Modular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B.subtilis RNase P protein

The bacterial RNase P holoenzyme catalyzes the formation of the mature 5′-end of tRNAs and is composed of an RNA and a protein subunit. Among the two folding domains of the RNase P RNA, the catalytic domain (C-domain) contains the active site of this ribozyme. We investigated specific binding of the Bacillus subtilis C-domain with the B.subtilis RNase P protein and examined the catalytic activity of this C-domain–P protein complex. The C-domain forms a specific complex with the P protein with a binding constant of ∼0.1 µM. The C-domain–P protein complex and the holoenzyme are equally efficient in cleaving single-stranded RNA (∼0.9 min–1 at pH 7.8) and substrates with a hairpin–loop 3′ to the cleavage site (∼40 min–1). The holoenzyme reaction is much more efficient with a pre-tRNA substrate, binding at least 100-fold better and cleaving 10–500 times more efficiently. These results demonstrate that the RNase P holoenzyme is functionally constructed in three parts. The catalytic domain alone contains the active site, but has little specificity and affinity for most substrates. The specificity and affinity for the substrate is generated by either the specificity domain of RNase P RNA binding to a T stem–loop-like hairpin or RNase P protein binding to a single-stranded RNA. This modular construction may be exploited to obtain RNase P-based ribonucleoprotein complexes with altered substrate specificity.

Enhanced phospholipase C-gamma1 activity produced by association of independently expressed X and Y domain polypeptides.

The X and Y domains of phospholipase C (PLC)-gamma1, which are conserved in all mammalian phosphoinositide-specific PLC isoforms and are proposed to interact to form the catalytic site, have been expressed as individual hexahistidine-tagged fusion proteins in the baculovirus system. Following coinfection of insect cells with recombinant viruses, association of X and Y polypeptides was demonstrated in coprecipitation assays. When enzyme activity was examined, neither domain possessed catalytic activity when expressed alone; however, coexpression of the X and Y polypeptides produced a functional enzyme. This reconstituted phospholipase activity remained completely dependent on the presence of free Ca2+. The specific activity of the X:Y complex was significantly greater (20- to 100-fold) than that of holoPLC-gamma1 and was only moderately influenced by varying the concentration of substrate. The enzyme activities of holoPLC-gamma1 and the X:Y complex exhibited distinct pH optima. For holoPLC-gamma1 maximal activity was detected at pH 5.0, while activity of the X:Y complex was maximal at pH 7.2.

Glutamate is required to maintain the steady-state potassium pool in Salmonella typhimurium.

In many bacteria, accumulation of K+ at high external osmolalities is accompanied by accumulation of glutamate. To determine whether there is an obligatory relationship between glutamate and K+ pools, we studied mutant strains of Salmonella typhimurium with defects in glutamate synthesis. Enteric bacteria synthesize glutamate by the combined action of glutamine synthetase and glutamate synthase (GS/GOGAT cycle) or the action of biosynthetic glutamate dehydrogenase (GDH). Activity of the GS/GOGAT cycle is required under nitrogen-limiting conditions and is decreased at high external ammonium/ammonia ((NH4)+) concentrations by lowered synthesis of GS and a decrease in its catalytic activity due to covalent modification (adenylylation by GS adenylyltransferase). By contrast, GDH functions efficiently only at high external (NH4)+ concentrations, because it has a low affinity for (NH4)+. When grown at low concentrations of (NH4)+ (< or = 2 mM), mutant strains of S. typhimurium that lack GOGAT and therefore are dependent on GDH have a low glutamate pool and grow slowly; we now demonstrate that they have a low K+ pool. When subjected to a sudden (NH4)+ upshift, strains lacking GS adenylyltransferase drain their glutamate pool into glutamine and grow very slowly; we now find that they also drain their K+ pool. Restoration of the glutamate pool in these strains at late times after shift was accompanied by restoration of the K+ pool and a normal growth rate. Taken together, the results indicate that glutamate is required to maintain the steady-state K+ pool -- apparently no other anion can substitute as a counter-ion for free K+ -- and that K+ glutamate is required for optimal growth.

