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Biomedical subjects

H B Gray

Publications and source records attributed to H B Gray.

At least 91 records · Page 5Linked to original sources
PubMed1983

BAL 31 nuclease as a probe in concentrated salt for the B-Z DNA junction.

The BAL 31 nuclease, an extracellular nuclease from A. espejiana, specifically recognizes and cleaves the salt induced conformational junction between B and Z-DNA. Short segments of (dC-dG) left-handed Z-helix, comprising approximately 1% of the total DNA, are specifically detected within two different recombinant plasmids. The BAL 31 enzyme is highly resistant to inactivation by the presence of high concentrations of a variety of electrolytes that stabilize left-handed helices, is active at physiological pH, and can be used to probe both linear and circular DNAs. Additionally, the nuclease cleaves left-handed (dC-dG)n only very poorly, if at all. Thus, the BAL 31 nuclease can be utilized as a probe for helical junctions and consequently for segments of left-handed DNA that might exist within predominantly right-handed naturally occurring genomes.

Bacteria↗
PubMed1982

Temperature dependence of the reduction potential of blue copper in fungal laccase.

Thin-layer spectroelectrochemical methods have been employed to measure the reduction potentials of the blue copper in Polyporus versicolor laccase (EC 1.10.3.2) between 7 degrees C and 41 degrees C (0.2 M sodium phosphate, pH 5.4). Thermodynamic parameters are: DeltaS degrees = -13.9 +/- 2 cal/mol-K; DeltaH degrees = -22.1 +/- 0.5 kcal/mol; E degrees (25 degrees C) = 780 +/- 3 mV vs. the normal hydrogen electrode. Comparison of the DeltaS degrees and DeltaH degrees values with those for single-site proteins suggests that the high potential of the blue copper in fungal laccase is attributable mainly to stabilization of the copper (I) center by enhanced ligand binding interactions and that protein solvation effects play a lesser role.

Journal Article↗
PubMed1982

Preparation and characterization of a pentaammineruthenium(III) derivative of horse heart ferricytochrome c.

A stable complex between pentaammineruthenium(III) and histidine-33 in horse heart ferricytochrome c is formed in the reaction between aquopentaammineruthenium(II) and the protein at pH 7. HPLC of the tryptic hydrolysate of the modified protein was employed to identify the pentaammineruthenium binding site. Spectroscopic measurements show that the integrity of the native structure in the vicinity of the heme c group is maintained in the ruthenium-modified protein. The reduction potentials are: heme c (Fe3+/2+), 0.26 V; Ru(NH3)5(His-33)3+/2+, 0.15 V (vs. normal hydrogen electrode).

Amino Acid Sequence↗
PubMed1981

Type I DNA topoisomerases from mammalian cell nuclei interlock strains and promote renaturation of denatured closed circular PM2 DNA.

Type I DNA topoisomerases from mouse ascites cell nuclei and from rat liver cell nuclei act on denatured viral closed circular PM2 DNA to produce molecules with a highly contracted structure as well as fully duplex non-supercoiled covalently closed circular molecules. Highly contracted DNA molecules contain a novel type of topological linkage in which a strand in one region of the double-stranded molecule passes between the strands in another region of the circular molecule one or more times. Since it is also found that the action of the topoisomerase promotes renaturation of complementary strands in denatured closed circular DNA, it is suggested that formation of contracted DNA structures proceeds through renatured, duplex intermediates with highly negative superhelix densities that contain small single-stranded regions.

Animals↗
PubMed1981

Reactions of nitric oxide with tree and fungal laccase.

The reactions of nitric oxide (NO) with the oxidized and reduced forms of fungal and tree laccase, as well as with tree laccase depleted in type 2 copper, are reported. The products of the reactions were determined by NMR and mass spectroscopy, whereas the oxidation states of the enzymes were monitored by EPR and optical spectroscopy. All three copper sites in fungal laccase are reduced by NO. In addition, NO forms a specific complex with the reduced type 2 copper. NO similarly reduces all of the copper sites in tree laccase, but it also oxidizes the reduced sites produced by ascorbate or NO reduction. A catalytic cycle is set up in which N2O, NO2-, and various forms of the enzyme are produced. On freezing of fully reduced tree laccase in the presence of NO, the type 1 copper becomes reoxidized. This reaction does not occur with the enzyme depleted in type 2 copper, suggesting that it involves intramolecular electron transfer from the type 1 copper to NO bound to the type 2 copper. When the half-oxidized tree laccase is formed in the presence of NO, a population of molecules exists which exhibits a type 3 EPR signal. A triplet EPR signal is also seen in the same preparation and is attributed to a population of the enzyme molecules in which NO is bound to the reduced copper of a half-oxidized type 3 copper site.

