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

---

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

Hepatitis B virions in plasma (Dane particles) are known to contain small circular DNA molecules. The experiments described here indicate that virions in plasma, as well as particles from hepatitis B virus-infected human liver, also contain viral DNA-RNA hybrid molecules, and deoxynucleotides can be incorporated into the DNA of these hybrids by DNA polymerase activities in the virions. Thus, two viral DNA synthetic reactions appear to take place in virions: repair of the single-stranded region of circular DNA molecules and synthesis or elongation of the DNA strand of DNA-RNA hybrid molecules. Centrifugation of virion nucleic acid to equilibrium in Cs2SO4 density gradients revealed the presence of viral DNA-RNA hybrid molecules over a density range of 1.45 to 1.60 g/cm3. Distinct species of hybrid molecules were found with an average density of 1.57 g/cm3 in Dane particles and 1.52 and 1.57 g/cm3 in particles from liver. Fractionation of nucleic acid from Cs2SO4 density gradients by gel electrophoresis demonstrated that the majority of hybrid molecules migrated faster than molecules with the density of pure DNA (1.42 g/cm3). One notable exception was the finding of DNA-RNA hybrid molecules migrating slower than open circular viral DNA. Characterization of viral DNA-RNA hybrids by heat denaturation Cs2SO4 density gradient fractionation, and recombinant M13-HBV single-stranded probe hybridization revealed that the hybrid molecules consisted of viral plus-strand RNA hydrogen bonded to viral minus-strand DNA sequences. Data obtained by pancreatic ribonuclease digestion revealed that the hybrid molecules at density 1.45 to 1.52 g/cm3 contained HBV RNA strands base paired over only part of their length in contrast to the hybrid species at density 1.57 g/cm3 which contained RNA strands apparently base paired over most of their length. Further characterization showed that the hybrid at 1.57 g/cm3 contained genome-length minus-strand viral DNA. The experiments rule out the possibility that the hybrid molecules are transcriptional complexes. Data presented in a companion manuscript indicate that the hybrid molecules may represent intermediates in the synthesis of viral DNA in the endogenous DNA polymerase reaction.
...
PMID:Hepatitis B virus particles of plasma and liver contain viral DNA-RNA hybrid molecules. 649 59

A complex of RNase A with a transition-state analog, uridine vanadate, has been studied by a combination of neutron and x-ray diffraction. The vanadium atom occupies the center of a distorted trigonal bipyramid, with the ribose oxygen O2' at the apical position. Contrary to expectations based on the straightforward interpretation of the known in-line mechanism of action of RNase, nitrogen NE2 of histidine-12 was found to form a hydrogen bond to the equatorial oxygen O8, while nitrogen NZ of lysine-41 makes a clear hydrogen bond to the apical oxygen O2'. Nitrogen ND1 of histidine-119 appears to be within a hydrogen-bond distance of the other apical oxygen, O7. Two other hydrogen bonds between the vanadate and the protein are made by nitrogen NE2 of glutamine-11 and by the amide nitrogen of phenylalanine-120. The observed geometry of the complex may necessitate reinterpretation of the mechanism of action of RNase.
...
PMID:Active site of RNase: neutron diffraction study of a complex with uridine vanadate, a transition-state analog. 657 1

The static accessibility modified discrete charge model for electrostatic interactions in proteins is extended to the prediction of the pH dependence of hydrogen exchange reactions. The exchange rate profiles of buried amide protons are shown to follow the calculated pH dependence of the electrostatic component of protein stability. Rate profiles are calculated for individual buried amide protons in ribonuclease S and bovine pancreatic trypsin inhibitor. The electrostatic free energy of stabilization of the protein and the energy required to bring the catalytic ion to an exchange site are expressed as an apparent, pH-dependent contribution to the activation energy. Changes in the electrostatic stabilization of the proteins affect the calculated exchange rate for buried amide protons by more than 1000, while local field effects raise or lower the predicted exchange rates by less than 100. The pH dependence of exchangeable protons at the protein surface, such as the C-2 imidazole protons, is shown to follow the estimated energy required to introduce the catalytic ion at the exchange site. These calculations are discussed in terms of current models for proton exchange which incorporate the dynamic nature of the structure to explain exchange data from the interior of a protein.
...
PMID:The pH dependence of hydrogen exchange in proteins. 682 49

