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:3.1.27.1 (RNase)
16,360 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The ribonuclease excreted by Bacillus amyloliquefaciens, Barnase, was co-crystallized with the deoxy-dinucleotide d(GpC). The crystal structure was determined by molecular replacement from a model of free Barnase previously derived by Mauguen et al. Refinement was carried out using data to 1.9 A resolution. The final model, which has a crystallographic R factor of 22%, includes 869 protein atoms, 38 atoms from d(GpC), a sulfate ion and 73 water molecules. Only minor differences from free Barnase are seen in the protein moiety, the root-mean-square C alpha movement being 0.45 A. The dinucleotide has a folded conformation. It is located near the active site of the enzyme, but outside the protein molecule and making crystal packing contacts with neighboring molecules. The guanine base is stacked on the imidazole ring of active site His102, rather than binding to the so-called recognition loop as it does in other complexes of guanine nucleotides with microbial nucleases. The deoxyguanosine is syn, with the sugar ring in C-2'-endo conformation; the deoxycytidine is anti and C-4'-exo. In addition to the stacking interaction, His102 hydrogen bonds to the free 5' hydroxyl, which is located near the position where the 3' phosphate group is found in other inhibitors of microbial ribonucleases. While the mode of binding observed with d(GpC) and Barnase would be non-productive for a dinucleotide substrate, it may define a site for the nucleotide product on the 3' side of the hydrolyzed bond.
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PMID:Crystal structure of a barnase-d(GpC) complex at 1.9 A resolution. 202 57

The absorbance peak in the near ultraviolet electron-transfer spectrum of the oxyvanadium constellation in the "transition-state-analogue complexes" obtained by treating the dephospho form of phosphoglucomutase with inorganic vanadate in the presence of either glucose 1-phosphate or glucose 6-phosphate, as described in an accompanying paper [Ray, W. J., Jr., Burgner, J. W., II, & Post, C. B. (1990) Biochemistry (second of four papers in this issue)], is centered at a wavelength of 312 nm. The position of this peak amounts to a change in oscillator frequency of about -5000 cm-1 relative to that of tetrahedral VO4(3-). To provide a rationale for this spectral change, the near ultraviolet spectra of the di- and monoanions of inorganic vanadate and a number of derivatives of these anions are compared with that of vanadium (V) in the enzymic complexes, in terms of both what is observed experimentally and what is expected from crystal field theory. Comparisons in water and in largely anhydrous solvents show that water is not an essential element in the coordination sphere of inorganic vanadate or its mono- or diesters and hence that the coordination number of V(V) in such compounds likely is four. These comparisons also show that loss of solvating water from a 4-coordinate vanadate on binding cannot provide a rationale for the spectra of the enzymic complexes. Other comparisons show that neither the binding of metal ions nor protonation nor the binding of vanadate at a site with an unusually high or an unusually low dielectric constant can provide such a rationale. Further comparisons with vanadates known to be pentacoordinate strongly suggest that the coordination number of V(V) in the transition-state-analogue complexes of phosphoglucomutase does not exceed four. In fact, from the standpoint of crystal field theory the marked red shift observed in the electron-transfer absorbance spectrum of the oxyvanadium constellation in these complexes is more reasonably interpreted in terms of a decreased coordination at vanadium (V), viz., in terms of a weakened bonding between vanadium and one or more of its coordinating oxygens. This decreased coordination could be produced by a physical stretching of the vanadate ester linkage. By contrast, the near ultraviolet spectrum of the transition-state-analogue complex that ribonuclease forms with an adduct of uridine and vanadate [Lindquist, R. N., Lynn, J. L., & Lienhard, G. E. (1973) J. Am. Chem. Soc. 95, 8762] is similar to spectra of pentacoordinate model compounds of vanadium(V).(ABSTRACT TRUNCATED AT 400 WORDS)
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PMID:The oxyvanadium constellation in transition-state-analogue complexes of phosphoglucomutase and ribonuclease. Structural deductions from electron-transfer spectra. 214 Jun 98

