Conformational preferences of modified nucleoside N(2)-methylguanosine (m(2)G) and its derivative N(2), N(2)-dimethylguanosine (m(2)(2)G) occur at 26th position (hinge region) in tRNA

Conformational preferences of the modified nucleosides N²-methylguanosine (m²G) and N², N²-dimethylguanosine (m₂²G) have been studied theoretically by using quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. Automated complete geometry optimization using semiempirical quantum chemical RM1, along with ab initio molecular orbital Hartree–Fock (HF-SCF), and density functional theory (DFT) calculations has also been made to compare the salient features. Single-point energy calculation studies have been made on various models of m²G26:C/A/U44 and m₂²G26:C/A/U44. The glycosyl torsion angle prefers “syn” (χ = 286°) conformation for m²G and m₂²G molecules. These conformations are stabilized by N(3)–HC2′ and N(3)–HC3′ by replacing weak interaction between O5′–HC(8). The N²-methyl substituent of (m²G26) prefers “proximal” or s-trans conformation. It may also prefer “distal” or s-cis conformation that allows base pairing with A/U44 instead of C at the hinge region. Thus, N²-methyl group of m²G may have energetically two stable s-trans m²G:C/A/U or s-cis m²G:A/U rotamers. This could be because of free rotations around C–N bond. Similarly, N², N²-dimethyl substituent of (m₂²G) prefers “distal” conformation that may allow base pairing with A/U instead of C at 44th position. Such orientations of m²G and m₂²G could play an important role in base-stacking interactions at the hinge region of tRNA during protein biosynthesis process.     

H(2)O(2)-induced O(2) production by a non-phagocytic NAD(P)H oxidase causes oxidant injury

Non-phagocytic NAD(P)H oxidases have been implicated as major sources of reactive oxygen species in blood vessels. These oxidases can be activated by cytokines, thereby generating O(2), which is subsequently converted to H(2)O(2) and other oxidant species. The oxidants, in turn, act as important second messengers in cell signaling cascades. We hypothesized that reactive oxygen species, themselves, can activate the non-phagocytic NAD(P)H oxidases in vascular cells to induce oxidant production and, consequently, cellular injury. The current report demonstrates that exogenous exposure of non-phagocytic cell types of vascular origin (smooth muscle cells and fibroblasts) to H(2)O(2) activates these cell types to produce O(2) via an NAD(P)H oxidase. The ensuing endogenous production of O(2) contributes significantly to vascular cell injury following exposure to H(2)O(2). These results suggest the existence of a feed-forward mechanism, whereby reactive oxygen species such as H(2)O(2) can activate NAD(P)H oxidases in non-phagocytic cells to produce additional oxidant species, thereby amplifying the vascular injury process. Moreover, these findings implicate the non-phagocytic NAD(P)H oxidase as a novel therapeutic target for the amelioration of the biological effects of chronic oxidant stress.     

Synthesis and structural characterization of cadmium(II) complexes with 2-(2-pyridyl)imino-N-(2-thiazolin-2-yl)thiazolidine (PyTT)

We have carried out the synthesis of the cadmium coordination compounds [Cd(NO₃)₂(PyTT)(H₂O)] (1) and [CdCl₂{(μ-Cl)₂CdCl(μ-Cl)(μ-PyTT)Cd}₂]_n (2), together with their structural determination by means of X-ray diffraction. The compounds were also characterized through elemental analysis and infrared spectroscopy. The first complex presents a distorted pentagonal bipyramidal geometry with the axial positions occupied by one oxygen atom from a water molecule and a second one from a nitrate ion which acts as a monodentate ligand, whereas the equatorial plane contains three nitrogen atoms from the organic moiety and two oxygen atoms coming from the other nitrate group, which is bidentate. The structure of the second complex consists of parallel sheets linked by van der Waals forces, each one made up of structural units [CdCl₂{(μ-Cl)₂CdCl(μ-Cl)(μ-PyTT)Cd}₂], which possesses two PyTT ligands, 10 bridging chloro ligands and 5 cadmium(II) centres belonging to three environment types: octahedral CdN₂Cl₄, octahedral CdCl₆, on which a centre of symmetry is located, and tetrahedral CdNCl₃, present in a 2:1:2 ratio.     

Partikelgestalt des Spargel-Virus 2 (asparagus virus 2) (Kurze Mitteilung)

Zwei Kernpolyedervirus‐Isolate der Kohleule aus Deutschland (MbKPV‐D) und Moldawien (MbKPV‐Ki) wurden im Biotest geprüft und der Genotyp mit Hilfe der Restriktionsenzym‐Fragmentanalyse (REN) untersucht. Beide Isolate ergaben eine gleiche biologische Aktivität. Die REN‐Profile zeigten weitestgehende Übereinstimmung in der DNA‐Struktur. Geringe Unterschiede wurden in den Profilen der Eco RI‐ und Hind III‐ Schnitte gefunden. Die erhaltenen REN‐Profile stimmen im wesentlichen mit den für ein niederländisches MbKPV‐Isolate beschriebenen Bandenmustern überein.     