Basidiomycota↗
PubMed1981

Spectroscopic studies of ascorbate oxidase. Electronic structure of the blue copper sites.

Low-temperature electronic absorption and room temperature circular dichroism (CD) and magnetic circular dichroism (MCD) spectra are reported for ascorbate oxidase. Bands attributable to d-d electronic transitions in the type 1 (blue) coppers (2B2 ground state) have been observed at 5800, 10000, and 12000 cm-1 (1725, 1000, and 835 nm). The three bands are assigned to the transitions 2B2 leads to 2E, 2B2 leads to 2B1, and 2B2 leads to 2A1, respectively, in the slightly flattened tetrahedral blue copper centers. The ligand field theoretical treatment predicts a type 1 copper reduction potential of 417 mV. The MCD spectrum of ascorbate oxidase contains one major band at 14000 cm-1 (710 nm) and a very weak feature at 13 200 cm-1 (550 nm). The intensities of the CD and MCD bands are consistent with two or three type 1 coppers in each enzyme molecule, and the near-infrared spectroscopic results suggest that the electronic structures of the blue coppers are closely similar.

Ascorbate Oxidase↗
PubMed1981

Extended x-ray absorption fine structure of copper in cytochrome c oxidase: Direct evidence for copper-sulfur ligation.

The copper x-ray fluorescence excitation spectrum of cytochrome c oxidase (ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1) has been recorded in the 245-270 K range. The beat pattern observed in the extended x-ray absorption fine structure can be accounted for only by postulating a combination of sulfur and nitrogen (or oxygen) ligands to the copper. The average Cu-S distance is 2.27 +/- 0.02 A and the average Cu-N (or Cu-O) distance is 1.97 +/- 0.02 A. The amplitudes require ca, 1-1.5 sulfurs and 2 nitrogens (or oxygens) per copper. The distribution of sulfur ligands between Cu(A) and Cu(B) sites is not known, although there is some evidence that two sulfur atoms are bound to Cu(A).

Journal Article↗
PubMed1980

Ethidium bromide-mediated renaturation of denatured closed circular DNAs. The nature of denaturation-resistant fractions of bacteriophage PM2 closed circular DNA.

Addition of the intercalating dye ethidium bromide (EtdBr) to a solution of alkali-denatured double-stranded closed circular PM2, PhiX174, or lambdab(2)b(5)c phage DNAs, under conditions such that the solution remains strongly alkaline, can result in the renaturation of up to 100% of the DNA upon neutralization of the solution. For a fixed time of incubation of the alkaline dye-containing solution before neutralization, there exists a minimum concentration of the dye below which no EtdBr-mediated renaturation is observed for each species of closed circular DNA examined. These minimum concentrations increase, for a given DNA, with increasing ionic strength and temperature. The kinetics of accumulation of forms renaturing upon neutralization of alkaline solutions, at fixed concentrations of dye and DNA, are dependent upon the molecular weight and superhelix density of the starting DNA. After extended periods of incubation at a fixed ionic strength and temperature, however, the profiles of percentage of DNA renatured as a function of ethidium concentration become very similar for all the closed circular DNAs tested and display a transition from an absence of dye-mediated renaturation to virtually 100% renaturation upon neutralization over a small range of dye concentration. Circular DNA containing one or more strand scissions remains strand-separated under all the conditions used to effect the renaturation of closed circular DNA. These findings indicate that configurations of closed circular DNA, in which at least some of the complementary bases are apposed, can be selectively stabilized and accumulate in the presence of ethidium in solutions containing 0.19 N hydroxide ion. The closed circular DNA of bacteriophage PM2 has properties distinct from those of the other DNAs of this study in that it has been shown to contain fractions which exist in the base-paired duplex form after neutralization of strongly alkaline solutions of this DNA incubated at ambient temperature, while no duplex DNA is observed after exposure to alkali and neutralization of solutions of closed circular DNA from other sources. (1,2) The fraction of denaturation-resistant PM2 DNA is shown in the present work to depend upon the temperature and time of incubation in alkali, but not upon the superhelix density of the starting DNA. PM2 closed circular DNA also behaves anomalously with respect to its kinetics of accumulation of forms renaturing upon neutralization of alkaline, EtdBr-containing solutions. Evidence is presented that the translocation of one of the strands of a closed circular molecule relative to the other, which is required for the molecule to exist in the denatured form at neutral pH, is a process to which PM2 DNA is less labile than the other closed circular DNAs of this study.

