Biomedical subjects

H B Gray

Publications and source records attributed to H B Gray.

At least 73 records · Page 4Linked to original sources

PubMed1989

Ethidium bromide-mediated renaturation of denatured closed circular DNAs: mechanistic aspects and fractionation of DNA on a molecular weight basis.

When closed circular duplex DNAs are exposed to alkali in the presence of ethidium bromide, from 0 to 100% of the DNA can be recovered as the fully base-paired duplex (native) form upon neutralization of the solutions. The fraction of native DNA depends on the concentration of ethidium bromide, time of incubation, ionic strength and temperature of the solutions before neutralization as well as the molecular weight and superhelix density of the DNA. Limiting ethidium concentrations exist below and above which 0 and 100% of the DNA, respectively, is recovered as native material under a given set of incubation conditions regardless of the length of time of incubation before neutralization. The strong molecular weight dependence of the fraction of DNA recovered in the native form after a given time of pre-neutralization incubation at ethidium concentrations between the limiting values noted above allows larger DNAs to remain fully denatured upon neutralization while smaller DNAs in the same mixture are fully renatured. This permits the rapid fractionation of mixtures of closed duplex DNAs on the basis of molecular weight when a technique for the separation of denatured from fully base-paired DNA is applied to such mixtures. Such a separation has been demonstrated through the marked enrichment of plasmid cloning vector DNA containing cloned inserts in the fractions that remain denatured after neutralization of alkaline solutions of these DNAs containing ethidium bromide.

Bacteriophages↗

PubMed1989

Effects of buried ionizable amino acids on the reduction potential of recombinant myoglobin.

The temperature dependences of the reduction potentials (E degrees') of wild-type human myoglobin (Mb) and three site-directed mutants have been measured by the use of thin-layer spectroelectrochemistry. Residue Val68, which is in van der Waals contact with the heme in Mb, has been replaced by Glu, Asp, and Asn. The changes in E degrees' and the standard entropy (delta S degrees') and enthalpy (delta H degrees') of reduction in the mutant proteins were determined relative to values for wild type; the change in E degrees' at 25 degrees C was about -200 millivolts for the Glu and Asp mutants, and about -80 millivolts for the Asn mutant. At pH 7.0, reduction of Fe(III) to Fe(II) in the Glu and Asp mutants is accompanied by uptake of a proton by the protein. These studies demonstrate that Mb can tolerate substitution of a buried hydrophobic group by potentially charged and polar residues and that such amino acid replacements can lead to substantial changes in the redox thermodynamics of the protein.

Asparagine↗

PubMed1989

Axial ligand replacement in horse heart cytochrome c by semisynthesis.

Semisynthesis has been employed to replace the axial methionine in horse heart cytochrome c with histidine. The reduction potential of the His-80 protein (cyt c-His-80) is 41 mV vs NHE (0.1 M phosphate; pH 7.0; 25 degrees C). The absorption spectra of oxidized and reduced cyt c-His-80 are very similar to those of the native protein in the porphyrin region, but the 695 nm band is absent in the oxidized His-80 protein.

Animals↗

PubMed1988

Circular intermediates with missing nucleotides in the conversion of supercoiled or nicked circular to linear duplex DNA catalyzed by two species of BAL 31 nuclease.

The extracellular nucleases from Alteromonas espejiana BAL 31 can catalyze the endonucleolytic and/or exonucleolytic hydrolysis of duplex DNA in response to a variety of alterations, either covalent or noncovalent, in DNA structure. The nuclease can exist as at least two kinetically and molecularly distinct protein species. The two species that have been studied, called the 'fast' (F) and 'slow' (S) nucleases, both readily convert negatively supercoiled DNAs to linear duplex molecules and accomplish this conversion through the formation of a circular duplex intermediate containing usually a single interruption in one strand. It is further shown that most of these intermediates contain gaps arising from the removal in a processive manner of one or more nucleotide residues after the introduction of the initial strand break (nick). Considering only the intermediates with gaps, the average number of missing residues is 6.3 +/- 0.5 and 2.8 +/- 0.3, respectively, for DNA acted upon by the F and S enzymes independently of the extent of conversion of supercoiled DNA. The nicks and gaps are bounded by 3'-hydroxyl and 5'-phosphoryl termini. When singly nicked circular DNA is used as the substrate, conversion to the linear duplex form occurs predominantly through a gapped circular intermediate with the same average numbers, within experimental error, of missing nucleotides for the respective nuclease species as found when supercoiled DNA is the substrate. The conversion to linear duplex DNA is much slower when nicked circular DNA is the substrate compared to that found when supercoiled DNA is the starting material.

