Structure of 5 S ribosomal RNA from Escherichia coli: identification of kethoxal-reactive sites in the A and B conformations.

The topographies of the A and B conformers of free 5 S RNA have been examined using kethoxal as a probe of single-stranded, accessible guanine residues. Each of the kethoxal-reactive guanines has been identified using diagonal electrophoresis, and the relative rate of modification at each site has been studied.Free 5 S RNA in the A form has several reactive guanines in addition to G₁₃ and G₄₁, which are the only two available for reaction in the intact 50 S ribosomal subunit (Noller &; Herr, 1974). The relative reactivities of these sites are G₄₁ ? G₁₃ > G₆₉ > G₂₄ > G₈₆ > G₁₀₇ > G₁₆, G₂₃, G₄₄. Modification at G₂₃ and G₄₄ reaches maximum values of only about 0.05 mol per mol 5 S RNA, suggesting that these residues are unreactive in the major conformer of the A form population. These results are compatible with a secondary structure model based on phylogenetic sequence conservation (Fox &; Woese, 1975), but imply that 12 of the 18 unpaired guanines in this model are involved in further molecular interactions.The modification pattern of the B conformer demands a different base-pairing arrangement and shows that the B form contains less structure than the A form. The relative reactivities in the B form are G₁₃ > G₁₀₂ > G₁₆ > G₂₄, G₄₄ > G₆₁, G₁₀₀ > G₂₃, G₅₁, G₁₀₇ > G₅₄, G₅₆. Several sites show plateaux at submolar modification levels, indicating the existence of some conformational heterogeneity in preparations of the B form of 5 S RNA. Heat-denatured 5 S RNA appears to contain a mixture of conformers including the A and B form.These results place limitations on certain structural and functional models for 5 S RNA. For example, G₄₄, which has often been implicated in base-pairing with tRNA, is accessible in the B form but not in the A form. Yet the B form does not bind the 5 S RNA-specific ribosomal proteins, nor is there evidence for its existence in the ribosome.     

Crystal Structure of d(gcGXGAgc) with X = G: a Mutation at X is Possible to Occur in a Base-Intercalated Duplex for Multiplex Formation

DNA fragments with the sequences d(gcGX[Y]_n Agc) (n = 1, X = A, and Y = A, T, or G) form base-intercalated duplexes, which is a basic unit for formation of multiplexes such as octaplex and hexaplex. To examine the stability of multiplexes, a DNA with X = Y = G and n = 1 was crystallized under conditions different from those of the previously determined sequences, and its crystal structure has been determined. The two strands are coupled in an anti-parallel fashion to form a base-intercalated duplex, in which the first and second residues form Watson-Crick type G:C pairs and the third and sixth residues form a sheared G:A pairs at both ends of the duplex. The G₄ and G₅ bases are stacked alternatively on those of the counter strand to form a long G column of G₃-G₄-G₅*-G₅-G₄*-G₃*, the central four Gs being protruded. In addition, the three duplexes are associated to form a hexaplex around a mixture of calcium and sodium cations on the crystallographic threefold axis. These structural features are similar to those of the previous crystals, though slightly different in detail. The present study indicates that mutation at the 4th position is possible to occur in a base-intercalated duplex for multiplex formations, suggesting that DNA fragments with any sequence sandwiched between the two triplets gcG and Agc can form a multiplex.     

Inorganic Carbon of Sediments in the Yangtze River Estuary and Jiaozhou Bay

JGOFS results showed that the ocean is a major sink for the increasing atmospheric carbon dioxide resulting from human activity. However, the role of the coastal seas in the global carbon cycling is poorly understood. In the present work, the inorganic carbon (IC) in the Yangtze River Estuary and Jiaozhou Bay are studied as examples of offshore sediments. Sequential extraction was used to divide inorganic carbon in the sediments into five forms, NaCl form, NH₃ H₂O form, NaOH form, NH₂OH HCl form and HCl form. Studied of their content and influencing factors were also showed that NaCl form < NH₃ H₂O form<NaOH form < NH₂OH HCl form<HCl form, and that their influencing factors of pH, Eh, Es, water content, organic carbon, organic nitrogen, inorganic nitrogen, organic phosphorus and inorganic phosphorus on inorganic carbon can be divided into two groups, and that every factor has different influence on different form or on the same form in different environment. Different IC form may transform into each other in the early diagenetic process of sediment, but NaCl form, NH₃ H₂O form, NaOH form and NH₂OH HCl form may convert to HCl form ultimately. So every IC form has different contribution to carbon cycling. This study showed that the contribution of various form of IC to the carbon cycle is in the order of NaOH form>NH₂OH HCl form>NH₃ H₂O form>NaCl form>HCl form, and that the contribution of HCl form contributes little to carbon cycling, HCl form may be one of end-result of atmospheric CO₂. So Yangtze River estuary sediment may absorb at least about 40.96×10¹¹ g atmospheric CO₂ every year, which indicated that offshore sediment play an important role in absorbing atmospheric CO₂.     