How photons start vision.

Recent studies have elucidated how the absorption of a photon in a rod or cone cell leads to the generation of the amplified neural signal that is transmitted to higher-order visual neurons. Photoexcited visual pigment activates the GTP-binding protein transducin, which in turn stimulates cGMP phosphodiesterase. This enzyme hydrolyzes cGMP, allowing cGMP-gated cationic channels in the surface membrane to close, hyperpolarize the cell, and modulate transmitter release at the synaptic terminal. The kinetics of reactions in the cGMP cascade limit the temporal resolution of the visual system as a whole, while statistical fluctuations in the reactions limit the reliability of detection of dim light. Much interest now focuses on the processes that terminate the light response and dynamically regulate amplification in the cascade, causing the single photon response to be reproducible and allowing the cell to adapt in background light. A light-induced fall in the internal free Ca2+ concentration coordinates negative feedback control of amplification. The fall in Ca2+ stimulates resynthesis of cGMP, antagonizes rhodopsin's catalytic activity, and increases the affinity of the light-regulated cationic channel for cGMP. We are using physiological methods to study the molecular mechanisms that terminate the flash response and mediate adaptation. One approach is to observe transduction in truncated, dialyzed photoreceptor cells whose internal Ca2+ and nucleotide concentrations are under experimental control and to which exogenous proteins can be added. Another approach is to observe transduction in transgenic mouse rods in which specific proteins within the cascade are altered or deleted.

X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B.

Hereditary deficiency of factor IXa (fIXa), a key enzyme in blood coagulation, causes hemophilia B, a severe X chromosome-linked bleeding disorder afflicting 1 in 30,000 males; clinical studies have identified nearly 500 deleterious variants. The x-ray structure of porcine fIXa described here shows the atomic origins of the disease, while the spatial distribution of mutation sites suggests a structural model for factor X activation by phospholipid-bound fIXa and cofactor VIIIa. The 3.0-A-resolution diffraction data clearly show the structures of the serine proteinase module and the two preceding epidermal growth factor (EGF)-like modules; the N-terminal Gla module is partially disordered. The catalytic module, with covalent inhibitor D-Phe-1I-Pro-2I-Arg-3I chloromethyl ketone, most closely resembles fXa but differs significantly at several positions. Particularly noteworthy is the strained conformation of Glu-388, a residue strictly conserved in known fIXa sequences but conserved as Gly among other trypsin-like serine proteinases. Flexibility apparent in electron density together with modeling studies suggests that this may cause incomplete active site formation, even after zymogen, and hence the low catalytic activity of fIXa. The principal axes of the oblong EGF-like domains define an angle of 110 degrees, stabilized by a strictly conserved and fIX-specific interdomain salt bridge. The disorder of the Gla module, whose hydrophobic helix is apparent in electron density, can be attributed to the absence of calcium in the crystals; we have modeled the Gla module in its calcium form by using prothrombin fragment 1. The arched module arrangement agrees with fluorescence energy transfer experiments. Most hemophilic mutation sites of surface fIX residues occur on the concave surface of the bent molecule and suggest a plausible model for the membrane-bound ternary fIXa-FVIIIa-fX complex structure: fIXa and an equivalently arranged fX arch across an underlying fVIIIa subdomain from opposite sides; the stabilizing fVIIIa interactions force the catalytic modules together, completing fIXa active site formation and catalytic enhancement.

The mode of action of aspirin-like drugs: effect on inducible nitric oxide synthase.

