenging the 2,2-diphenyl-1-picrylhydrazyl radical by glutathione and its novel analog, containing α-glutamyl residue in place of the γ-glutamyl moiety, were studied using different ratios of reagents. At low concentrations of the peptides, the process was described as a bimolecular reaction obeying the stoichiometric ratio 1:1. However, at excess of peptides the formation of a non-covalent complex between the reagents was discovered and characterized by dissociation constants K = 0.61 mM for glutathione and K = 0.27 mM for the glutathione α-glutamyl analog, respectively. The complex formation was followed by a reaction step that was characterized by the similar rate constant k = 0.02 s⁻¹ for both peptides. Thus, the apparently different antioxidant activity of these two peptides, observed under common assay conditions, was determined by differences in the formation of this non-covalent complex.     

Tryptophanase in aqueous methanol: the solvent effects and a probable mechanism of the hydrophobic control of substrate specificity

To shed light on the mechanism of hydrophobic control in reactions of microbial tryptophanase the direct effect of the solvent hydrophobicity on affinities of amino acid inhibitors was first examined. Values of inhibition constants (K_i) for a variety of amino acids were determined in 37.5% aqueous methanol, and no general correlation between the change of K_i, on passing from water to aqueous methanol, and amino acid hydrophobicity was found. The solvent effects on the separate stages of the external aldimine formation (K_D) and deprotonation to form a quinonoid intermediate (K_q) were determined for the reactions of tryptophanase with 2-oxindolyl- -alanine and -alanine by stopped-flow technique. For 2-oxindolyl- -alanine, which is a close transition-state analogue for the enzyme reaction with natural substrate, the decrease in the affinity in aqueous methanol is associated exclusively with the α-proton abstraction stage but not with the preceding formation of external aldimine. We conclude that the environment of amino acid side chains in the active site cannot be considered to be permanently hydrophobic irrespective of the bound amino acid. We suggest that complexes of tryptophanase with amino acids may exist either in a hydrophobic, presumably “closed”, conformation, where bound amino acids are isolated from the solvent, or in an accesible to solvent, “open”, conformation, depending on the structure of the bound amino acid and stage of the catalytic mechanism. For 2-oxindolyl- -alanine the transfer from an open to a closed conformation probably accompanies deprotonation of the external aldimine. The change of the active site hydrophobicity may provide an efficient way of modulating the relative acid–base properties of the catalytic groups to ensure the movement of protons in the “correct” direction depending on the elementary stage of catalysis.     

An assay for angiotensin-converting enzyme using capillary zone electrophoresis

A sensitive and rapid method was developed for angiotensin-converting enzyme (ACE) activity determination by capillary zone electrophoresis. Hippuryl-l-histidyl-l-leucine, a synthetic tripeptide, was used as the ACE-specific substrate. Capillary zone electrophoresis was employed to separate the products of the enzymatic reaction and the ACE activity was determined by quantification of hippuric acid, a result of the enzymatic reaction on the tripeptide. The capillary electrophoresis was performed in a 27 cm x 75 micrometer i.d. fused-silica capillary using 200 mM boric acid-borate buffer (pH 9.0) as a run buffer with an applied voltage of 8.1 kV at a capillary temperature of 23 degrees C. The electrophoresis was monitored at 228 nm. Each electrophoretic run requires only a nanoliter of the enzymatic reactant solution, at only 6 min, rendering a powerful tool for the ACE assay.     

Metabolic Engineering for Microbial Production of Aromatic Amino Acids and Derived Compounds

Metabolic engineering to design and construct microorganisms suitable for the production of aromatic amino acids and derivatives thereof requires control of a complicated network of metabolic reactions that partly act in parallel and frequently are in rapid equilibrium. Engineering the regulatory circuits, the uptake of carbon, the glycolytic pathway, the pentose phosphate pathway, and the common aromatic amino acid pathway as well as amino acid importers and exporters that have all been targeted to effect higher productivities of these compounds are discussed.     

Macroevolutionary trends of atomic composition and related functional group proportion in eukaryotic and prokaryotic proteins

To fully explore the trends of atomic composition during the macroevolution from prokaryote to eukaryote, five atoms (oxygen, sulfur, nitrogen, carbon, hydrogen) and related functional groups in prokaryotic and eukaryotic proteins were surveyed and compared. Genome-wide analysis showed that eukaryotic proteins have more oxygen, sulfur and nitrogen atoms than prokaryotes do. Clusters of Orthologous Groups (COG) analysis revealed that oxygen, sulfur, carbon and hydrogen frequencies are higher in eukaryotic proteins than in their prokaryotic orthologs. Furthermore, functional group analysis demonstrated that eukaryotic proteins tend to have higher proportions of sulfhydryl, hydroxyl and acylamino, but lower of sulfide and carboxyl. Taken together, an apparent trend of increase was observed for oxygen and sulfur atoms in the macroevolution; the variation of oxygen and sulfur compositions and their related functional groups in macroevolution made eukaryotic proteins carry more useful functional groups. These results will be helpful for better understanding the functional significances of atomic composition evolution.     

Production of functional recombinant tyrosine hydroxylase by the BPV-1 expression plasmids in the cell cultures

Bovine papilloma virus type-1 (BPV-1)-based expression plasmids TkBPVTH and CGalBPVTH encoding the rat tyrosine hydroxylase (TH) enzyme have been designed for the development of gene therapy for experimental Parkinson's disease. The aim of the present work was to examine the transfection of BPVTH plasmids to express a dopaminergic transgene in the monkey CV1-P fibroblast, rat C6 glioma and human NHA astrocyte cell cultures. The biological function of the transgene was estimated by analyzing the production of recombinant TH mRNA and protein, and the synthesis of L-dopa and dopamine. The highest transfection efficiency was obtained using TkBPVTH plasmids (5 microg). Furthermore, the expression of TkBPVTH plasmids was associated with significant synthesis of TH enzyme and L-dopa in the C6 and NHA cell cultures.     