Glutathione and glutathione metabolizing enzymes in yeasts

Total glutathione content, glutathione peroxidase, glutathione transferase and glutathione reductase activities have been measured in 12 species of yeasts. All the strains tested contained glutathione, though in different amounts, as well as the above mentioned enzymes. To discriminate between the selenium-dependent and the selenium-independent form, glutathione peroxidase activity has been measured with both H₂O₂ and cumene hydroperoxide. Rhodotorula glutinis appeared to be the only strain in which the selenium-dependent form was not found, but this yeast exhibited the highest level of selenium-independent glutathione peroxidase activity as compared to the other strains.     

Über den Hemm-Mechanismus mitochondrialer Glutamat-Oxalacetat-Transaminase in SO2-begasten Erbsen

Summary The effect of SO₂-fumigation on the mitochondrial and cytoplasmic form of GOT in peas has been tested. GOT is represented by two distinct proteins in peas and therefore its activity may be taken as a measure of action of certain effectors on different components of the cell. An optical method for the direct measurement of GOT activity in crude plant extracts has been established. Using this method it could be shown that the mitochondrial GOT in SO₂-fumigated peas is inhibited while at the same time the cytoplasmic form of the enzyme remains uneffected. The mechanism of inhibition of mitochondrial GOT by SO ₃ ^-- /HSO ₃ ^- has been analyzed and could be shown to be of the mixed type. This investigation confirms an earlier observation that differential effects of SO₂ on single compartments of the cell may occur.

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Abkürzungen GOT Glutamat-Oxalacetat-Transaminase - GDH Glutamat-dehydrogenase - PLP Pyridoxalphosphat     

Properties of NADPH-cytochrome P-450 reductase purified from rabbit liver microsomes.

NADPH-cytochrome P-450 reductase has been purified to electrophoretic homogeneity from rabbit liver microsomes by a procedure that may be used in conjunction with the isolation of the major forms of cytochrome P-450. The purified reductase is active in a reconstituted hydroxylation system containing P-450LM₂ or P-450LM₄. The enzyme contains one molecule each of FMN and FAD per polypeptide chain having an apparent minimal molecular weight of 74,000. Immunological techniques provided evidence for only a single form of the reductase; lower molecular weight forms occasionally seen are believed to be due to degradation by contaminating microsomal or bacterial proteases. Upon anaerobic photochemical reduction, the rabbit liver reductase undergoes spectral changes highly similar to those previously described by Vermilion and Coon for the rat liver enzyme; the fully reduced rabbit liver enzyme is converted to the three-electron-reduced form by the addition of NADP and then to the stable one-electron-reduced form by exposure to oxygen. The CD spectra of the fully oxidized enzyme, one-electron-reduced form (air-stable semiquinone), three-electron-reduced form, and fully reduced form are presented. The results obtained provide evidence that the FMN and FAD are in highly different environments in the enzyme, as also indicated by the different redox potentials and oxygen reactivities of the flavins.     

Sequence of the high-activity equine erythrocyte carbonic anhydrase: N-terminal polymorphism (acetyl-ser/acetyl-thr) and homologies to similar mammalian isozymes

The amino acid sequence of the high-activity equine erythrocyte carbonic anhydrase (CA-II) has been determined. Two different N-termini are noted, the C₁ form having an N-acetyl-serine and the C₂ form an N-acetyl-threonine. The sequence of the equine enzyme is most homologous to the human CA-II isozyme, with 224 of the 259 residues being identical.This investigation was supported in part by United States Public Health Service Grant CA-1786 from the National Cancer Institute.     

