A GFP fluorescence-based approach to determine detergent insolubility of the human serotonin1A receptor

Insolubility in non-ionic detergents such as Triton X-100 is a widely used biochemical criterion for characterization of membrane domains. We report here a novel green fluorescent protein fluorescence-based approach to directly determine detergent insolubility of specific membrane proteins. We have applied this method to explore the detergent resistance of an important G-protein coupled receptor, the serotonin1A (5-HT1A) receptor. Our results show, for the first time, that a small yet significant fraction of the 5-HT1A receptor exhibits detergent insolubility. These results are validated by control experiments involving fluorescent lipid probes and protein markers. Our results assume relevance in the context of localization of the 5-HT1A receptor in membrane domains and its significance in receptor function and signaling.     

Structure—chemical approach to organization of information on metabolic charts

A nontraditional approach to construction of metabolic charts is proposed. It is based on the discovery of symmetry in the structure of the network of metabolic reactions. So if compounds and reactions are located on the metabolic chart according to their chemical features, the chart structure will acquire a periodic pattern. The charts thus created have a natural two-dimensional coordinate system of the metabolic network. Points on the X-axis correspond to number of carbon atoms in the carbon skeleton of compounds in columns and points on the Y-axis correspond to number of -COOH groups in compounds filing in series of rows on the charts. As a result this coordinate system sections the field of the charts into rectangular blocks each of which containing compounds with the same numbers of carbon atoms and the same numbers of -COOH groups. The latter substantially improves the charts and makes them a more valid source of metabolic data possessing heuristic properties. The periodicity of the metabolic network structure enables us easily to remember information about biochemical reactions and their products. The charts can also be used as a universal key for any biological database information that is systematically connected with the metabolic information. The charts can be important for medicine and pharmacology because they can help to understand the metabolic processes involved in decomposition of a particular drug or to find the chain of reactions blocked or initiated by administering this drug into a living organism.Translated from Biokhimiya, Vol. 69, No. 12, 2004, pp. 1691–1699.Original Russian Text Copyright © 2004 by Malygin.     

X-ray crystallographic and kinetic correlation of a clinically observed human fumarase mutation

Fumarase catalyzes the reversible conversion of fumarate to S- malate during the operation of the ubiquitous Kreb's cycle. Previous studies have shown that the active site includes side chains from three of the four subunits within the tetrameric enzyme. We used a clinically observed human mutation to narrow our search for potential catalytic groups within the fumarase active site. Offspring homozygous for the missense mutation, a G-955-C transversion in the fumarase gene, results in the substitution of a glutamine at amino acid 319 for the normal glutamic acid. To more fully understand the implications of this mutation, a single-step site-directed mutagenesis method was used to generate the homologous substitution at position 315 within fumarase C from Escherichia coli. Subsequent kinetic and X-ray crystal structure analyses show changes in the turnover number and the cocrystal structure with bound citrate.     

Assessing metabolic activity in aging Caenorhabditis elegans: concepts and controversies

It is widely believed that normal by-products of oxidative metabolism and the subsequent molecular damage inflicted by them couple the aging process to metabolic rate. Accordingly, high metabolic rates would be expected to accelerate aging, and life-extending interventions are often assumed to act by attenuating metabolic rate. Notorious examples in Caenorhabditis elegans are food restriction, mutation in the Clock genes and several genes of the insulin-like signalling pathway. Here we discuss how metabolic rate can be accurately measured and normalized, and how to deal with differences in body size. These issues are illustrated using experimental data of the long-lived mutant strains clk-1(e2519) and daf-2(e1370). Appropriate analysis shows that metabolic rates in wildtype and in the clk-1 mutant are very similar. In contrast, the metabolic rate profiles point to a metabolic shift toward enhanced efficiency of oxidative phosphorylation in the daf-2 worms.     

Regulation of energy metabolism in liver

Energy metabolism in liver has to cope with the special tasks of this organ in intermediary metabolism. Main ATP-generating processes in the liver cell are the respiratory chain and glycolysis, whereas main ATP-consuming processes are gluconeogenesis, urea synthesis, protein synthesis, ATPases and mitochondrial proton leak. Mitochondrial respiratory chain in the intact liver cell is subject to control mainly by substrate (hydrogen donors, ADP, oxygen) transport and supply and proton leak/slip. Whereas hormonal control is mainly on substrate supply to mitochondria, proton leak/slip is supposed to play an important role in the modulation of the efficiency of oxidative phosphorylation.     

