Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.27.4 (ribonuclease)
 6,621 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The amino acid sequences of the pancreatic ribonucleases from impala Thomson's gazelle, nilgai and two types of water buffalo were studied from several enzymic digests. Peptides were positioned by homology with other ribonucleases of known sequence. Only peptides that differ in amino acid composition from the corresponding peptides of ox and goat ribonuclease were sequenced. The primary structures of pancreatic ribonucleases from 11 species of the Bovidae family are known to date. The evolutionary rate of bovid ribonucleases is 2--3 times lower than the average rate observed in all mammals. A possible explanation is that the presence of a stable symbiotic system in the rumen of grass-eating ruminants has caused a slowing down of the evolutionary rate of pancreatic ribonuclease in this taxon. The subfamily of the Bovinae (five species) exhibits a slightly higher evolutionary rate; most replacements in the Bovinae occur near residues 34--36, the most commonly observed carbohydrate attachment site in ribonucleases.
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PMID:Primary structures of pancreatic ribonucleases from Bovidae. Impala, Thomson's gazelle, nilgai and water buffalo. 735 35

The crystal structure of purine-specific ribonuclease (RNase) U2 from Ustilago sphaerogena has been solved by the molecular replacement methods using RNase T1 as a search model. The structure, with 114 amino acid residues, 141 water molecules, and a sulfate ion, is refined to an R factor of 0.143 at 1.8 A resolution. As evidenced by the electron densities, residues 49 and 50 are revised to Glu 49 and Asp 50, respectively, and also Asp 45 is identified as a beta-isomerized form to L-isoaspartate with a beta-peptide linkage. RNase U2 consists of a beta-hairpin at residues from 7 to 14, a 4.4-turn alpha-helix from 16 to 32, a central beta-sheet with five strands, and a protruding beta-turn from 74 to 77. As for the catalytic site residues, His 41, Glu 62, and Arg 85 are located as constituents of the central beta-sheet, and Tyr 39 and His 101 are situated at either end of the beta-sheet. The side chains of Tyr 39, Glu 62, Arg 85, and His 101 are hydrogen-bonded to the sulfate ion which marks the RNA phosphate position. Though the side chain of His 41 is pointing away from the sulfate, small conformational adjustments of His 41 enable the side chain to interact with either the phosphate or the ribose group of RNA. The loop region from Tyr 44 to Asp 50 is ascribed to the base recognition site where Glu 49 is involved in adenine recognition. beta-Isomerized Asp 45 suggests that this region is conformationally flexible and alterable.
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PMID:Crystal structure of Ustilago sphaerogena ribonuclease U2 at 1.8 A resolution. 749 61

Metallothioneins (MTs) are low-molecular-weight cytosolic proteins that are induced by cellular stress as well as exposure to various heavy metals including mercury. Excessive residues of mercury have recently been identified in various fish species of the lower Ouachita River system in Arkansas. Fillets of mature largemouth bass (Micropterus salmoides) collected from Woodard Lake, an ox-bow lake of the Ouachita River, possessed muscle residues of mercury ranging from 0.3 to 1.0 ppm (micrograms/g). To assess the usefulness of using MT expression as a biomarker of mercury exposure, livers and fillets were obtained from feral bass of Woodard Lake. Ouachita served as a control site having mercury residues below detection. Analyses using a ribonuclease protection assay with winter flounder MT cDNA revealed that bass had significantly elevated levels of MT mRNA which correlated (r2 = 0.756) with the levels of mercury in muscle fillets. To further explore the water quality of Woodard Lake, 10 juvenile channel catfish were housed in cages and placed where feral collections were made in both sites for 2 weeks. Mercury was not detected in muscle or liver and no significant difference in hepatic MT mRNA was observed. These data demonstrate that MT mRNA expression can be used as a tool to assess exposure to heavy metals and suggest that the elevated levels of mercury in large predatory fish may be due to trophic magnification rather than a single point-source exposure.
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PMID:Expression of hepatic metallothionein messenger RNA in feral and caged fish species correlates with muscle mercury levels. 749 68

We have carried out a differential scanning calorimetry study into the pH effect on the thermal denaturation of ribonuclease A at several concentrations of the osmolyte sarcosine. In order to properly analyze these data, we have elaborated the thermodynamic theory of the linkage between temperature, cosolvent, and pH effects. The denaturation heat capacity increases with sarcosine concentration. The effects of temperature and sarcosine concentration on the denaturation enthalpy and entropy values are well described by convergence equations, with convergence temperatures of around 100 degrees C for the enthalpy and around 112 degrees C for the entropy; we suggest that these effects might be related to a solvent-induced alteration of the apolar-group-hydration contribution to the folding thermodynamics. From our data, we estimate that about 70 extra molecules of water are thermodynamically bound upon ribonuclease denaturation in diluted aqueous solutions of sarcosine; this number is 6-9 times smaller than that predicted on the basis of the following two premises: (a) the osmolyte is strongly excluded from the surface of both the native and the denatured protein and (b) the denatured state is a fully solvated chain. We suggest that at least one of these two premises does not hold. We briefly comment on the potential use of cosolvent effects on thermal denaturation to evaluate the degree of hydration of denatured proteins (thus providing an independent measure of the consequence of their possible residual structure) and, also, on the possibility of finding substances that are more efficient protein stabilizers than known osmolytes are.
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PMID:An osmolyte effect on the heat capacity change for protein folding. 754 26

