Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.1.26.9 (ribonuclease)
6,589 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Van der Waals (vdW) interaction energies between different atom types, energies of hydrogen bonds (H-bonds), and atomic solvation parameters (ASPs) have been derived from the published thermodynamic stabilities of 106 mutants with available crystal structures by use of an originally designed model for the calculation of free-energy differences. The set of mutants included substitutions of uncharged, inflexible, water-inaccessible residues in alpha-helices and beta-sheets of T4, human, and hen lysozymes and HI ribonuclease. The determined energies of vdW interactions and H-bonds were smaller than in molecular mechanics and followed the "like dissolves like" rule, as expected in condensed media but not in vacuum. The depths of modified Lennard-Jones potentials were -0.34, -0.12, and -0.06 kcal/mole for similar atom types (polar-polar, aromatic-aromatic, and aliphatic-aliphatic interactions, respectively) and -0.10, -0.08, -0.06, -0.02, and nearly 0 kcal/mole for different types (sulfur-polar, sulfur-aromatic, sulfur-aliphatic, aliphatic-aromatic, and carbon-polar, respectively), whereas the depths of H-bond potentials were -1.5 to -1.8 kcal/mole. The obtained solvation parameters, that is, transfer energies from water to the protein interior, were 19, 7, -1, -21, and -66 cal/moleA(2) for aliphatic carbon, aromatic carbon, sulfur, nitrogen, and oxygen, respectively, which is close to the cyclohexane scale for aliphatic and aromatic groups but intermediate between octanol and cyclohexane for others. An analysis of additional replacements at the water-protein interface indicates that vdW interactions between protein atoms are reduced when they occur across water.
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PMID:Interatomic potentials and solvation parameters from protein engineering data for buried residues. 1214 53

A new method for the bonding of diethylamine(DEA) on the surface of silica to prepare novel hydrophilic packings for HPLC has been studied. After allyl glycidyl ether being synthesized, the Si-DEA anion-exchange bonded phase was prepared by the reaction of the double bond in allyl group with Si-H silica. The bonded phases obtained were characterized by elemental analysis, diffuse reflectance infrared Fourier transform(DRIFT) spectroscopy and HPLC evaluation. The methods were used for both porous silica and monodisperse non-porous silica. The contents of carbon, hydrogen and nitrogen of porous Si-DEA packing (MPS-DEA) were 3.31%, 0.95% and 1.34% respectively and those of monodisperse non-porous Si-DEA packing (NPS-DEA) were 2.55%, 0.97% and 0.96% respectively. The diethylamine absorption peak can be observed at 2970 cm-1 from the Si-DEA silica DRIFT spectrum. These data revealed that the diethylamine had been bonded on MPS-DEA and NPS-DEA packings. In HPLC tests, nucleotides and nucleosides such as cytosine, uracil, cytidine-5'-monophosphate, adenosine-5'-monophosphate, inosine-5'-monophosphate and guanosine-5'-monophosphate were satisfactorily separated on the porous anion-exchange packing (MPS-DEA), and a group of proteins (lysozyme, ribonuclease, ovalbumin, bovine serum albumin, insulin and gamma-globulin) were separated within 15 minutes successfuly. All test results indicated that the new method for preparing better anion-exchange silica packings is effective for both porous silica and monodiperse non-porous silica.
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PMID:[Preparation and evaluation of new ion-exchange chromatographic stationary phase for the use in high performance liquid chromatography]. 1255 75

Sakaguchi, Genji (National Institute of Health, Tokyo, Japan), Sumiko Sakaguchi, and Nobuko Imai. Comparative gel filtration of toxin grecursor and trypsin-activated toxin of Clostridium botulinum type E. J. Bacteriol. 87:401-407. 1964.-Precursor of type E botulinus toxin was highly purified from bacterial cells by extraction, ammonium sulfate precipitation, ribonuclease digestion, and chromatography on CM-Sephadex. The sample free from ribonucleic acid had a toxicity of 5.1 x 10(5)ld(50) per mg of nitrogen before activation and 8.3 x 10(7)ld(50) per mg of nitrogen after activation. This precursor and its activated product were subjected to gel filtration on a column of Sephadex G-200. No evidence for smaller fractions was obtained. Both precursor and trypsin-activated toxin were eluted in the void volume with 0.05 or 1 m acetate buffer (pH 6.0) or with 0.05 or 0.5 m phosphate buffer (pH 7.5). Intact trypsin and its degradation products were separated from toxin. The toxins eluted with the acetate buffers had potencies of 1.2 x 10(8) and 1.3 x 10(8)ld(50) per mg of N, while those eluted with the phosphate buffers showed lower toxicities. Possible mechanisms involved in the activation process are discussed.
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PMID:COMPARATIVE GEL FILTRATION OF TOXIN PRECURSOR AND TRYPSIN-ACTIVATED TOXIN OF CLOSTRIDIUM BOTULINUM TYPE E. 1415 Oct 63