Differential mechanism of light-induced and oxygen-dependent restoration of the high-potential form of cytochrome b559 in Tris-treated Photosystem II membranes

The effect of illumination and molecular oxygen on the redox and the redox potential changes of cytochrome b₅₅₉ (cyt b₅₅₉) has been studied in Tris-treated spinach photosystem II (PSII) membranes. It has been demonstrated that the illumination of Tris-treated PSII membranes induced the conversion of the intermediate-potential (IP) to the reduced high-potential (HP^Fe2+) form of cyt b₅₅₉, whereas the removal of molecular oxygen resulted in the conversion of the IP form to the oxidized high-potential (HP^Fe3+) form of cyt b₅₅₉. Light-induced conversion of cyt b₅₅₉ from the IP to the HP form was completely inhibited above pH 8 or by the modification of histidine ligand that prevents its protonation. Interestingly, no effect of high pH or histidine modification was observed during the conversion of the IP to the HP form of cyt b₅₅₉ after the removal of molecular oxygen. These results indicate that conversion from the IP to the HP form of cyt b₅₅₉ proceeds via different mechanisms. Under illumination, conversion of the IP to the HP form of cyt b₅₅₉ depends primarily on the protonation of the histidine residue, whereas under anaerobic conditions, the conversion of the IP to the HP form of cyt b₅₅₉ is driven by higher hydrophobicity of the environment around the heme iron resulting from the absence of molecular oxygen.     

New interpretation of the redox properties of cytochrome b559 in photosystem II

A model of heme–quinone redox interaction has been developed for cytochrome b559 in photosystem II. The quinone Q_C in the singly protonated form may function as an interacting quinone. The electrostatic effect between the charges on the heme iron of the cytochrome and Q_CH leads to appearance of three forms of the cytochrome with different redox potentials. A simple and effective mechanism of redox regulation of the electron transfer pathways in photosystem II is proposed.     

Purification and properties of two forms of hepatic phenylalanine:pyruvate transaminase from glucagon treated rats.

Two forms of phenylalanine:pyruvate transaminase (EC 2.6.1. aminotransferases, the exact EC number has not been assigned) termed A and B were obtained from the liver supernatant fraction of glucagon-treated rats by DEAE-Sephadex A-50 column chromatography. Each of the two forms was further purified by hydroxylapatite, Sephadex G-100 chromatography, and preparative gel electrophoresis. Both the A and B forms have been purified to homogeneity as judged by analytical and sodium dodecyl sulfate polyacrylamide gel electrophoresis. Moreover, histidine was found to be a competitive inhibitor of phenylalanine with both purified proteins. These findings conclusively support the view that phenylalanine:pyruvate transaminase and histidine:pyruvate transaminase reactions are catalyzed by the same protein. The overall purification was 710-fold for the A form and 1200-fold for the B form. The apparent molecular weight for both A and B are 74,000 ±6000 as determined by gel filtration. Sodium dodecyl sulfate gel electrophoresis revealed that the A form has two identical subunits of molecular weight 42,000, whereas the B form has two nonidentical subunits of molecular weight 42,000 and 44,000. The amino acid composition for the A and B forms of the enzyme are different. The major differences are in glycine, alanine and leucine. The isoelectric point for A was 7.8 and for B was 7.3. However, the A and B forms of the enzyme are of immunological identity. The substrate specificity determined for both the A and B form was phenylalanine >asparagine >alanine >leucine >histidine. The K_m for phenylalanine was 7.70 mm for the A form, 6.00 mm for the B form. For histidine, the K_m was 13.70 mm for the A form, 12.50 mm for the B form.     

The effect of quaternary structure on the state of the α and β subunits within nitrosyl haemoglobin: Low temperature photodissociation and the ESR spectra

Photodissociation of nitrosyl haemoglobin and nitrosyl hybrids, in which either the α or β subunit is in the nitrosyl form has been studied at liquid helium temperature (4.2°K) by electron spin resonance and optical absorption spectroscopy. In the presence of inositol hexaphosphate, the photodissociated form of nitrosyl haemoglobin showed an anomalous absorption spectrum in the near infrared region. The experiments with nitrosyl hybrids showed that the α^NO subunit within the T state haemoglobin is predominantly responsible for the anomalous photodissociated form and the ESR spectrum with three distinct hyperfines. The ESR spectrum of α₂^NOβ₂^deoxy with inositol hexaphosphate appeared to be very similar to that of the 5-coordinated NO-haem complexes but the absorption spectrum of its photodissociated form was similar to none of protoporphyrin Fe(II) derivatives so far reported. This result suggests that the anomalous photodissociated form may be attributable to some structural distortion of porphyrin or a new electronic state of the haem with different spin state from that of deoxyhaemoglobin.     