Nitric oxide synthesized by inducible nitric oxide synthase (iNOS) has been implicated as a mediator of inflammation in rheumatic and autoimmune diseases. We report that exposure of lipopolysaccharide-stimulated murine macrophages to therapeutic concentrations of aspirin (IC50 = 3 mM) and hydrocortisone (IC50 = 5 microM) inhibited the expression of iNOS and production of nitrite. In contrast, sodium salicylate (1-3 mM), indomethacin (5-20 microM), and acetaminophen (60-120 microM) had no significant effect on the production of nitrite at pharmacological concentrations. At suprapharmacological concentrations, sodium salicylate (IC50 = 20 mM) significantly inhibited nitrite production. Immunoblot analysis of iNOS expression in the presence of aspirin showed inhibition of iNOS expression (IC50 = 3 mM). Sodium salicylate variably inhibited iNOS expression (0-35%), whereas indomethacin had no effect. Furthermore, there was no significant effect of these nonsteroidal anti-inflammatory drugs on iNOS mRNA expression at pharmacological concentrations. The effect of aspirin was not due to inhibition of cyclooxygenase 2 because both aspirin and indomethacin inhibited prostaglandin E2 synthesis by > 75%. Aspirin and N-acetylimidazole (an effective acetylating agent), but not sodium salicylate or indomethacin, also directly interfered with the catalytic activity of iNOS in cell-free extracts. These studies indicate that the inhibition of iNOS expression and function represents another mechanism of action for aspirin, if not for all aspirin-like drugs. The effects are exerted at the level of translational/posttranslational modification and directly on the catalytic activity of iNOS.

Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase.

Escherichia coli RuvC protein is a specific endonuclease that resolves Holliday junctions during homologous recombination. Since the endonucleolytic activity of RuvC requires a divalent cation and since 3 or 4 acidic residues constitute the catalytic centers of several nucleases that require a divalent cation for the catalytic activity, we examined whether any of the acidic residues of RuvC were required for the nucleolytic activity. By site-directed mutagenesis, we constructed a series of ruvC mutant genes with similar amino acid replacements in 1 of the 13 acidic residues. Among them, the mutant genes with an alteration at Asp-7, Glu-66, Asp-138, or Asp-141 could not complement UV sensitivity of a ruvC deletion strain, and the multicopy mutant genes showed a dominant negative phenotype when introduced into a wild-type strain. The products of these mutant genes were purified and their biochemical properties were studied. All of them retained the ability to form a dimer and to bind specifically to a synthetic Holliday junction. However, they showed no, or extremely reduced, endonuclease activity specific for the junction. These 4 acidic residues, which are dispersed in the primary sequence, are located in close proximity at the bottom of the putative DNA binding cleft in the three-dimensional structure. From these results, we propose that these 4 acidic residues constitute the catalytic center for the Holliday junction resolvase and that some of them play a role in coordinating a divalent metal ion in the active center.

Catalytic domain of human immunodeficiency virus type 1 integrase: identification of a soluble mutant by systematic replacement of hydrophobic residues.

The integrase protein of human immunodeficiency virus type 1 is necessary for the stable integration of the viral genome into host DNA. Integrase catalyzes the 3' processing of the linear viral DNA and the subsequent DNA strand transfer reaction that inserts the viral DNA ends into host DNA. Although full-length integrase is required for 3' processing and DNA strand transfer activities in vitro, the central core domain of integrase is sufficient to catalyze an apparent reversal of the DNA strand transfer reaction, termed disintegration. This catalytic core domain, as well as the full-length integrase, has been refractory to structural studies by x-ray crystallography or NMR because of its low solubility and propensity to aggregate. In an attempt to improve protein solubility, we used site-directed mutagenesis to replace hydrophobic residues within the core domain with either alanine or lysine. The single substitution of lysine for phenylalanine at position 185 resulted in a core domain that was highly soluble, monodisperse in solution, and retained catalytic activity. This amino acid change has enabled the catalytic domain of integrase to be crystallized and the structure has been solved to 2.5-A resolution [Dyda, F., Hickman, A. B., Jenkins, T. M., Engelman, A., Craigie, R. & Davies, D. R. (1994) Science 266, 1981-1986]. Systematic replacement of hydrophobic residues may be a useful strategy to improve the solubility of other proteins to facilitate structural and biochemical studies.