Enhancement in oxygen uptake by high-cell-density cultivations has been achieved previously by expression of the bacterial hemoglobin gene from Vitreoscilla. The Vitreoscilla hemoglobin (VHb) gene was expressed in the yeast Yarrowia lipolytica to study the effect of expression in this commercially important yeast. The expression of VHb in this yeast was found to enhance growth, contrary to reported observations in wild-type Saccharomyces cerevisiae in which there was no significant growth enhancement. VHb-expressing Y. lipolytica exhibited higher specific growth rate, enhanced oxygen uptake rate, and higher respiratory activity. We report the beneficial effects of VHb expression on growth under microaerobic as well as under nonlimiting dissolved oxygen conditions. Earlier studies in Y. lipolytica have demonstrated inhibition of mycelia formation by respiratory inhibitors and poor nitrogen source, conditions poor for growth. VHb(+) Y. lipolytica cells were more efficient at forming mycelia, indicating better utilization of available oxygen as compared with the VHb(-) cells. Expression of VHb was also found to increase the levels of enzyme ribonuclease secreted into the medium, a property that may be beneficial for producing heterologous proteins in Y. lipolytica.
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PMID:Expression of vitreoscilla hemoglobin improves growth and levels of extracellular enzyme in Yarrowia lipolytica. 1459 78

Carnivorous plants usually grow in nutrient-deficient habitats, and thus they partly depend on insects for nitrogen and phosphate needed for amino acid and nucleotide synthesis. We report that a sticky digestive liquid from a sundew, Drosera adelae, contains an abundant amount of an S-like ribonuclease (RNase) that shows high amino acid-sequence similarity to S-like RNases induced by phosphate starvation or wounding in normal plants. By giving leaves an RNase "coat", D. adelae seems to achieve two requirements simultaneously to adapt itself to its specific surroundings: it obtains phosphates from insects, and defends itself against pathogen attack.
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PMID:An S-like ribonuclease gene is used to generate a trap-leaf enzyme in the carnivorous plant Drosera adelae. 1622 72

Homogenates of leaflets of desiccated tomato plants show increased ribonuclease activity compared to homogenates of turgid controls. Much of this increase is independent of changes in translocation to and from the leaflet. Interruption of translocation through living cells by detachment of leaflets or steam damage to the petiolules produces increased ribonuclease activity, but this activity is increased further when excised leaflets are allowed to wilt. Increases in ribonuclease often parallel or precede increases in the soluble nitrogen content. Further increases in activity occur when excised leaves become yellow. Exposure of leaflets to CO(2)-free air has little effect on activity at low-light intensity (120 ft-c). These results suggest that water stress directly affected ribonuclease activity at the cellular level.
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PMID:Ribonuclease activity of stressed tomato leaflets. 1665 36

Rice grains (Oryza sativa L.) from three varieties and three pairs of lines with different protein content were collected at 4-day intervals from 4 to 32 days after flowering. The samples were analyzed for protein, free amino nitrogen, ribonucleic acid, protease activity, and ribonuclease activity. In addition, the capacity of the intact grain to incorporate amino acids was determined for the three pairs of lines. The maximal level of free amino nitrogen and the capacity of the developing grain to incorporate amino acids were consistently found to be higher in the samples with the high protein content in the mature grain. The ribonucleic acid content of the grain tended to be higher in the high protein samples.
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PMID:Biochemical factors affecting protein accumulation in the rice grain. 1665 40