DNA, Circular↗

PubMed1988

Long-range electron transfer in myoglobin.

The distance and driving-force dependences of electron transfer (ET) in a set of four surface-ruthenated myoglobins, in which the heme prosthetic group has been systematically replaced by a series of metalloporphyrins of differing excited-state redox potentials, have provided information on the magnitude [Hab(12.7 A) approximately 6.3 x 10(-3) cm-1] and decay [beta approximately 0.8 A-1, where kET alpha exp [-beta(d - do)]] of protein-mediated donor-acceptor electronic coupling. A reorganization energy lambda approximately 1.3 eV, due to coordination and solvation changes both at and between the ET sites, has been estimated using a rate expression that allows electron-vibration coupling to classical and quantum mechanical modes. The contribution to lambda from the porphyrin and peptide matrix is approximately 0.7 eV. Specific electron-tunneling pathways in the protein have been evaluated.

Electron Transport↗

PubMed1987

Electron transfer from cytochrome b5 to iron and copper complexes.

The rates of electron transfer from the tryptic fragment of bovine liver cytochrome b5 to FeIIINTA, FeIIIATP, CuIINTA, CuIIATP, and CuIIHis have been measured by anaerobic stopped-flow techniques. The rates of reduction of the Fe(III) complexes are independent of ionic strength, enhanced at low pH, and slightly inhibited by ZnIINTA. Saturation kinetics are observed with CuIINTA (kappa et = 0.05 s-1, K = 8.6 M-1), CuIIHis (kappa et = 0.2 s-1, K = 2.6 X 10(3) M-1), and CuIIATP (kappa et = 0.6 s-1, K = 4.5 X 10(3) M-1), thereby indicating that binding of Cu(II) to the protein occurs prior to electron transfer. 1H NMR resonances of the three surface histidines and some neighboring residues have been assigned by two-dimensional NMR techniques. NMR titration experiments show unequivocally that CuIINTA binds preferentially at a site near His-26 and Tyr-27.

Animals↗

PubMed1987

Spectrochemical studies on the blue copper protein azurin from Alcaligenes denitrificans.

Spectroscopic and electrochemical studies, incorporating electronic spectra, electron paramagnetic resonance (EPR) spectra, resonance Raman (RR) spectra, and measurements of the redox potential, have been carried out on the blue copper protein azurin, from Alcaligenes denitrificans. These data are correlated with the refined crystal structure of this azurin and with corresponding data for other blue copper proteins. The electronic spectrum, characterized by an intense (epsilon = 5100 M-1 cm-1) charge-transfer band at 619 nm, the EPR spectral parameters (g perpendicular = 2.059, g parallel of = 2.255, A parallel of = 60 X 10(-4) cm-1), and the resonance Raman spectrum are similar to those obtained from other azurins and from plastocyanins. Both the electronic spectrum and the EPR spectrum are unchanged over the pH range 4-10.5, but major changes occur above pH 12 and below pH 3.5. A small reversible change occurs at pH approximately 11.4. In the RR spectrum the Cu-S stretching mode is shown to contribute to all of the five principal RR peaks. Deuterium substitution produces shifts in at least seven of the peaks; these shifts may be attributable, at least in part, to the NH...S hydrogen bond to the copper-ligated Cys-112. Measurements of the redox potential, using spectroelectrochemical methods, over the temperature range 4.8-40.0 degrees C, give values for delta H0' and delta S0' of -55.6 kJ mol-1 and -97.0 J K-1 mol-1, respectively. The redox potential of A. denitrificans azurin at pH 7.0, Eo', is 276 mV. These data are interpreted in terms of a copper site, in azurin, comprising three strong bonds, in an approximately trigonal plane, from Cys-112, His-46, and His-117 and much longer axial approaches from Met-121 and the peptide carbonyl oxygen of Gly-45. Spectral differences within the azurin family and between azurin and plastocyanin are attributed to differences in the strengths of these axial interactions. Likewise, the distinctly lower Eo values for azurins, as compared with plastocyanins, are related to the more copper(II)-like site in azurin [with a weaker Cu-S(Met) interaction and a Cu-O interaction not found in plastocyanin]. On the other hand, the relative constancy of the EPR parameters between azurin and plastocyanin suggests they are not strongly influenced by weakly interacting axial groups.