Evolução estrutural e performance catalítica de nanopartículas de AuPd de composição variável

Nanopartículas bimetálicas de AuPd têm mostrado excelente atividade catalítica em reações de oxidação. O entendimento dos efeitos da variação da composição e morfologia das nanopartículas bimetálicas em suas propriedades catalíticas é fundamental para a preparação de catalisadores cada vez mais ativos e seletivos. Neste trabalho foram estudadas nanopartículas bimetálicas de AuPd de composição variável suportadas sobre um suporte constituído por nanopartículas de magnetita revestidas por sílica. O efeito da calcinação e da redução com hidrogênio sobre a morfologia e composição das nanopartículas bimetálicas foi acompanhado pelas técnicas de TEM, XEDS, XAS, XRD e XPS. A correlação entre estrutura, composição e atividade catalítica dos catalisadores preparados foi estudada pelo acompanhamento de reações de oxidação de monóxido de carbono e de oxidação de álcool benzílico. As amostras não calcinadas apresentaram segregação metálica em todas as composições estudadas. Após a etapa de calcinação, maior segregação metálica foi encontrada, com a formação de óxido de paládio na superfície das nanopartículas, exceto na amostra mais rica em ouro. O tratamento das amostras oxidadas com hidrogênio foi capaz de reduzir os metais oxidados na superfície das nanopartículas, mas um enriquecimento em paládio na superfície e maior segregação entre ouro e paládio foram observados. Uma melhora na atividade catalítica na oxidação de monóxido de carbono foi observada juntamente com um aumento na composição de paládio, além disso, observou-se uma maior atividade catalítica em relação às nanopartículas não calcinadas para as amostras calcinadas e reduzidas. Para a oxidação de álcool benzílico um aumento na atividade catalítica de até cinco vezes foi observado após a calcinação dos catalisadores, com maior atividade para a amostra de composição Au1Pd2. A queda na atividade catalítica após a redução dos catalisadores mostrou que a presença de óxido de paládio na superfície das nanopartículas é fundamental para que seja observada uma maior atividade catalítica.

Spectroscopic, calorimetric, and catalytic evidences of hydrophobicity on Ti-MCM-41 silylated materials for olefin epoxidations

Hydrophobic Ti-MCM-41 samples prepared by post-synthesis silylation treatment demonstrate to be highly active and selective catalysts in olefins epoxidation by using organic hydroperoxides as oxidizing agents in liquid phase reaction systems. Epoxide yields show important enhancements with increased silylation degrees of the Ti-mesoporous samples. Catalytic studies are combined and correlated with spectroscopic techniques (e.g. XRD, XANES, UV-Visible, 29Si MAS-NMR) and calorimetric measurements to better understand the changes in the surface chemistry of Ti-MCM-41 samples due to the post-synthesis silylation treatment and to ascertain the role of these trimethylsilyl groups incorporated in olefin epoxidation. In such manner, the effect of the organic moieties on solids, and both water and glycol molecules contents on the catalytic activity and selectivity are analyzed in detail. Results show that the hydrophobicity level of the samples is responsible for the decrease in water adsorption and, consequently, the negligible formation of the non-desired glycol during the catalytic process. Thus, catalyst deactivation by glycol poisoning of Ti active sites is greatly diminished, this increasing catalyst stability and leading to practically quantitative production of the corresponding epoxide. The extended use of these hydrophobic Ti-MCM-41 catalysts together with organic hydroperoxides for the highly efficient and selective epoxidation of natural terpenes is also exemplified.

The role of mesoporosity and Si/Al ratio in the catalytic etherification of glycerol with benzyl alcohol using ZSM-5 zeolites