Previous work from our laboratory has implicated hormone-induced plasma membrane movement (i.e., endo- and exocytosis) in water and electrolyte transport by the epithelial cells that line the ducts in the liver (i.e., cholangiocytes). To further explore the cellular mechanisms regulating ductal bile secretion, we infused somatostatin and/or secretin intravenously into rats 2 wk after either bile duct ligation (BDL), a procedure that induces selective proliferation of cholangiocytes, or sham surgery and measured bile flow and biliary constituents. We also determined the effect of somatostatin on basal and secretin-induced exocytosis by purified cholangiocytes isolated from rat liver after BDL. Finally, we studied the expression of the somatostatin receptor gene by both ribonuclease (RNase) protection and nuclear run-on assays using cDNA encoding for two subtypes of the somatostatin receptor gene (i.e., SSTR1 and SSTR2). In vivo, somatostatin infusion caused a dose-dependent bicarbonate-poor decrease (57% maximal decrease below baseline; P < 0.05) in bile flow in BDL but not in sham-operated rats; in contrast, secretin caused a dose-dependent bicarbonate-rich choleresis (228% maximal increase above baseline; P < 0.05) in BDL but not in sham-operated rats. Simultaneous or prior infusion of somatostatin inhibited the secretin-induced hypercholeresis in BDL rats. In vitro, somatostatin had no effect on basal exocytosis by cholangiocytes isolated from BDL rats; however, somatostatin inhitibed (88% maximal inhibition; P < 0.05) secretin-induced exocytosis by cholangiocytes in a dose-dependent fashion. In addition, somatostatin inhibited secretin-induced increases in levels of adenosine 3',5'-cyclic monophosphate (cAMP) in cholangiocytes isolated from BDL rats.(ABSTRACT TRUNCATED AT 250 WORDS)
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PMID:Somatostatin inhibits secretin-induced ductal hypercholeresis and exocytosis by cholangiocytes. 763 87

Peptide-water interactions of a ribonuclease C-peptide analogue, RN-24 (Suc-AETAAAKFLRAHANH2), which exhibits significant helicity, have been studied in solution using homonuclear 2D and 3D NMR cross-relaxation experiments. Dipolar peptide proton-water proton interactions are indicated by a large number of NOESY-type cross peaks at the H2O resonance frequency, most of them with opposite sign relative to the diagonal. Some cross peaks arise from intrapeptide cross relaxation to labile protons of histidine, threonine, lysine and arginine side chains. The observed peptide-water interactions are rather uniformly distributed, involving peptide backbone and side chains equally. The data are consistent with rapid fluctuations of the conformational ensemble and the absence of peptide regions that are highly shielded from bulk solvent, even in a peptide that exhibits high propensities for formation of helical secondary structure.
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PMID:Hydration of the partially folded peptide RN-24 studied by multidimensional NMR. 764 54

Molecular dynamics simulations are used to investigate the unfolding reaction of an isolated beta-hairpin formed by residues 85 to 102 of barnase, a ribonuclease from Bacillus amyloliquefaciens. This peptide was considered following evidence from experimental studies that it may act as an initiation site for barnase folding by adopting a native-like conformation early during the folding process. Three successive molecular dynamics simulations of about 300 ps each were carried out for an all-atom model of the hairpin in water at 300 K, 450 K, and 600 K, respectively. A detailed analysis of all three simulations is presented. In particular we investigate the behavior of the backbone hydrogen bonds, and of hydrophobic interactions between side-chains, where distinction is made between contributions from native and non-native contacts, respectively. Furthermore, we investigate peptide water interactions and monitor the presence and size of empty cavities. The behavior of the hairpin in the three simulations, when considered sequentially, describes a process whereby a native-like conformation evolves to an unfolded state. Unfolding starts at the beginning of the 450 K simulation with the loss of two hydrogen bonds at the free hairpin extremities. At about the same time, the centrally located H-bonds are weakened and exchange more frequently with water, but the turn tightens up as the beta-sheet extends into the turn region. All this is accompanied by a volume expansion and the formation of a large hydrophobic side-chain cluster promoted by both native and highly fluctuating non-native apolar contacts involving residues 87 to 90 and 95 to 99. This collapsed but more loosely packed state, essentially stabilized by hydrophobic interactions, is stable throughout the entire 450 K simulation and for about 150 ps at 600 K, after which point it proceeds rapidly to completely denatured conformations. This behavior presents clear analogies with known features of the unfolding reaction of complete proteins. It may indicate that this beta-hairpin has a well-defined conformation on its own, which would be in agreement with its role as an initiation site for folding.
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PMID:Unfolding simulations of the 85-102 beta-hairpin of barnase. 765 Jul 41