The NMR titration curves of proton chemical shifts were observed for the C2 protons of histidine residues in intact bovine pancreatic RNAase A (EC 3.1.27.5) and carboxyalkylated RNAase A. By comparing the methyl region of NMR spectra, the 250-340 nm region of circular dichoic spectra, and the NMR titration curves of tyrosine ring protons among intact and modified RNAase A, it was ascertained that the carboxyalkylation of histidine residues at position 12 or 119 did not make any appreciable conformational changes to RNAase A. With the pK values determined for intact and modified RNAase A, the microscopic pK values and molar ratios of tautomers were estimated for His-12 and His-119 by means of the procedure described in the preceding paper. The estimated microscopic pK values of tautomers were 6.2 for the N1-H tautomer of His-12, more than 8 for the N3-H tautomer of His-12, 7.0 for the N1-H tautomer of His-119, and 6.4 for the N3-H tautomer of His-119, respectively. These values were interpreted in terms of the microscopic environments surrounding the histidine residues. The microscopic structure estimated in the present study was discussed, comparing it with those from X-ray crystallography and hydrogen-tritium (or hydrogen-deuterium) exchange technique.
...
PMID:1H-NMR study on the tautomerism of the imidazole ring of histidine residues. II. Microenvironments of histidine-12 and histidine-119 of bovine pancreatic ribonuclease A. 683 91

Hydrogen exchange has been studied in a single crystal of RNase A [ribonuclease (pancreatic), EC 3.1.27.5] in the course of a neutron structure investigation. Refinement of the occupancies of amide hydrogens provided information about the kind of isotope present in each site and also provided estimates of the errors associated with the measurement. Twenty-eight of the 120 peptide amide hydrogens were found to be at least partially protected from exchange during approximately 1 year required for crystal preparation and data collection. Most of the protected hydrogens were involved in hydrogen bonds with main-chain carbonyl groups. A contiguous region of the beta-sheet containing residues 75, 106--109, 116, and 118 had a large number of protected hydrogens, indicating its low flexibility and the lack of accessibility to solvent. Residues 11--13 from the alpha-helix near the amino terminus were protected, in good agreement with a model of cooperative unwinding of this helix, starting from the free (amino) end.
...
PMID:Hydrogen exchange in RNase A: neutron diffraction study. 695 Nov 86

A method for mapping all base-paired stems in both elongation and initiator tRNAs is described using double-stranded-specific ribonuclease V1 from the venom of the cobra Naja naja oxiana. 32p-end-labeled RNA is first partially digested with double-strand-specific V1 nuclease under near physiological conditions, and the resultant fragments are than electrophoretically fractionated by size in adjacent lanes of a polyacrylamide gel run in 90% formamide. After autoradiography, the base-paired nucleotides are definitively located by comparing V1 generated bands with fragments of known length produced by both Neurospora endonuclease and base-specific ribonucleases. Using the substrates yeast tRNAPhe an E, coli tRNAfMet of known three-dimensional structure, we find V1 nuclease to cleave entirely within every base-paired stem. Our studies also reveal that nuclease V1 will digest paired nucleotides not hydrogen-bonded by standard Watson-Crick base-pairing. In yeast tRNAPhe cleavage of both wobble base-pairs and nucleotides involved in tertiary base-base hydrogen bonding is demonstrated.
...
PMID:Mapping tRNA structure in solution using double-strand-specific ribonuclease V1 from cobra venom. 703 4