A comparative study of the influence of three different acid solids as catalysts (conventional zeolites Z15c with Si/Al = 19.5 and Z40c with Si/Al = 48.2, and a hierarchical zeolite Z40c-H with Si/Al = 50.0) for the etherification of glycerol with benzyl alcohol was performed. The catalytic activity and selectivity of these zeolites was elucidated at different catalyst contents. Three different ethers (3-benzyloxy-1,2-propanediol, which is a mono-benzyl-glycerol ether (MBG) and 1,3-dibenzyloxy-2-propanol, which is a di-benzyl-glycerol ether (DBG) and dibenzyl ether (DBz) were identified as the main products. MBG was the major product of the reaction catalyzed by the microporous Z15c zeolite with low Si/Al molar ratio, whereas DBG was formed in higher yield with the use of microporous Z40c and hierarchical Z40c-H zeolites, both of them having a similar high Si/Al molar ratio (≈50). MBG is a value-added product and it is obtained with good yield and selectivity when using the conventional zeolite Z15c as a catalyst. Under the best conditions tested, i.e., 25 mg of catalyst for 8 h at 120 °C, a 62% of conversion was obtained without the need of solvent, with an excellent 84% selectivity toward the MBG and no formation of DBz.

Enhancement of the hydrogenation activity of a Pd-tridecilamine (TDA) complex by confinement in carbon nanotubes

An active hydrogenation Pd complex has been immobilised by impregnation on CNTs submitted to several treatments that lead to important differences in their surface chemistry and in the proportion of tubes with both ends open. Most of the hybrid catalysts are more active than the complex in homogeneous phase, but the support properties have an important impact in the catalytic activity. In general, the more developed the surface chemistry, the lower the activity. However, when CNTs are open at both ends, the Pd complex can enter the tubular cavity and an important enhancement of the catalytic activity due to a confinement effect is observed.

Development of magnetic carbon xerogels for catalytic wet peroxide oxidation

Hybrid magnetic carbon composites have been recently proposed as the next step in the evolution of catalysts for catalytic wet peroxide oxidation (CWPO), with several synergistic effects arising from the combination of the high catalytic activity of metal species with the proven catalytic properties of carbon-based materials in CWPO [1]. Bearing this in mind, this work sought the development of novel magnetic carbon xerogels, composed by interconnected carbon microspheres with iron (Fe) and/or cobalt (Co) microparticles embedded in their structure. As inferred from the extensive characterization performed, materials with distinctive properties were obtained upon inclusion of different metal precursors during the sol-gel polymerization of resorcinol and formaldehyde, followed by thermal annealing.

Alteration of natural ³⁷Ar activity concentration in the subsurface by gas transport and water infiltration

High ³⁷Ar activity concentration in soil gas is proposed as a key evidence for the detection of underground nuclear explosion by the Comprehensive Nuclear Test-Ban Treaty. However, such a detection is challenged by the natural background of ³⁷Ar in the subsurface, mainly due to Ca activation by cosmic rays. A better understanding and improved capability to predict ³⁷Ar activity concentration in the subsurface and its spatial and temporal variability is thus required. A numerical model integrating ³⁷Ar production and transport in the subsurface is developed, including variable soil water content and water infiltration at the surface. A parameterized equation for ³⁷Ar production in the first 15 m below the surface is studied, taking into account the major production reactions and the moderation effect of soil water content. Using sensitivity analysis and uncertainty quantification, a realistic and comprehensive probability distribution of natural ³⁷Ar activity concentrations in soil gas is proposed, including the effects of water infiltration. Site location and soil composition are identified as the parameters allowing for a most effective reduction of the possible range of ³⁷Ar activity concentrations. The influence of soil water content on ³⁷Ar production is shown to be negligible to first order, while ³⁷Ar activity concentration in soil gas and its temporal variability appear to be strongly influenced by transient water infiltration events. These results will be used as a basis for practical CTBTO concepts of operation during an OSI.

Preparation and catalytic properties of ZrO2-Al2O3 composite oxide supported nickel catalysts for methane reforming with carbon dioxide

ZrO2-Al2O3 composite oxides and supported Ni catalysts were prepared, and characterized by N-2 adsorption/desorption, X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) techniques. The catalytic performance and carbon deposition was also investigated. This mesoporous composite oxide is shown to be a promising catalyst support. An increase in the catalytic activity and stability of methane and carbon dioxide reforming reaction was resulted from the zirconia addition, especially at 5wt% ZrO2 content. The Ni catalyst supported ZrO2-Al2O3 has a strong resistance to sintering and the carbon deposition in a relatively long-term reaction.