Internally quenched fluorogenic protease substrates: Solid-phase synthesis and fluorescence spectroscopy of peptides containing ortho-aminobenzoyl/dinitrophenyl groups as donor-acceptor pairs

Summary A general procedure, using the commonly employed solid-phase peptide synthesis methodology for obtaining internally quenched fluorogenic peptides with ortho-aminobenzoyl/dinitrophenyl groups as donor-acceptor pairs, is presented. The essential feature of this procedure is the synthesis of an N -Boc or-Fmoc derivative of glutamic acid with the -carboxyl group bound to N-(2,4-dinitrophenyl)-ethylenediamine (EDDnp), which provides the quencher moiety attached to the C-terminus of the substrate. The fluorescent donor group, ortho-aminobenzoic acid (Abz), is incorporated into the resin-bound peptide in the last coupling cycle. Depending on the resin type used, Abz-peptidyl-Gln-EDDnp or Abz-peptidyl-Glu-EDDnp is obtained. Using the procedure described above, substrates for human renin and tissue kallikreins were synthesised. Spectrofluorimetric measurements of Abz bound to the -amino group of proline showed that strong quenching of Abz fluorescence occurs in the absence of any acceptor group.     

Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism

The esterification of lauric acid with geraniol catalyzed by the commercially immobilized lipase preparation from Mucor miehei, Lipozyme(R), was studied in well-stirred flasks. The enzyme support was characterized in terms of its internal and external surface area, protein location, and protein content. It was found that the enzyme was mainly located on the external surface of the support, therefore, internal diffusional limitations were not important. It was also shown that the protein content of the support depends on the size of the particle, with smaller particles containing higher amounts of protein per unit weight. Under the conditions studied, the reaction was not under external mass transfer limitations, and the initial reaction rate depended on the size of the support particles. This was mainly due to the different protein contents on the support as a function of particle size and not to internal or external mass transfer limitations. Also, it was found that the inhibition exerted by water was predominantly a physical effect due to its accumulation around the enzyme. It was also found that the reaction was substrate inhibited by lauric acid, but not by geraniol. (c) 1995 John Wiley & Sons, Inc.     

Fluorescent Bone Viewed through Toenails of Living Animals: a Method to Observe Bone Regrowth

We have developed a new method to observe bone and to document growth in living animals. The technique involves injecting calcein, a fluorescent calcium deposition marker, waiting approximately 4 hr for it to clear the vascular system, and observing bone directly through the toenails of lightly anesthetized living animals. Bone regrowth can be monitored in situ by amputating the digit through the nail plate, waiting the desired number of days, and injecting a second fluorescent label, alizarin red. Bone that has regrown since the amputation appears as a red area distal to the green calcein label on toes of lightly anesthetized animals when viewed under FITC fluorescence. This method has been used to demonstrate blocked bone synthesis and to quantitate significant differences in bone growth in control and experimental toes of individual animals. Advantages of this method include its simplicity, the use of fewer animals to collect sequential data, and increased reliability of repeated microscopic measurements using the same animal.     

The intensity of respiration and heat emission from seedlings of Festuca pratensis (Hud.) and Hordeum vulgare L. during pathogenesis caused by Bipolaris sorokiniana (Sacc.) Shoem

The presented work was conducted on seedlings of spring barley and meadow fescue which differ in the degree of sensitivity to leaf spot pathogen Bipolaris sorokiniana (Sacc.) Shoem. The seedling reaction to inoculation with mycelium and conidia was examined in glasshouse conditions on the basis of respiration intensity and heat production. The leaf respiration was measured using Clark-type electrode, while heat emission was evaluated by means of isotermic microcalorimeter. The measurements were performed after 1, 3, 6, 10, 24, 48, 72, 168 and 240 hours since the inoculation moment. Leaves of meadow fescue were characterized by the most intense respiration at the 6^th hour, while barley leaves at the 24^th and 72^nd hour after inoculation. In the case of meadow fescue the greatest heat production was noted in the period between 24 and 168 hours after inoculation. Simultaneously, at the 48^th hour the smallest rate of respiration was observed. Barley leaves emitted the greatest amount of heat only in the first 3 hours of the pathogenesis. In these hours the smallest respiration rate was noted. The observed, opposing reaction of respiration intensity and heat emission in the infected seedlings of both species may illustrate a disorder in metabolic processes in plants during pathogenesis. The plants studied differed in the time of their reaction to pathogen attack: barley responded earlier in heat production, while fescue extended respiration rate in the first hours after inoculation. This is clearly observable, when coefficients of metabolic inefficiency (heat rates per mole O₂) are compared. In the case of barley the highest rates were noticed just after inoculation, whereas in fescue at the 48^th hour. In both species attack of pathogen caused high metabolic efficiency.     

Phytochrome regulation of nuclear gene expression in plants

The photoregulation of gene expression in higher plants was extensively studied during the 1980s, in particular the light-responsive cis -acting elements and trans -acting factors of the Lhcb and rbcS genes. However, little has been discovered about: (1) which plant genes are regulated by light, and (2) which photoreceptors control the expression of these genes. In the 1990s, the functional analysis of the various photoreceptors has progressed rapidly using photoreceptor-deficient mutants, including those of the phytochrome gene family. More recently however, advanced techniques for gene expression analysis, such as fluorescent differential display and DNA microarray technology, have become available enabling the global identification of genes that are regulated by particular photoreceptors. In this paper we describe distinct and overlapping effects of individual phytochromes on gene expression in Arabidopsis thaliana.