Stereospecific formation of alpha-hydroxycarboxylato oxo peroxo complexes of vanadium(V). Crystal structure of (NBu4)2[V2O2(O2)2(L-lact)2] x 2H2O and (NBu4)2[V2O2(O2)2(D-lact)(L-lact)] x 2H2O

An overview of structurally characterized alpha-hydroxycarboxylatodioxo- and alpha-hydroxycarboxylatooxoperoxovanadates(V) is presented and the geometric parameters of the V2O2 bridging core are discussed. The first case of a stereospecific formation of oxoperoxovanadates(V) is reported: The crystal structures of the isomeric compounds (NBu4)2[V2O2(O2)2(L-lact)2] x 2H2O and (NBu4)2[V2O2(O2)2(D-lact)(L-lact)] x 2H2O (lact = C3H4O3(2-), the anion of the lactic acid) differ mainly in the arrangement of the V2O2 core and in mutual orientation of the V=O bonds. The complexes with achiral ligands adopt the same structural type as the complexes formed from a racemic mixture of a chiral ligand, while the structure obtained using an enantiopure L,L-hydroxycarboxylate is different.     

Synthesis,spectral and magnetical characterization of monomeric [Cu(2-NO2bz)2(3-pyme)2(H2O)2] and polymeric [Cu{3,5-(NO2)2bz}2(3-pyme)2]n

Two new complexes of composition [Cu(2-NO₂bz)₂(3-pyme)₂(H₂O)₂] (1) and/or [Cu{3,5-(NO₂)₂bz}₂(3-pyme)₂] (2) (3-pyme = 3-pyridylmethanol, ronicol or 3-pyridylcarbinol, 2-NO₂bz = 2-nitrobenzoate and 3,5-(NO₂)₂bz = 3,5-dinitrobenzoate) have been prepared and studied by elemental analysis, electronic, infrared and EPR spectroscopy, magnetic susceptibility measurements and the structure of both complexes has been solved. Complex (1) shows an unusual molecular type of structure consisting of the [Cu(2-NO₂bz)₂(3-pyme)₂(H₂O)₂] molecules held together by hydrogen bonds and van der Waals interactions. Complex (2) exhibits a polymeric chain-like structure [Cu{3,5-(NO₂)₂bz}₂(3-pyme)₂]_n with copper atoms doubly bridged by two 3-pyridylmethanol molecules and the polymeric molecules are held together by van der Waals interactions. Complex (1) exhibits a magnetic moment μ_eff = 1.84 B.M. at 300 K that remains nearly constant within the temperature region (5–300 K). Further cooling results in lowering the magnetic moment to μ_eff = 1.82 B.M. at 1.8 K. The magnetic susceptibility temperature dependence obeys Curie–Weiss law with Curie constant of 0.423 cm³ K mol⁻¹ and with Weiss constant of −0.06 K. The magnetic moment of (2) exhibits a small increase with a decrease in the temperature (μ_eff = 1.80 B.M. at 300 K and μ_eff = 1.85 B.M. at 1.8 K) with Curie constant of 0.409 cm³ K mol⁻¹ and with Weiss constant of +1.1 K, which can indicate a very weak ferromagnetic interaction between the copper atoms within the chain. Applying the molecular field model resulted in obtaining zJ′ values −0.08 cm⁻¹ for complex (1), and −0.07 cm⁻¹ for complex (2), respectively, that could characterize intermolecular and interchain interactions transmitted through π–π stacking.     

Molecular-Mechanical studies of the mismatched base analogs of d(CGCGAATTCGCG)2:d(CGTGAATTCGCG)2, d(CGAGAATTCGCG)2, d(CGCGAATTCACG)2, d(CGCGAATTCTCG)2, and d(CGCAGAATTCGCG)·d(CGCGAATTCGCG)

Molecular-mechanical simulations have been carried out on “mismatched base” analogs of the DNA double-helical structure d(CGCGAATTCGCG)₂, in which the base pairs CG at the 3 and 10 positions have been replaced by CA, AG, TC, and TG base pairs, as well as an insertion analog in which an extra adenine has been incorporated into one strand of the above structure between bases 3 and 4. The results of these simulations (calculated relative stabilities, structures, and nmr ring-current shifts) have been compared with calorimetric and nmr data. The calculated relative stabilities of the double-helical parent dodecamer and the various “wobble” base pairs qualitatively correlate with the experimental melting temperatures. The base-pairing structure for the GT wobble pair is in agreement with that previously determined from nmr experiments. For the GA base pair, the structure with both bases anti has a slightly more favorable energy from base pairing and stacking than a structure with non-Watson-Crick H-bonding with adenine syn, in agreement with nmr experiments. The CA wobble base is calculated to favor an adenine 6NH₂ …? cytosine N3 H-bond over cytosine 4NH₂ …? adenine N1, again, in agreement with nmr experiments. There is no definitive experimental data on the TC base pair, but the existence of (somewhat long and weak) H-bonds involving cytosine 4NH₂ …? thymine 4CO and cytosine N3 …? thymine HN3 seems reasonable. We find a structure in which the extra adenine base of the insertion analogs sits “inside” the double helix.     