Undegraded free and membrane-bound polysomes were isolated from developing kernels of Zea mays L. frozen in liquid nitrogen. Freezing in liquid nitrogen was a prerequisite for preserving polysome structure in stored kernels. Membrane-bound polysomes from 22-day post-pollination kernels ground in high pH buffers containing 50 mm Mg(2+) contained unique classes of large polysomes. These large polysomes were sensitive to ribonuclease, and electron micrographs verified that they were not formed by aggregation. The membrane-bound polysomes were the principal site of zein synthesis, since the major protein synthesized in vitro was similar to purified zein in its ethanol solubility and mobility on sodium dodecyl sulfate polyacrylamide gels.
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PMID:Storage Protein Synthesis in Maize: Isolation of Zein-synthesizing Polyribosomes. 1665 63

The indole ring of the canonical amino acid tryptophan (Trp) possesses distinguished features, such as sterical bulk, hydrophobicity and the nitrogen atom which is capable of acting as a hydrogen bond donor. The introduction of an amino group into the indole moiety of Trp yields the structural analogs 4-aminotryptophan ((4-NH(2))Trp) and 5-aminotryptophan ((5-NH(2))Trp). Their hydrophobicity and spectral properties are substantially different when compared to those of Trp. They resemble the purine bases of DNA and share their capacity for pH-sensitive intramolecular charge transfer. The Trp --> aminotryptophan substitution in proteins during ribosomal translation is expected to result in related protein variants that acquire these features. These expectations have been fulfilled by incorporating (4-NH(2))Trp and (5-NH(2))Trp into barstar, an intracellular inhibitor of the ribonuclease barnase from Bacillus amyloliquefaciens. The crystal structure of (4-NH(2))Trp-barstar is similar to that of the parent protein, whereas its spectral and thermodynamic behavior is found to be remarkably different. The T(m) value of (4-NH(2))Trp- and (5-NH(2))Trp-barstar is lowered by about 20 degrees Celsius, and they exhibit a strongly reduced unfolding cooperativity and substantial loss of free energy in folding. Furthermore, folding kinetic study of (4-NH(2))Trp-barstar revealed that the denatured state is even preferred over native one. The combination of structural and thermodynamic analyses clearly shows how structures of substituted barstar display a typical structure-function tradeoff: the acquirement of unique pH-sensitive charge transfer as a novel function is achieved at the expense of protein stability. These findings provide a new insight into the evolution of the amino acid repertoire of the universal genetic code and highlight possible problems regarding protein engineering and design by using an expanded genetic code.
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PMID:Aminotryptophan-containing barstar: structure--function tradeoff in protein design and engineering with an expanded genetic code. 1678 15

Despite the therapeutic potential of tempol (4-hydroxy-2,2,6,6-tetra-methyl-1-piperidinyloxy) and related nitroxides as antioxidants, their effects on peroxidase-mediated protein tyrosine nitration remain unexplored. This posttranslational protein modification is a biomarker of nitric oxide-derived oxidants, and, relevantly, it parallels tissue injury in animal models of inflammation and is attenuated by tempol treatment. Here, we examine tempol effects on ribonuclease (RNase) nitration mediated by myeloperoxidase (MPO), a mammalian enzyme that plays a central role in various inflammatory processes. Some experiments were also performed with horseradish peroxidase (HRP). We show that tempol efficiently inhibits peroxidase-mediated RNase nitration. For instance, 10 muM tempol was able to inhibit by 90% the yield of 290 muM 3-nitrotyrosine produced from 370 muM RNase. The effect of tempol was not completely catalytic because part of it was consumed by recombination with RNase-tyrosyl radicals. The second-order rate constant of the reaction of tempol with MPO compound I and II were determined by stopped-flow kinetics as 3.3 x 10(6) and 2.6 x 10(4) M(-1) s(-1), respectively (pH 7.4, 25 degrees C); the corresponding HRP constants were orders of magnitude smaller. Time-dependent hydrogen peroxide and nitrite consumption and oxygen production in the incubations were quantified experimentally and modeled by kinetic simulations. The results indicate that tempol inhibits peroxidase-mediated RNase nitration mainly because of its reaction with nitrogen dioxide to produce the oxammonium cation, which, in turn, recycles back to tempol by reacting with hydrogen peroxide and superoxide radical to produce oxygen and regenerate nitrite. The implications for nitroxide antioxidant mechanisms are discussed.
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PMID:Inhibition of myeloperoxidase-mediated protein nitration by tempol: Kinetics, mechanism, and implications. 1849 4


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