What to Learn from a Comparative Genomic Sequence Analysis of <Emphasis Type="Italic">L</Emphasis>-Carnitine Dehydrogenase

Summary. In contrast to eukaryotic cells certain eubacterial strains have acquired the ability to utilize L-carnitine (R-(–)-3-hydroxy-4-(trimethylamino)butyrate) as sole source of energy, carbon and nitrogen. The first step of the L-carnitine degradation to glycine betaine is catalysed by L-carnitine dehydrogenase (L-CDH, EC 1.1.1.108) and results in the formation of the dehydrocarnitine. During the oxidation of L-carnitine a simultaneous conversion of the cofactor NAD⁺ to NADH takes place. This catabolic reaction has always been of keen interest, because it can be exploited for spectroscopic L-carnitine determination in biological fluids – a quantification method, which is developed in our lab – as well as L-carnitine production.Based on a cloned L-CDH sequence an expedition through the currently available prokaryotic genomic sequence space began to mine relevant information about bacterial L-carnitine metabolism hidden in the enormous amount of data stored in public sequence databases. Thus by means of homology-based and context-based protein function prediction is revealed that L-CDH exists in certain eubacterial genomes either as a protein of approximately 35 kDa or as a homologous fusion protein of approximately 54 kDa with an additional putative domain, which is predicted to possess a thioesterase activity. These two variants of the enzyme are found on one hand in the genome sequence of bacterial species, which were previously reported to decompose L-carnitine, and on the other hand in gram-positive bacteria, which were not known to express L-CDH. Furthermore we could not only discover that L-CDH is located in a conserved genetic entity, which genes are very likely involved in this L-carnitine catabolic pathway, but also pinpoint the exact genomic sequence position of several other enzymes, which play an essential role in the bacterial metabolism of L-carnitine precursors.     

Limiting Partial Molar Volumes of Electrolytes in 2-Methyl-2-Butanol <Emphasis Type="Bold">+</Emphasis> Water Mixtures at 298.15 K

Partial molar volumes at infinite dilution, V⁰₂, of alkali–metal halides (LiCl, NaCl KCl RbCl CsCl, NaBr, KBr, KI), tetra-n-alkylammonium bromides, R₄NBr (R=Me, Et, n-Pr, n-Bu, n-Pen), NaBPh₄, and Ph₄PCl have been determined in binary solvent mixtures of water with 2-methyl-2-butanol covering the water-rich region and the alcohol-rich region at 298.15 K. V⁰₂ for alkali–metal halides show relatively little dependence on the solvent composition. However, in the case of hydrophobic electrolytes the observed effects are more pronounced. A good linear dependence between V⁰₂(R₄NBr) and the molecular weight of the tetra-n-alkylammonium cation is found. Limiting single-ion volumes have been obtained using the assumption that V⁰(Ph₄P⁺)–V⁰(BPh^–₄)=2.0 cm³-mol^–1. The trends in the single-ion volumes are discussed in both solvent regions.     

Three-dimensional structural features and the toxicity of aminobenzenes and phenols

There are many organic pollutants in the environment, such as polychlorinated biphenyl, polycyclic aromatic hydrocarbons, dichlorodiphenyl-trichloroethane (DDT), and polychlorinated naphthalene. These organic pollutants are persistent,liposoluble and easily cumulated in organism; consequently, the potential toxicity will be high. Risk assessment of industrial chemicals is currently carried out using scanty experimental data, because many of these chemicals have very little or no test data. S…     

Influence of ethanol oxidation rate on the lactate/pyruvate ratio and phosphorylation state of the liver in fed rats.

The effect of the ethanol oxidation rate on the interaction between the phosphorylation state (the [ATP]/[ADP] X [HPO4]2- ratio) and the redox state (the free [NAD+]/[NADH] ratio) of the liver cytosol was studied in intact fed rats. The rate of ethanol oxidation was inhibited to different degrees with pyrazole. The ethanol oxidation rate had no influence on the liver lactate level but correlated significantly with the pyruvate level. Accordingly, a significant correlation was also found between the ethanol oxidation rate and the lactate/pyruvate ratio. The rate of ethanol oxidation correlated significantly with the liver 3-phosphoglycerate level. No change in the glyceraldehyde-3-phosphate level was found. No correlation was found between the ethanol oxidation rate and the glyceraldehyde-3-phosphate/3-phosphoglycerate redox couple. Ethanol administration slightly increased the liver ATP level, but the simultaneous administration of pyrazole eliminated this effect. Other adenine nucleotides and HPO4 2- were not changed. The changes in the rate of ethanol oxidation had no effect on the phosphorylation state in the fed liver. It is assumed that in the fed liver the phosphorylation state is so well stabilized that the redox level has no influence.     