Compartment-dependent management of H(2)O(2) by peroxisomes

Peroxisomes (PO) are essential and ubiquitous single-membrane-bound organelles whose ultrastructure is characterized by a matrix and often a crystalloid core. A unique feature is their capacity to generate and degrade H(2)O(2) via several oxidases and catalase, respectively. Handling of H(2)O(2) within PO is poorly understood and, in contrast to mitochondria, they are not regarded as a default H(2)O(2) source. Using an ultrasensitive luminometric H(2)O(2) assay, we show in real time that H(2)O(2) handling by matrix-localized catalase depends on the localization of H(2)O(2) generation in- and outside the PO. Thus, intact PO are inefficient at degrading external but also internal H(2)O(2) that is generated by the core-localized urate oxidase (UOX). Our findings suggest that, in addition to the PO membrane, the matrix forms a significant diffusion barrier for H(2)O(2). In contrast, matrix-generated H(2)O(2) is efficiently degraded. We further show that the tubular structures in crystalloid cores of UOX are associated with and perpendicularly oriented toward the PO membrane. Studies on metabolically active liver slices demonstrate that UOX directly releases H(2)O(2) into the cytoplasm, with the 5-nm primary tubules in crystalloid cores serving as exhaust conduits. Apparently, PO are inefficient detoxifiers of external H(2)O(2) but rather can become an obligatory source of H(2)O(2)--an important signaling molecule and a potential toxin.     

Spectroscopic investigations of Er(3+) :CdO-Bi(2) O(3) -B(2) O(3) glasses

This article reports on the optical properties of Er³⁺ ions doped CdO–Bi₂O₃–B₂O₃ (CdBiB) glasses. The materials were characterized by optical absorption and emission spectra. By using Judd–Ofelt theory, the intensity parameters Ω_λ (λ = 2, 4, 6) and also oscillatory strengths were calculated from the absorption spectra. The results were used to compute the radiative properties of Er³⁺:CdBiB glasses. The concentration quenching and energy transfer from Yb³⁺–Er³⁺ were explained. The stimulated emission cross‐section, full width at half maximum (FWHM) and FWHM × values are also calculated for all the Er³⁺:CdBiB glasses. Copyright © 2011 John Wiley & Sons, Ltd.     

Conformational analysis of the tetranucleotides m6(2)A-m6(2)A-U-m6(2)A(m6(2)A = N6-dimethyladenosine) and U-m6(2)A-U-m6(2)A and of the hybrid dA-r(U-A). A one- and two-dimensional NMR study

A 1H-NMR investigation was carried out on the tetranucleotides U-m6(2)A-U-m6(2)A and m6(2)A-m6(2)A-U-m6(2)A (m6(2) = N6-dimethyladenosine) as well as on the hybrid trinucleotide dA-r(U-A). An extensive comparison with m6(2)A-U-m6(2)A and other relevant compounds is made. Previous proton NMR studies on trinucleotides have shown that purine-pyrimidine-purine sequences prefer to adopt a mixture of states which have as a common feature that the interior pyrimidine residue bulges out, whereas the flanking purine residues stack upon each other. A stacking interaction on the 3' side of the bulge is known to have no measurable effect on the bulge population. Chemical-shift data, ribose ring conformational analysis and information from NOE experiments now show unambiguously that the moderate U(1)-m6(2)A(2) stack in U-m6(2)A-U-m6(2)A diminishes the population of bulged-out structures in favour of a regular stack. This tendency towards conformational transmission in the downstream 5'----3' direction is fully confirmed by the fact that the strong m6(2)A(1)-m6(2)A(2) stack in the tetranucleotide m6(2)A-m6(2)A-U-m6(2)A virtually precludes the formation of bulged-out structures. The conformational characteristics of dA-r(U-A) appear comparable with those of m6(2)A-U-m6(2)A, which indicates that the presence of a 2'-hydroxyl group in the first purine residue is not a necessary prerequisite for the formation of a bulge.     