Melanin concentrating hormone (MCH) is a key neuroendocrine peptide which is involved in the regulation of body color in teleost fish. Antigenically similar peptides exist in higher vertebrates including rodents and man. The precise function(s) of these peptides in these higher vertebrates has yet to be fully elucidated, although regulatory roles in stress-induced or corticotropin-releasing hormone-stimulated ACTH release and/or water balance have been proposed. The salmon, rat, and human MCH cDNA clones have been isolated and sequenced. We isolated and characterized the structure of the rat MCH gene. In addition to providing the complete nucleotide sequence of this gene, we demonstrate that there is a single copy of this gene in the rat genome. The structure of the rat MCH gene indicates that the MCH mRNA is encoded by three exons. Using primer extension and RNase protection assays, the transcriptional start sites of hypothalamic MCH mRNA were determined, allowing us to define the promoter region of this gene. We also characterize the central nervous system distribution of expression of the MCH gene by Northern blot analysis, demonstrating that the MCH mRNA is found predominantly if not exclusively within the hypothalamus.
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PMID:Nucleotide sequence and tissue-specific expression of the rat melanin concentrating hormone gene. 226 Oct 81

The attempt is made to find new correlations between local structural characteristics of proteins and the hydrogen exchange rates of their individual main-chain amides, and to relate such correlations to possible mechanisms of hydrogen exchange. It is found that in bovine pancreatic trypsin inhibitor (BPTI) the surface area buried by a particular residue and its neighbors correlates with the exchange rate of the main-chain amide of that residue. As the area buried by a particular fragment can be associated with the stabilization of the protein structure by this fragment, the correlation suggests a role for the energetics of the local unfolding in the mechanism of hydrogen exchange. Calculations based on the assumption that the exchange mechanism involves local unfolding lead to quantitative agreement between the calculated and experimentally measured exchange rates for 80% of the amides of BPTI that are buried or hydrogen bonded to the main-chain or to internal water molecules. The same degree of correlation is found between the calculated exchange rates and partial exchange data for ribonuclease S, hen lysozyme and cytochrome c. A similarly strong correlation is found between calculated exchange rates and the exchange rates of ribonuclease A determined by neutron diffraction in the crystal. The criteria of correlation are, however, less stringent in this case because of the experimental errors, which are larger than for solution data. It is suggested that the observed correlation be used for predictions of hydrogen exchange rates in proteins.
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PMID:Correlation between calculated local stability and hydrogen exchange rates in proteins. 244 80

The incubation of peripheral blood smears in distilled water frequently used for the control of the digestion with ribonuclease produced distinct changes of basophilic ribonucleic acid containing structures in peripheral lymphocytes. The alteration of these structures was apparently produced by the activity of the endogenous ribonuclease since it was reduced or prevented by the lowering of the temperature or addition of the ribonuclease inhibitor. In addition, marked differences were found between peripheral blood lymphocytes of healthy persons and patients suffering from chronic lymphocytic leukaemia with respect to the sensitivity of lymphocytic basophilia to the incubation in distilled water.
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PMID:The lymphocytic basophilia after incubation of blood smears in distilled water. 246 51

Along with classical lipopolysaccharide (LPS), O-specific material not precipitated by ultracentrifugation has been isolated from the water-phenol extract of S. sonnei avirulent strain 9090 possessing complete antigenic properties. The purification of O-antigen contained in the supernatant fluid has been carried out by the gel filtration of the fluid, previously treated with ribonuclease, in a column packed with Sephadex G-100. The polysaccharide nature of O-antigen thus obtained, the absence of lipid A and KDO and the low content of hexoses, or core-specific saccharides of S. sonnei LPS, in this antigen make it possible to classify this material with O-components of microbial cells, described by different authors as "native protoplasmic polysaccharide" or "L-hapten" and formed by polymers of LPS O-side chains. The content of this component in S. sonnei strains under study is, on the average, 2.5% of the weight of dry microbial substance. L-hapten preparations obtained in the course of our investigations have been found to contain two O-specific antigens detected by immunoelectrophoresis and immunodiffusion, as well as by sedimentation in saccharose gradient, where they form peaks corresponding to 4.3 S and 10.8 S. This polysaccharide O-antigen is supposed to be capable of interaction with ribosomal particles and suitable for use as a component of ribosomal dysentery vaccines.
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PMID:[O-specific L-hapten in the composition of Shigella sonnei]. 248 42