Bacteriophages↗
PubMed1980

Coordination environment and fluoride binding of type 2 copper in the blue copper protein ascorbate oxidase.

The coordination environment of the type 2 (nonblue) copper in native ascorbate oxidase (L-ascorbate:oxygen oxidoreductase, EC 1.10.3.3) and of a derivative of the enzyme having the type 1 (blue) copper reversibly bleached has been examined by electron paramagnetic resonance (EPR) spectroscopy. In the g[unk] region of the spectrum of bleached ascorbate oxidase, a seven-line superhyperfine pattern is seen that is attributed to the presence of three nitrogen-donor ligands to a type 2 copper having tetragonal geometry. The superhyperfine splitting patterns in the g parallel region of the EPR spectra of native and bleached ascorbate oxidase show that as many as two fluorides may bind to type 2 copper. Because fluoride inhibits the enzyme competitively with respect to ascorbic acid, it is proposed that the type 2 copper is part of the ascorbate binding site.

Journal Article↗
PubMed1979

A rapid method for the purification of supercoiled PM2 DNA by affinity chromatography on H1 histone covalently coupled to agarose.

A simple and rapid method is described for the purification of supercoiled PM2 DNA by affinity chromatography on columns of H1 histone covalently coupled to agarose. The method does not require the use of intercalating agents or ultracentrifugation procedures. Under the conditions most appropriate for purification, elution is carried out in a single step with buffered 0.7 M NaCl after the sample has been loaded onto the column in buffered 0.2 M NaCl. The DNA eluted at the higher salt concentration consists of supercoiled closed circular DNA at greater than 90% purity independently of the ratio of supercoiled to nicked circular DNA in the input mixture.

Bacteriophages↗
PubMed1979

Extracellular nucleases of Alteromonas espejiana BAL 31.IV. The single strand-specific deoxyriboendonuclease activity as a probe for regions of altered secondary structure in negatively and positively supercoiled closed circular DNA.

The dependence of the initial rate of introduction of the first single-chain scission (initial nicking rate) into covalently closed circular phage PM2 DNA by the single strand-specific nuclease from Alteromonas espejiana BAL 31 upon the superhelix density (sigma) of the DNA has been examined. The initial nicking rate decreases with decreasing numbers of negative superhelical turns (decreasing values of -sigma), which behavior is characteristic of other single strand-specific nucleases as reported earlier. In contrast to earlier work, the initial nicking rates of closed circular DNAs by the action of the Alteromonas nuclease have been shown to be readily measurable at values of -sigma as low as 0.02. However, even at the elevated concentrations of enzyme and extended digestion periods required to cause nicking at an appreciable rate at near-zero values of sigma, closed circular DNA containing very few superhelical turns (form IO DNA) is not cleaved at a detectable rate. When this DNA is rendered positively supercoiled by ethidium bromide (EtdBr), it is not affected by the nuclease until very high positive values of sigma are attained, at which low rates of cleavage can be detected at elevated enzyme concentrations. The effects of EtdBr on the enzyme activity have been tested and are entirely insufficient to allow the interpretation of zero nicking rates as the result of inhibition of the nuclease activity by the dye. Positively supercoiled DNA is concluded not to contain regions having significant single-stranded character until values of sigma are reached which are very much higher than the values of -sigma for which negatively supercoiled DNAs behave as if they contain unpaired or weakly paired bases.

DNA, Circular↗
PubMed1978

Magnetic susceptibility studies of laccase and oxyhemocyanin.