Conformations of model compounds of proteins. I. Acetylglycine N-methylamide

Infrared spectra in the region 4000–60 cm^?1 have been measured for acetylglycine N-methylamide and its deuterium homologs, CD₃CONHCH₂CONHCH₃, CH₃-CONHCD₂CONHCH₃, CH₂CONHCH₂CONHCD₃, and CH₃CONDCH₂CONDCH₃. Normal frequencies have also been calculated for these molecules with various conformations. The spectra show that this compound has two crystalline modifications, form A and form B. The frequencies and their isotope shifts show that the molecular conformation (Ψ, ?) of form B is near (0, 120) and that of form A near (180, 120). The short-range factors determining the conformation of peptide backbone having glycine residues are discussed.     

Synthesis of a New Template with a Built-in Adjuvant and Its Use in Constructing Peptide Vaccine Candidates Through Polyoxime Chemistry

Synthetic lipopeptides are showing promise as vaccine candidates, but until now it has been very difficult to prepare them in homogeneous form. We describe the synthesis and characterization of a new water-soluble, four-branched template with a built-in lipophilic adjuvant (Pam₃Cys). Through the use of oxime chemistry, we attached four copies of an unprotected influenza virus peptide and characterized the product (13kDa) by reversed-phase HPLC and electrospray ionization mass spectrometry. Several other such constructions were made using the new template and different peptides. We seem to have a general method for making synthetic lipopeptides in homogeneous form.     

Microheterogeneity of the inner core region of yeast manno-protein

The inner core linkage region fragment from Saccharomyces cerevisiae mannan has been fractionated into 6 components and their structures have been analyzed. They form a family of homologous oligosaccharides (Man₁₂GNAc to Man₁₇GNAc) with 6 or 7 mannose units in α1→6 linkage attached to N-acetylglucosamine by a β1→4 linkage, and with different amounts of side chain mannose units attached by α1→2 and α1→3 linkage.     

Structural Basis for the Association of the Redox-sensitive Target of Rapamycin FATC Domain with Membrane-mimetic Micelles

The target of rapamycin (TOR) is a conserved eukaryotic Ser/Thr kinase that regulates cellular growth in response to the nutrient and energy state. TOR signaling plays an important role in the development of diseases such as cancer, obesity, and diabetes and in different redox-sensitive processes (hypoxia, apoptosis, and aging). Because TOR has been detected at different cellular membranes and in the nucleus, its localization may influence the specific signaling readout. To better understand how TOR can associate with different membranes, the lipid-binding properties of the redox-sensitive yeast TOR1 FATC domain (y1fatc) have been characterized by solution NMR spectroscopy. Binding studies with different lipids indicate that y1fatc interacts specifically with a membrane-mimetic environment but appears not to recognize a specific lipid headgroup. In both, the structures of oxidized and reduced micelle-bound y1fatc, residues Ile-2456 to Trp-2470 of the lipid-binding motif form a hydrophobic bulb that has a rim of charged residues. The diffusion constants for both micelle-bound states are consistent with the rotational correlation times from the analysis of the ¹⁵N relaxation data. Based on the K_d values, the oxidized form (K_d ∼ 0.31 mm) binds dodecyl phosphocholine micelles slightly tighter than the reduced form (K_d ∼ 1.86 mm). Binding studies with y1fatc in which one or both tryptophans (Trp-2466 and Trp-2470) were replaced by alanine suggest that these residues are important for the exact positioning in the membrane and that the other aromatic (His-2462, Tyr-2463, and Phe-2469) and aliphatic residues (Ile-2456, Leu-2459, Ile-2464, and Pro-2468) in the lipid-binding motif contribute significantly to the affinity.     

Nitrous Acid Reactivation of Ultraviolet-Irradiated Transforming DNA from Hemophilus influenzae

Partial recovery of ultraviolet-damaged denatured or native transforming DNA from Hemophilus influenzae, has been obtained by exposing the irradiated DNA in the denatured form to nitrous acid. Some factors that affect this recovery are described. An erythromycin marker (E₂₀) was not reactivated. The UV damage reactivable by nitrous acid is different from that repaired by the photoreactivating enzyme from bakers' yeast. The pretreatment with nitrous acid affords a slight protection for denatured C₂₅ DNA and Sm₂₅₀ DNA against ultraviolet irradiation, but this pretreatment sensitized the E₂₀ DNA to this irradiation.     