To study the interaction and the role of the metal ion in the reaction catalyzed by Escherichia coli ribonuclease HI (E. coli RNase HI), substrate analogues containing a phosphorothioate linkage or 2'-modified nucleosides at the cleavage site were used. In the presence of Mg2+, Mn2+, Co2+, Zn2+, or Cd2+, the phosphorothioate linkage with the RP-configuration was cleaved, while the SP-isomer was not. Kinetic studies showed that Mn2+ and Cd2+ facilitated the cleavage of the phosphorothioate to only a small extent, which indicated the absence of an interaction between the metal ion and this phosphate residue. The interaction of the metal ion with the 2'-functional group was analyzed by Mg(2+)-titration experiments using the -OH, -NH2, and -F substrates. From Hill plots, it was found that the KMg values were almost the same. These results are evidence of an interaction between Mg2+ and the 2'-functional group by the formation of an outer-sphere complex with a water molecule. The Hill coefficient of 1.0 for the -OH substrate indicated that a single Mg2+ ion is required for the catalysis.
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PMID:Role of the Mg2+ ion in the Escherichia coli ribonuclease HI reaction. 770 24

The backbone dynamics of Escherichia coli ribonuclease HI (RNase HI) in the picosecond to nanosecond time scale were characterized by a combination of measurements of 15N-NMR relaxation (T1, T2, and NOE), analyzed by a model-free approach, and molecular dynamics (MD) simulation in water. The MD simulations in water were carried out with long-range Coulomb interactions to avoid the artificial fluctuation caused by the cutoff approximation. The model-free analysis of the 15N-NMR relaxation indicated that RNase HI has a rotational correlation time of 10.9 ns at 27 degrees C. The generalized order parameter (S2) for the internal motions varied from 0.15 to 1.0, with an average value of 0.85, which is much larger than that of the RNase H domain of HIV-1 reverse transcriptase (0.78). Large internal motions (small order parameters) were observed in the N-terminal region (Leu2-Lys3), the loop between beta-strands A and B (Cys13-Gly15), the turn between alpha-helix I and beta-strand D (Glu61, His62), the loop between beta-strand D and alpha-helix II (Asp70-Tyr71), the loop between alpha-helices III and IV (Ala93-Lys96), the loop between beta-strand E and alpha-helix V (Gly123-His127), and the C-terminal region (Gln152-Val155). The effective correlation time observed in these regions varied from 0.45 ns (Glu61, Lys96) to 2.2 ns (Leu14). The order parameters calculated from the MD agreed well with those from the NMR experiment, with a few exceptions. The distributions of most of the backbone N-H vectors obtained by MD are approximately consistent with the diffusion-in-a-cone model. These distributions, however, were elliptic, with a long axis perpendicular to the plane defined by the N-H and N-C alpha vectors. Distributions supporting the axial fluctuation model or the jump-between-two-cones model were also observed in the MD simulation.
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PMID:Characterization of the internal motions of Escherichia coli ribonuclease HI by a combination of 15N-NMR relaxation analysis and molecular dynamics simulation: examination of dynamic models. 775 90

All of the individual carboxyl groups (the side-chain carboxyl groups of Asp and Glu, and the C-terminal alpha-carboxyl group) in Escherichia coli ribonuclease HI, which is an enzyme that cleaves the RNA strand of a RNA/DNA hybrid, were pH-titrated, and their ionization constants (pKa) were determined from an analysis of the pH-dependent chemical shifts of the carboxyl carbon resonances obtained from 1H-13C heteronuclear two-dimensional NMR. The pKa values in the enzyme varied widely among individual residues, for example, in the unusual pKa values for two important catalytic residues, Asp10 (pKa 6.1) and Asp70 (pKa 2.6). Moreover, remarkable two-step titrations were observed for these carboxylates. The binding of Mg2+ ion to the enzyme, which is the cofactor necessary for catalytic activity, caused no significant change in the pKa values of the carboxyl groups, except for that of Asp10. The variations of the pKas that were dependent on the microenvironment in the protein were theoretically reproduced to compare with the experimental results by a numerical calculation, using a continuum electrostatic model. Most of the significant pKa decreases were brought about through strong electrostatic interactions with the neighboring basic amino acids, Arg or Lys. The pKa shifts and the two-step titrations of Asp10 and -70, which are close to each other, were interpreted to be due to the neighboring effect of two functional groups, as observed in the interacting titratable groups of a dicarboxyl compound or in the active site carboxylates of lysozyme and aspartic protease. The role of Asp10 in the catalytic action is either to be the proton donor to the RNA moiety or the binding partner of the Mg2+ ion cofactor. Asp70, on the other hand, is considered to be the proton acceptor from a water molecule.
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PMID:Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR. 790 91


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