Alcaligenes↗

PubMed1986

Chemical and biological properties of pentaammineruthenium-bleomycin complexes.

The reaction of [(H2O)(NH3)5RuII]2+ with bleomycin forms at least two stable products following oxidation to the Ru(III) analog. Spectroscopic and electrochemical measurements indicate monodentate binding of [(NH3)5RuIII] to the imidazole and pyrimidine moieties, with coordination to the latter involving the exocyclic amine nitrogen. DNA cleavage studies show the complexes to be ineffective in DNA strand scission. In vitro biological studies reveal these adducts to be cytotoxic.

Animals↗

PubMed1986

Spectroelectrochemical study of cytochrome c oxidase: pH and temperature dependences of the cytochrome potentials. Characterization of site-site interactions.

The cytochrome a and a3 sites in uninhibited, detergent-solubilized cytochrome c oxidase have been studied under a wide range of conditions using thin-layer spectroelectrochemistry. The observed absorbance changes at the alpha and Soret absorbance maxima have been used together to estimate the extents of reduction of cytochromes a and a3, using the absorbance properties of these cytochromes deduced from previous measurements employing ligand inhibition of cytochrome a3. The resulting Nernst plots, combined with the results of parallel studies on the carbon monoxide-inhibited enzyme (Ellis, W. R., Jr., Wang, H., Blair, D. F., Gray, H. B., and Chan, S. I. (1986) Biochemistry 25, 161-167; Wang, H., Blair, D. F., Ellis, W. R., Jr., Gray, H. B., and Chan, S. I. (1986) Biochemistry 25, 167-171), indicate that the cytochrome a site participates in anticooperative thermodynamic interactions which involve all three of the other metal sites in the protein. Using an analysis which resolves the intrinsic thermodynamic properties of the cytochromes from the effects of the intersite interactions, the pH, temperature, and ionic strength dependences of the cytochrome reduction potentials have been measured. The standard entropy of reduction of cytochrome a in the native enzyme is large and negative, in agreement with measurements on the carbon monoxide-inhibited enzyme. The reduction potential of cytochrome a is only moderately (less than -30 mV/pH unit) dependent upon pH, which implies that its reduction is linked to the uptake, on the average, of only about 0.5 protons at pH 7.0, and significantly less at the higher pH values relevant to the mitochondrial matrix. The thermodynamic properties of cytochrome a3 were found to be different in the two enzyme batches studied: in one batch, the cytochrome a3 reduction potential decreased steeply (about -56 mV/pH unit) with increasing pH, indicating stoichiometric (1 H+/e-) coupling of protonation to reduction. In the other batch, the cytochrome a3 potential was insensitive to pH below pH 7.5 and decreased at higher pH values in a manner suggesting coupling to an ionizable group with pKa near 7.8. The temperature dependence of the cytochrome a3 reduction potential indicates that its standard entropy of reduction is more positive than that of myoglobin, another high-spin metalloprotein heme, and significantly more positive than that of cytochrome a.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1986

Long-range electron transfer in heme proteins.

Kinetic experiments have conclusively shown that electron transfer can take place over large distances (greater than 10 angstroms) through protein interiors. Current research focuses on the elucidation of the factors that determine the rates of long-range electron-transfer reactions in modified proteins and protein complexes. Factors receiving experimental and theoretical attention include the donor-acceptor distance, changes in geometry of the donor and acceptor upon electron transfer, and the thermodynamic driving force. Recent experimental work on heme proteins indicates that the electron-transfer rate falls off exponentially with donor-acceptor distance at long range. The rate is greatly enhanced in proteins in which the structural changes accompanying electron transfer are very small.

Animals↗

PubMed1986

Spectroelectrochemical study of the cytochrome a site in carbon monoxide inhibited cytochrome c oxidase.