The palladium complexes of a C3-bridged di(benzimidazol-2-ylidene) ligand via cleavage of a dibenzotetraazafulvalene

Reduction of the N1, N1′-C₃-bridged di(benzimidazol-2-thione) (5) with a sodium/potassium alloy leads to the N1, N1′-C₃-bridged dibenzotetraazafulvalene (6). One equivalent of 6 reacts with palladium diiodide to give the dicarbene complex 1,3-(2,2-dimethylpropane)-N1,N1′-bis(N3-ethylbenzimidazol-2-ylidene)palladium diiodide (7). The X-ray crystal structure analysis of 7 reveals a slightly distorted square-planar coordination environment for the palladium center and a C_carbene-Pd-C_carbene angle of 85.0(15)°. The carbene planes are oriented almost perpendicular (82.7° and 79.3°) to the PdI₂C₂ plane.     

Enantioselective synthesis and biological evaluation of 5-o-carboranyl pyrimidine nucleosides

Base-modified carborane-containing nucleosides such as 5-o-carboranyl-2'-deoxyuridine (CDU) when combined with neutrons have potential for the treatment of certain malignancies. Lack of toxicity in various cells, high accumulation in cancer cells and intracellular phosphorylation are desirable characteristics for modified nucleosides used in boron neutron capture therapy (BNCT) for brain tumors and other malignancies. The aim of this work was to synthesize the two beta-enantiomers of several 5-o-carboranyl-containing nucleosides. These derivatives may possess favorable properties such as high lipophilicity, high transportability, the ability to be phosphorylated, and resistance to catabolism. Beta-isomers of 2',3'-dihydroxynucleosides and analogues containing a heteroatom in the sugar moiety were also synthesized. Carboranyl pyrimidine nucleosides were prepared either from the parent beta-D-nucleoside, beta-L-nucleoside, or by a coupling reaction. The dioxolane derivative 7 was prepared by a coupling reaction between protected 5-o-carboranyluracil (8, CU) and the corresponding protected heterocycle. Specific catalysts were used during the N-glycosylation process to favor the formation of the beta-isomer. Biological evaluation of these new chiral 5-o-carboranyl pyrimidine derivatives indicated that most of these compounds have low toxicity in a variety of normal and malignant cells and achieved high cellular levels in a lymphoblastoid cell line. Increasing the number of hydroxyl groups on the sugar moiety decreased the cellular accumulation and serum binding to different extents. Five compounds were identified for further biological evaluation as potential agents for BNCT.     

Effect of 2-deoxy- -glucose on acetylcholine and histamine levels in gastric juice of pylorus-ligated rats anesthetized with urethane

Acetylcholine (ACh) in gastric juice was detected and measured by pretreatment of acetylcholinesterase inhibitor, 1 mM eserine (1 ml/rat, p.o.), in pylorus-ligated rats, by liquid chromatography with electrochemical detection. In order to elucidate whether or not the ACh level in gastric juice reflects the activity of cholinergic neurons, the effect of 2-deoxy- -glucose (2-DG), a vagus stimulant, on the levels of ACh, histamine and gastric acid in gastric juice was investigated in pylorus-ligated rats anesthetized with urethane (1.25 g/kg, i.p.). Under the non-anesthetic condition, ACh, histamine and gastric acid levels were 100±25 pmol/h, 120±10 ng/h, and 240±32 μequiv./h, respectively. These levels were completely inhibited by urethane anesthesia. Under the anesthetized condition, 2-DG (50–200 mg/kg, i.v.) significantly increased ACh and histamine levels in gastric juice, as well as acid secretion. The 2-DG (200 mg/kg, i.v.)-induced increases in these levels were completely inhibited by vagotomy. These results suggest that ACh level measured in gastric juice reflects the activity of cholinergic transmission. Furthermore, these results also support the conclusion that vagus stimulation facilitates not only cholinergic transmission but also histaminergic transmission related to gastric acid secretion.     

Solution-state characteristics of the ultraviolet A-induced visible fluorescence from proteins

In response to illumination by ultraviolet-A (UV-A) light, proteins in solid form are now known to display a visible blue fluorescence, ostensibly on account of excitation transitions of loosely-held electrons within peptide bond orbitals engaged in hydrogen bonding. Because the CO and NH atom groups in peptide bonds are generally engaged in extensive hydrogen bonding in globular proteins even in aqueous solution, one could argue that proteins in solution must also display this novel blue fluorescence. Here, using high concentrations to enhance detectability, two globular proteins, γ-crystallin, and lysozyme, are shown to fluoresce visibly, exhibiting: (a) two excitation maxima, at ∼315 nm and ∼385 nm, (b) maximal emission at 425 nm in 100 mg/ml lysozyme and 465 nm in 100 mg/ml γ-crystallin, (c) a time-resolved emission decay that is best fitted by a sum of three exponentials with lifetimes of 3.14, 0.46, and 9.08 ns, respectively, and comparable relative amplitudes of around 30--40 percent each, and (d) a weak CD spectrum displaying a positive band at ∼385 nm and a negative band at ∼465 nm. While the wavelength of maximal emission (^emλ_max) in lysozyme is the same for all protein concentrations, the ^emλ_max of γ-crystallin varies with protein concentration, suggesting a certain degree of conformation dependence.