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:3.1.27.5 (RNase)
17,967 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A semisynthetic RNase, RNase-(1-118).(111-124), consisting of a noncovalent complex between residues 1-118 of RNase (obtained from the proteolytic digestion of RNase A), and a synthetic 14-residue peptide containing residues 111-124 of RNase, exhibits 98% of the enzymatic activity of bovine pancreatic ribonuclease A (EC 3.1.27.5). The replacement of aspartic acid-121 by asparagine in this semisynthetic RNase to form the "D121N" analog reduces kcat/Km to 2.7% of the value for RNase A. In the present work, 1H NMR spectroscopy has been used to probe the ionization states of His12, His105, and His119 in this catalytically defective semisynthetic RNase. A comparison of the observed resonances of D121N with those previously determined by others for RNase A enabled us to assign the C2 proton NMR resonances to individual residues; the assignment of His119 was confirmed by titrating D121N with the fully deuterated peptide, [Asn121]-RNase-(111-124). The observed pKa values of His12, His105, and His119 decrease 0.18, 0.16, and 0.02 pH unit, respectively, as a result of the D121N replacement. Values calculated by using a finite difference algorithm to solve the Poisson-Boltzmann equation (the DELPHI program, version 3.0) and a refined 2.0-A coordinate set for the crystal structure of D121N differ significantly for active site residues His12 (delta pKa = -0.58) and His119 (delta pKa = -0.55) but not for His105 (delta pKa = -0.10). The elmination of bound water from the calculations reduced, but did not reconcile, these discrepancies (His12, delta pKa = -0.36; His119, delta pKa = -0.41).
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PMID:Histidine pKa shifts accompanying the inactivating Asp121----Asn substitution in a semisynthetic bovine pancreatic ribonuclease. 189 58

The side-chains of phenylalanine and tyrosine residues in proteins are frequently found to be involved in pairwise interactions. These occur both within repeating elements of secondary structure and in tertiary and quaternary interactions. It has been suggested that they are important in protein folding and stability, and non-bonded potential energy calculations indicate that a typical aromatic-aromatic interaction has an energy of between -1 and -2 kcal/mol and contributes between -0.6 and -1.3 kcal/mol to protein stability. There is such an aromatic pair on the solvent-exposed face of the first alpha-helix of barnase, the small ribonuclease from Bacillus amyloliquefaciens. The edge of the aromatic ring of Tyr17 interacts with the face of that of Tyr13. The two residues have been mutated both singly and pairwise to alanine, and their free energies of unfolding determined by denaturation with urea. Application of the double-mutant cycle analysis gives an interaction energy of -1.3 kcal/mol for the aromatic pair in the folded protein relative to solvation by water in the unfolded protein. This value is similar to that calculated from the change in surface-accessible area between the rings on the formation of the pair. Analysis of a further double-mutant cycle in which the Tyr residues are mutated to Phe indicates that the aromatic-aromatic interactions of Tyr/Tyr and Phe/Phe make identical contributions to protein stability. However, Tyr is preferred to Phe by 0.3(+/- 0.04) kcal/mol at the solvent-exposed face of the alpha-helix.
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PMID:Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles. 201 Sep 20

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 solution stability of bovine pancreatic ribonuclease A (RNase) in phosphate buffer (pH 4.0, 6.4, and 10.0) at 45 degrees C decreased with increasing pH. Soluble aggregates were formed at each pH and corresponded qualitatively to the loss of enzymatic activity in the samples. Freeze drying of RNase resulted in no immediate loss of enzymatic activity in both the presence and absence of phosphate buffer salts. Freeze-dried RNase stored at 45 degrees C lost enzymatic activity and formed nondissociable aggregates at rates described by the following rank order of formulation contents: distilled water less than pH 6.4 phosphate buffer, less than pH 4.0 phosphate buffer less than pH 10.0 phosphate buffer. The amount of residual moisture remaining in the freeze-dried cakes was directly related to the rate of enzymatic activity loss and aggregate formation. The degradation rate was also directly related to the concentration of phosphate buffer salts added to the freeze-dried formulation.
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PMID:Stability of ribonuclease A in solution and the freeze-dried state. 207 55

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

The influence of substitution of the isotopic composition of the medium on the mechanical properties of immobilized crystals and films from bovine pancreatic ribonuclease and hen egg white lysozyme was investigated. The order of magnitude of the observed effects indicates that the contribution of the electrostatic interaction to the observed isotopic effect may be considered inessential. The absence of aggregation in the H2O and D2O medium under experimental conditions is demonstrated by the method of the low angle dispersion of X-rays. The observed effects of D2O on the mechanical behavior of crystals and films of proteins may be accounted for by the strengthening of molecular interactions in the samples.
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PMID:[Changes in mechanical characteristics of immobilized crystals and films of globular proteins during substitution of D2O for H2O]. 216 Dec 59

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


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