GPI 6150 prevents H(2)O(2) cytotoxicity by inhibiting poly(ADP-ribose) polymerase

GPI 6150 (1,11b-dihydro-[2H]benzopyrano[4,3,2-de]isoquinolin-3-one) is a novel inhibitor of poly(ADP-ribose) polymerase (PARP). It has demonstrated efficacy in rodent models of focal cerebral ischemia, traumatic brain injury, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine damage to dopaminergic neurons, regional myocardial ischemia, streptozotocin-induced diabetes, septic shock, and arthritis. Here we report the structure of GPI 6150, its enzymatic characteristics, and biochemical property in cytoprotection. As a competitive PARP inhibitor (K(i) = 60 nM), GPI 6150 protected the P388D1 cells against hydrogen peroxide cytotoxicity, by preventing PARP activation and the depletion of NAD(+), the substrate for PARP. To address the concerns of potential side effects of PARP inhibition, we tested GPI 6150 and found it had no effect on the repair and expression of a plasmid DNA damaged by N-methyl-N'-nitro-N-nitrosoguanidine. Neither did it affect dehydrogenases with NAD co-enzyme. GPI 6150 was much less potent to inhibit mono-ADP-ribosyltransferase. There was no selectivity for GPI 6150 between PARP isozymes. These attributes render GPI 6150 a useful tool to probe the functions of PARP.     

Photochemical synthesis method of tungsten(II) complexes [WCl2(CO)3PPh3)2] and [WCl2(CO)2(dppe)]

The photochemical oxidation reaction of W(CO)₆ to [W(CO)₄Cl₂]₂ with CCl₄ was applied in the synthesis of [WCl₂(CO)₃(PPh₃)₂] and [WCl₂(CO)₂₋- (dppe)].     

High CO(2) Requiring Mutant of Anacystis nidulans R(2)

Some physiological characteristics of a mutant (E₁) of Anacystis nidulans R₂, incapable of growing at air level of CO₂, are described. E₁ is capable of accumulating inorganic carbon (C_i) internally as efficiently as the wild type (R₂). The apparent photosynthetic affinity for C_i in E₁, however, is some 1000 times lower than that of R₂. The kinetic parameters of ribulose 1,5-bisphosphate carboxylase/oxygenase from E₁ are similar to those observed in R₂. The mutant appears to be defective in its ability to utilize the intracellular C_i pool for photosynthesis and depends on extracellular supply of Ci in the form of CO₂. The very high apparent photosynthetic K_m (CO₂) of the mutant indicate a large diffusion resistance for CO₂. Data obtained here are used to calculate the permeability coefficient for CO₂ between the bulk medium and the carboxylation site of cyanobacteria.     

Photoreduction of O(2) Primes and Replaces CO(2) Assimilation

A mass spectrometer with a membrane inlet system was used to monitor directly gaseous components in a suspension of algae. Using labeled oxygen, we observed that during the first 20 seconds of illumination after a dark period, when no net O₂ evolution or CO₂ uptake was observed, O₂ evolution was normal but completely compensated by O₂ uptake. Similarly, when CO₂ uptake was totally or partially inhibited, O₂ evolution proceeded at a high (near maximal) rate. Under all conditions, O₂ uptake balanced that fraction of the O₂ evolution which could not be accounted for by CO₂ uptake.     

Hemoproteins affect H(2)O(2) removal from rat tissues

The capacity of rat liver homogenates and mitochondria to remove H(2)O(2) was determined by comparing their ability to slow fluorescence generated by a H(2)O(2) 'detector' with that of desferrioxamine solutions. H(2)O(2) was produced by glucose oxidase-catalysed glucose oxidation. The capacity to remove H(2)O(2) was expressed as equivalent concentration of desferrioxamine. The method showed changes in the capacity of H(2)O(2) removal after treatment with ter-butylhydroperoxide or glutathione. The H(2)O(2) removal capacity of homogenates and mitochondria from rat liver, heart, and skeletal muscle was compared with their overall antioxidant capacity. For homogenates, the order of both antioxidant and H(2)O(2) removal capacities was liver>heart>muscle. For mitochondria, the order of the antioxidant capacities mirrored that of the homogenates, while the order of the H(2)O(2) removal capacities was heart>muscle>liver. Because H(2)O(2) removal is not only due to H(2)O(2)-metabolizing enzymes, but also to hemoproteins that convert H(2)O(2) into more reactive radicals via Fenton reaction, the higher concentration of cytochromes in mitochondria of cardiac and skeletal muscles can explain the above discrepancy. A higher H(2)O(2) removal capacity was found to be associated with a higher rate of H(2)O(2) release by mitochondria, indicating that the order of H(2)O(2) release rate mirrors that of H(2)O(2) production rate. We suggest that the different capacities of the mitochondria from the three tissues to produce reactive oxygen species are due to differences in the concentration of respiratory mitochondrial chain components in the reduced form.