Semiempirical potential energy calculations have been carried out to locate possible binding sites for purine nucleoside phosphates at the RNase S active center. The nucleobase of adenosine or 8-oxoadenosine was shown to be accommodated at the pyrimidine binding site of the enzyme provided the nucleoside must be "syn". The mutual orientation of 8-oxoadenosine carbonyl group and NH-group of Thr-45 suggests a formation of a corresponding hydrogen bond in the enzyme--nucleotide complex. The formation of the hydrogen bond was postulated earlier to be essential for specific recognition of the substrate by RNase. The results obtained are in good agreement with the postulate. The "leaving group" binding site at the RNase S active center was found to be nonspecific toward conformation (syn-anti) of purine nucleotides studied. In addition, optimal conformation of dinucleosidemonophosphate bound to the enzyme active site was estimated for Pyr-P-Pur substrates.
...
PMID:[Theoretical conformational analysis of noncovalent complexes of purine nucleotides with ribonuclease]. 712 59

The analysis of the absorption spectra of model compounds of tyrosine and phenylalanine residues by means of fourth-derivative spectrophotometry is able to separate the contribution of the two chromophores, thus allowing the study of each one. Fourth-derivative analysis resolves the two main vibrational bands of tyrosine, giving rise to two peaks which are sensitive to changes in the environment of the phenolic ring. The parameters obtained from the fourth-derivative spectra were found to depend on the strength of the hydrogen bonds formed by the OH group of tyrosine, as well as on the heterogeneity of tyrosine environments. It is also shown that the fourth-derivative tyrosine peaks are not perturbed by broad bands, such as that arising from ionized tyrosine chromophores. The peaks arising from the phenylalanine model, although less sensitive than those of tyrosine, were found to depend on the polarity of the environment. As a check of the method, it is applied to the study of tyrosine and phenylalanine residues of calf thymus histone H1 and bovine pancreatic ribonuclease A.
...
PMID:The state of tyrosine and phenylalanine residues in proteins analyzed by fourth-derivative spectrophotometry. Histone H1 and ribonuclease A. 714 Jul 49

Replicating DNA of human adenovirus type 2, identified as partly single-stranded viral DNA in which [3H]thymidine is readily incorporated, was found to be separated into two fractions by chromatography on hydroxyapatite. Whereas one of the these fractions was eluted with 180 mM phosphate, the other one was eluted at the same concentration, 240 mM, as fully double-stranded DNA. The physical properties of the 180 and 240 mM fractions, in particular their buoyant densities in solutions of CsCl and Cs2SO4, were compared both before and after treatment by various enzymes such as Neurospora crassa nuclease, pancreatic ribonuclease, ribonuclease H and the Klenow fragment of DNA polymerase I of Escherichia coli, used alone or in various combinations. Unlike the 240 mM fraction, the 180 mM fraction was found to include a substantial amount of single-stranded DNA, some of it being hydrogen-bonded to RNA. Both of these features confer to the 180 mM fraction the high buoyant density in cesium salt solution which was described, for several adenoviruses, as one of the characteristic properties of replicating DNA.
...
PMID:Two classes of replicating molecules of adenovirus type 2 DNA. 724 95

A method for the kinetic determination of peptide exchange using stable isotope enrichment is described. Synthetic 90% enriched (epsilon-13C)His 12 ribonuclease (RNase) (1-15) peptide was used as a probe to follow peptide exchange in the RNase S system by 13C nuclear magnetic resonance spectroscopy. The rate constant, k1, for dissociation of the RNase S complex containing the synthetic (1-15) peptide was found to be (4.1 +/- 0.3) x 10(-4) s-1 and its dissociation constant Kd, (0.2 +/- 0.8) x 10(-7) M, was greater than that of RNase S with natural S-peptide (residues 1 to 20) by a factor of five at 4 degrees C. This differences corresponds to the difference of the enthalpy of binding between the (1-15) and (1-20) peptides, which we determined to be 1.7 +/- 0.4 kcal/mol. This small enthalpy difference may originate from hydrogen bonding between Ser 16 and His 48 in the RNase S complex.
...
PMID:Direct observation of peptide exchange by stable isotope enrichment. 735 73


<< Previous 1 2 3 4 5 6 7 8 9 10 Next >>

---