The magnetic susceptibility of Rhus vernicifera laccase has been remeasured over the temperature range 5-260 K. In contrast to our previous results [Solomon, E.I., Dooley, D. M., Wang R.-H., Gray, H.B., Cerdonio, M., Mogno, F. & Romani, G. L. (1975) J. Am. Chem. Soc. 98, 1029-1031] linear chi versus T-1 behavior was observed. The susceptibility of Limulus polyphemus oxyhemocyanin has also been measured in the range 5-260 K. Only weak paramagnetism, attributable to dissolved oxygen and a small amount of paramagnetic impurities, was observed. Analysis of the data establishes a lower limit of 550 cm-1 for J, consistent with our earlier work. The temperature dependence of the susceptibility of laccase is quantitatively accounted for by the presence of two paramagnetic copper ions (types 1 and 2) per enzyme molecule. Curie law behavior at low temperatures rules out significant interaction between the two coppper types, indicating that these redox centers are well separated (several angstroms) and are not connected by bridging ligands. Formulation of the type 3 site as binuclear Cu(II) requires J greater than or equal to 500 cm-1.

Animals↗
PubMed1978

Coordination environment and fluoride binding of type 2 copper in the blue copper oxidase ceruloplasmin.

The electron paramagnetic resonance (EPR) spectra of the blue copper oxidase ceruloplasmin [ferroxidase, iron (II):oxygen oxidoreductase, EC 1.16.3.1] and of a derivative having the type I (blue) copper centers reversibly bleached are reported. The EPR spectrum of bleached ceruloplasmin has a seven-line superhyperfine structure in the g : formula: (see text) region that is attributed to the presence of three nitrogen-donor type 2 copper ligands. The EPR data suggest further that the type 2 copper in ceruloplasmin possesses a tetragonal coordination gometry. In the presence of varying amounts of fluoride, superhyperfine splitting patterns in the g : formula: (see text) region of both ceruloplasmin derivatives indicate that a maximum of two fluorides may be bound to the type 2 copper.

Ceruloplasmin↗
PubMed1978

Extracellular nucleases of pseudomonas BAL 31. III. Use of the double-strand deoxyriboexonuclease activity as the basis of a convenient method for the mapping of fragments of DNA produced by cleavage with restriction enzymes.

We have previously characterized an extracellular nuclease from Pseudomonas BAL 31 which, in addition to other activities, displays a double-strand exonuclease activity which progressively shortens both strands of linear duplex DNA molecules from both termini. This degradation is accomplished without the introduction of detectable scissions away from the ends of the duplexes. When this nuclease is used to produce a series of progressively shortened samples from a linear duplex DNA, subsequent digestion of these samples with a site-specific restriction endonuclease and analysis of the resulting fragments by gel electrophoresis permits the rapid establishment of the order of the restriction enzyme fragments through the entire genome. This is accomplished by noting from the electropherograms the order in which the various restriction enzyme fragments become noticeably shortened or disappear. Using this method, the five cleavage sites for the endonuclease Hpa I and the single cleavage sites for the nucleases Hpa II and Pst I have been mapped in PM2 bacteriophage DNA. In a more stringent test of the method, 18 of the 24 fragments produced by cleavage of coliphage lambdab2b5c DNA with the Pst I nuclease have been mapped, and five of the six remaining fragments have been assigned to small regions of the genome.

DNA Restriction Enzymes↗
PubMed1977

A sensitive endonuclease probe for lesions in deoxyribonucleic acid helix structure produced by carcinogenic or mutagenic agents.

The highly single strand-specific extracellular nuclease of Pseudomonas BAL 31 is shown to cleave non-supercoiled closed circular duplex PM2 bacteriophage DNA containing regions of altered helix structure produced in vitro by irradiation with ultraviolet light or by treatment with the carcinogen, N-acetoxy-N-2-acetylaminofluorene. Untreated samples of this DNA are affected very little by the nuclease. The unwinding of the DNA helix associated with the above treatment renders the closed circular DNA positively supercoiled compared to untreated samples. The extent of unwinding can be accurately measured and correlated with the average number of lesions per molecule of DNA by monitoring the alterations of the electrophoretic patterns, relative to those observed for untreated DNA, of such DNA in agarose gels. Interstrand cross-links and mismatched base pairs produced by treatment of non-supercoilded circular duplex DNA with the mutagen, nitrous acid, do not detectably unwind the DNA helix. The nitrous acid-treated DNA provides substrates for cleavage by the Pseudomonas nuclease which are likely to be the interstrand cross-links rather than the mismatched base pairs. Use of the Pseudomonas nuclease in conjunction with agarose gel electrophoresis can provide a powerful method for the detection of damage in duplex DNA such as that introduced by carcinogenic and mutagenic agents.

Acetoxyacetylaminofluorene↗