Crystallographic evidence for a CO/CO<Subscript>2</Subscript> tunnel gating mechanism in the bifunctional carbon monoxide dehydrogenase/acetyl coenzyme A synthase from<Emphasis Type="Italic"> Moorella thermoacetica</Emphasis>

Acetyl coenzyme A synthase (ACS) acts in concert with carbon monoxide dehydrogenase (CODH) to catalyze the formation of acetyl-coenzyme A from CO₂-derived CO and CH₃⁺ molecules. Recent crystal structures have shown that the three globular domains constituting the ACS subunit may be arranged in either a closed or an open conformation. A long hydrophobic tunnel network allows diffusion of CO between the CODH and the ACS active sites in the closed form, but it is blocked in the open form. On the other hand, the active site of ACS is only accessible for coenzyme A and the methyl donating protein in the open domain conformation. Although several metal compositions have been observed for this active site, present consensus is that it consists of a Ni-Ni-[Fe₄S₄] cluster. The observed conformational changes of ACS and the resulting different substrate accessibilities of the catalytic central nickel are reviewed here in the context of a putative CO₂/CO tunnel gating mechanism.     

Kinetics of carbon monoxide and oxygen binding to hemoglobin in human red blood cell suspensions studied by laser flash photolysis

The reaction kinetics of the binding of CO and O₂ to hemoglobin (Hb) in human red blood cell (RBC) suspensions have been examined using a 300 ns dye laser to photodissociate HbCO or HbO₂. Fast (halftime1?0 μs) and slow (5?ms) processes were seen after photolysis. The results indicate that neither the rate constants nor the activation energies for the binding of CO to the fast reacting form of Hb in the RBC are significantly different from that measured in solution in spite of the different environments. Rate constants determined for O₂ binding in RBC were intermediate between rates observed for reaction with fast and slow reacting forms of Hb and probably consist of contributions from each. The slow recombination of CO and O₂ probably has contributions both from reaction with slow reacting forms of Hb and from ligand that had diffused away from the RBC after photolysis.     

Cytidinium H-Phosphonate Monohydrate,bis 2′-Deoxycytidinium H-Phosphonate and 2′-Deoxycytromium H-Phosphonate -Structures and Properties

Abstract

The crystal structures of cytidinium H-phosphonate monohydrate, bis 2′-deoxycytidinium H-phosphonate and 2′-deoxycytidinium H-phosphonate have been determined by single crystal X-ray diffraction and FTIR spectroscopy. The influence of protonation and hydrogen bond formation on geometry of the cytidine fragment has been studied. All three compounds have similar geometry and conformation but they form different H-bond networks. Contrary to the phosphates of cytidine and deoxycytidine, the phosphonates do not form direct base pairs but they strongly interacts with H₃PO₃ acid and/or its anions present in the crystal lattice. This seems to be more favourable than the base-base interactions. As a result a pleated sheets are formed consisting from alternating columns of the cations and anions. The sheets are joined by additional O-H… O=P bonds giving a 3D network.     

Investigating Gabapentin Polymorphism Using Solid-State NMR Spectroscopy

Solid-state NMR spectroscopy (SSNMR), coupled with powder X-ray diffraction (PXRD), was used to identify the physical forms of gabapentin in samples prepared by recrystallization, spray drying, dehydration, and milling. Four different crystalline forms of gabapentin were observed: form I, a monohydrate, form II, the most stable at ambient conditions, form III, produced by either recrystallization or milling, and an isomorphous desolvate produced from desolvating the monohydrate. As-received gabapentin (form II) was ball-milled for 45 min in both the presence and absence of hydroxypropylcellulose (HPC). The samples were then stored for 2 days at 50°C under 0% relative humidity and analyzed by ¹³C SSNMR and PXRD. High-performance liquid chromatography was run on the samples to determine the amount of degradation product formed before and after storage. The ¹H T ₁ values measured for the sample varied from 130 s for the as-received unstressed material without HPC to 11 s for the material that had been ball-milled in the presence of HPC. Samples with longer ¹H T ₁ values were substantially more stable than samples that had shorter T ₁ values. Samples milled with HPC had detectable form III crystals as well. These results suggest that SSNMR can be used to predict gabapentin stability in formulated products.