Theoretical study of alkyl-pi and aryl-pi interactions. Reconciling theory and experiment

Quantum mechanical and quantum mechanical/molecular mechanical calculations in conjunction with continuum solvation models have been used to analyze CH-pi interactions in model systems of aryl- and alkyl-aromatic interactions, as well as in a model folding system designed to study those interactions. High level calculations reproduced accurately the interaction of CH-pi interactions in both alkyl- and aryl-based model systems. Dispersion effects dominate the interaction, but the electrostatics term is also relevant for aryl CH-pi interactions. Theoretical calculations were also used to examine the influence of CH-pi interactions in determining the conformational flexibility of folding models. Finally, a critical comparison of the results obtained from high level calculations on model systems and the experimental data derived for folding models in apolar solvents was carried out, which allowed us to reconcile the apparent discrepancy found between both data.     

Characterization of N-terminal processing of group VIA phospholipase A<Subscript>2</Subscript> and of potential cleavage sites of amyloid precursor protein constructs by automated identification of signature peptides in LC/MS/MS analyses of proteolytic digests

Dysregulation of proteolytic processing of the amyloid precursor protein (APP) contributes to the pathogenesis of Alzheimer's Disease, and the Group VIA phospholipase A(2) (iPLA(2)beta) is the dominant PLA(2) enzyme in the central nervous system and is subject to regulatory proteolytic processing. We have identified novel N-terminal variants of iPLA(2)beta and previously unrecognized proteolysis sites in APP constructs with a C-terminal 6-myc tag by automated identification of signature peptides in LC/MS/MS analyses of proteolytic digests. We have developed a Signature-Discovery (SD) program to characterize protein isoforms by identifying signature peptides that arise from proteolytic processing in vivo. This program analyzes MS/MS data from LC analyses of proteolytic digests of protein mixtures that can include incompletely resolved components in biological samples. This reduces requirements for purification and thereby minimizes artifactual modifications during sample processing. A new algorithm to generate the theoretical signature peptide set and to calculate similarity scores between predicted and observed mass spectra has been tested and optimized with model proteins. The program has been applied to the identification of variants of proteins of biological interest, including APP cleavage products and iPLA(2)beta, and such applications demonstrate the utility of this approach.     

Synthesis of Functionalized (2-Thienylcarbonyl)thiazoles and 4-(2-Thienyl)pyridines by Reaction of (2-Thienylcarbonyl)thioacetanilides and their Enamine Derivatives

Summary. The condensation of two molecules of 2-(2-thienylcarbonyl)thioacetanilides catalyzed by piperidine yielded thiazole derivatives as confirmed by X-ray crystal structure analysis. The reaction of malononitrile with 3-morpholino-3-(2-thienyl)acrylic acid thioanilides furnished 6-amino-1-aryl-4-(2-thienyl)-1,2-dihydro-2-thioxopyridine-5-carbonitriles. A similar reaction of malononitrile with 3-morpholino-3-(2-thienyl)acrylic acid anilides provided 2-oxopyridine-5-carbonitriles.     

Aminoalkylation with Aldehydes Mediated by Solid Lithium Perchlorate

Summary. The solid LiClO₄-mediated one-pot reaction of aldehydes with secondary amines and C nucleophiles afforded the corresponding aminoalkylation products in high yields. Unlike the previous reported procedure, the aminoalkylation of aldehyde was achieved in the presence of only 0.5 equivalents of solid lithium perchlorate in dichloromethane as the solvent with good to high yields at room temperature.     

The application of NMR and MS methods for detection of adulteration of wine,fruit juices,and olive oil. A review

This review covers two important techniques, high resolution nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), used to characterize food products and detect possible adulteration of wine, fruit juices, and olive oil, all important products of the Mediterranean Basin. Emphasis is placed on the complementary use of SNIF-NMR (site-specific natural isotopic fractionation nuclear magnetic resonance) and IRMS (isotope-ratio mass spectrometry) in association with chemometric methods for detecting the adulteration.     

Cooperative effects in phospholipid monolayers induced by a peptide from HIV-1 capsid protein

The study of interactions between biological molecules and model membranes is essential for the understanding of a number of physiological mechanisms involved in viral infections and dissemination. In this paper, the analysis of the interaction between a peptide from the p24 protein of Human Immunodeficiency Virus type 1 (HIV-1) and a phospholipid monolayer has pointed to a cooperative response in which very small amounts of peptide p24-1 (e.g. 0.05 mol%) can lead to measurable effects. Monolayer surface pressure and surface potential isotherms were affected for peptide concentrations as low as 0.05 mol%, with saturation at 0.5 mol%. The expansion effect from p24-1 is confirmed by changes in morphology of the monolayers using Brewster angle microscopy. Even though p24-1 is disordered in aqueous solutions, the interaction with dipalmitoyl phosphatidylcholine (DPPC) causes it to adopt an alpha-helix structure, as shown by circular dichroism (CD) data for multilamellar vesicles (MLV). The expansion of the phospholipid monolayer in a cooperative way may imply that p24-1 has potential antiviral activity, by participating in the cell rupture, with no need of specific receptors in the membrane.