The interactions of tryptophan-59 (TRP-59) and its protein environment in ribonuclease-T1 (RNAse-T1) were examined in a 50-ps molecular dynamics simulation. The simulation used was previously shown to demonstrate a fluorescence anisotropy decay that closely agreed with the experimentally determined limiting anisotropy for RNAse-T1 (Axelsen, P. H., C. Haydock, and F. G. Prendergast. 1988. Biophys. J. 54:249-258). Further characterization of TRP-59 side chain dynamics and its protein environment has now been completed and correlated to other photophysical properties of this protein. Angular fluctuations of the side chain occur at rates of 1-10 cycles/ps and are limited to +/- 0.3 radians in all directions. Side chain motions are primarily limited by nonpolar collisions, although most side chain atoms have some collisional contact with polar atoms in the adjacent protein matrix or water. The steric relationship between PRO-39 and TRP-59 changes abruptly at 16 ps into the simulation. Two types of interaction with water are observed. First, a structural water appears to H-bond with the greater than N-H group of TRP-59. Second, water frequently contacts the six-atom ring. The electrostatic field experienced by the TRP-59 rings appears to be relatively constant and featureless regardless of ring orientation. We make the following interferences from our data: The fluorescent emission of TRP-59 may be red-shifted relative to TRP in nonpolar solvents either as a result of specific interactions with the structural water or relaxations of proximal bulk water and polar protein moieties. The quenching efficiency of polar interactions with TRP-59 must be extremely low given their frequency and the high quantum yield of RNAse-T1. This low efficiency may be due to restricted and unfavorable interaction geometries. PRO-39 is located near two titratable HIS residues in RNAse-T1 and may be involved in pH-dependent fluorescence phenomena by virtue of a metastable interaction with TRP-59. The interaction of bulk water with TRP-59 illustrates features of the gated transition state model for transient exposure to exogenously added collisional quenching agents. The restrictive environment of TRP-59 suggests that extrinsic quenching can only occur via interactions with the edge of the indole six-atom ring and that the efficiency of a quencher in a protein environment is likely to be a function of molecular symmetry.
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PMID:Molecular dynamics of tryptophan in ribonuclease-T1. II. Correlations with fluorescence. 250 98

A detailed study of the NH resonances of Ribonuclease-S-peptide (1-19 N-terminal fragment of Ribonuclease A) has been carried out in H2O, pH 3.0, in the temperature range 1-31 degrees, and ionic strength 0-1 M. Individual assignments of all NH amide signals have been achieved by means of extensive double resonance experiments. The folding of S-peptide at low temperature has been monitored by examination of the several NH resonance parameters: first, the nonlinearity of chemical shift vs. temperature plots; second, the selective broadening observed for signals assigned to residues 3-13; and third, the decrease of 3JHNCH coupling constants belonging to this region of the polypeptide chain. All these results are in agreement with the formation of a folded structure at low temperature, which is similar to the one found for the S-peptide in the RNase S crystal.
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PMID:NH resonances of Ribonuclease S-peptide in aqueous solution. Low temperature n.m.r. study. 257 22

ESR studies on spin-labeled amorphous RNase A as a function of varying concentrations of sorbed H2O and D2O will be presented. A relaxation analysis of saturation transfer (ST-)ESR spectra of 14N(1H) nitroxide spin-label molecules essentially fixed at amino acid residue His-105 will be given. A characteristic correlation has been observed between the microdynamic behavior--expressed by the rotational correlation times of the paramagnetic label--and the macroscopic thermodynamic entropy for the sorption process of H2O and D2O at RNase. This correlation is particularly pronounced at low water concentrations, vis., nH2O/nprotein less than or equal to 100. A significant difference in this concentration range exists between the two systems "RNase-H2O" and "RNase-D2O", which is manifested not only by the thermodynamic data but also by the microdynamic behavior extracted from the corresponding non-linear ESR absorption line shapes.
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PMID:Thermodynamic and magnetic resonance studies on the hydration of polymers: II. Protein-water interactions in powered ribonuclease. 283 82

Rapid and sensitive methods are needed for the detection of enteric viruses to ensure proper drinking water quality. Gene probes have been shown to be useful for this purpose. Previously, samples to be assayed were treated with a series of phenol-chloroform extractions to release the viral nucleic acid. We have developed a more rapid procedure for liberating or exposing the genome of poliovirus for probing. In this study, a poliovirus model was used to test the ability of heat (65 degrees C for 30 min) for release or exposure of viral nucleic acid. Several different RNase inhibitors were tested for their ability to prevent viral RNA degradation. A comparison of the two methods indicates phenol-chloroform extraction is not necessary before probing. In addition to saving 2-4 h of time, maximum sensitivity levels were consistently obtained using this novel procedure.
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PMID:A novel method for liberating viral nucleic acid for assay of water samples with cDNA probes. 284 56


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