The reduction potential of the cytochrome a site in the carbon monoxide derivative of beef heart cytochrome c oxidase has been studied under a variety of conditions by thin-layer spectroelectrochemistry. The reduction potential exhibits no ionic strength dependence and only a 9 mV/pH unit dependence between pH 6.5 and 8.5. The weak pH dependence indicates that protonation of the protein is not stoichiometrically linked to oxidoreduction over the pH range examined. The temperature dependence of the reduction potential implies a relatively large standard entropy of reduction of cytochrome a. The measured thermodynamic parameters for reduction of cyctochrome a are (all relative to the normal hydrogen electrode) delta Go'(25 degrees C) = -6.37 kcal mol-1, delta Ho' = -21.5 kcal mol-1, and delta So' = -50.8 eu. When cytochrome c is bound to the oxidase, the reduction potential of cytochrome a and its temperature dependence are not measurably affected. Under all conditions studied, the cytochrome a site did not exhibit simple Nernstian n = 1 behavior. The titration behavior of the site is consistent with a moderately strong anticooperative interaction between cytochrome a and CuA [Wang, H., Blair, D. F., Ellis, W. R., Jr., Gray, H. B., & Chan, S. I. (1985) Biochemistry (following paper in this issue)].

Animals↗

PubMed1986

Temperature dependence of the reduction potential of CuA in carbon monoxide inhibited cytochrome c oxidase.

The temperature dependence of the reduction potential of the CuA site in carbon monoxide inhibited cytochrome c oxidase has been measured with a spectroelectrochemical method adapted to the relatively weak near-infrared absorption of this copper ion. These measurements, together with parallel measurements on the 604-nm absorption due to Fea, indicate that an interaction between CuA and Fea causes the reduction potential for one of these sites to be decreased by approximately 40 mV upon reduction of the other. The temperature dependence of the CuA reduction potential indicates a relatively large and negative standard entropy of reduction of CuA (delta So' = -48.7 +/- 2.3 eu). Possible implications of the intersite redox interaction and the large standard entropy of reduction of the CuA site are discussed.

Animals↗

PubMed1984

Terminally directed hydrolysis of duplex ribonucleic acid catalyzed by a species of the BAL 31 nuclease from Alteromonas espejiana.

The extracellular nuclease activities of Alteromonas espejiana sp. BAL 31 are mediated by at least two distinct protein species that differ in molecular weights and catalytic properties. The two species that have been purified to homogeneity and characterized, the "fast" (F) and "slow" (S) enzymes, both possess an exonuclease activity that shortens both strands of duplex DNA, with the F nuclease displaying a much greater (approximately 19-fold) turnover number for this degradation than the S species. In the present article, it is shown that the F species also mediates the terminally directed hydrolysis of a linear duplex RNA, gradually shortening molecules of this substrate through a mechanism that results in the removal of nucleotides from both the 3' and the 5' ends. This degradation proceeds with very infrequent introduction of scissions away from the termini as demonstrated by gel electrophoretic examination of the products of partial degradation, both in duplex form and after denaturation by reaction with CH3HgOH, and by electron microscopic characterization of duplex partially degraded molecules. The apparent Michaelis constant and turnover number have been determined. At equimolar enzyme concentrations in the limit of high substrate concentration, the F nuclease will degrade duplex RNA at a rate 0.021 +/- 0.010 (S.D.) times that for a duplex DNA of comparable guanine + cytosine content. The S species, by contrast, shows very little activity against the duplex RNA substrate relative to that of the F enzyme.

Endodeoxyribonucleases↗

PubMed1984

A single apurinic site can elicit BAL 31 nuclease-catalyzed cleavage in duplex DNA.

The extracellular nuclease from Alteromonas espejiana BAL 31 is a highly sensitive endonucleolytic probe for lesions that distort the helical structure of duplex DNA. The nuclease can be isolated as two distinct molecular species, the 'fast' (F) and 'slow' (S) species, which have different kinetic properties. When nonsupercoiled, covalently closed circular phage PM2 DNA containing apurinic sites introduced by heating at acid pH was incubated with individual fractions from a chromatographic column which separated the two nuclease species, cleavage of the DNA was observed which was greatly in excess of control levels using nonmodified DNA. The initial rates of such cleavage clearly paralleled the peaks of both absorbance and nuclease activity against single-stranded and linear duplex substrates. When samples of apurinic DNA were incubated with pooled fractions from the same column representing pure F and S nucleases, respectively, the rate and extent of the cleavage observed was dependent upon the average number of apurinic sites per molecule. Cleavage was readily detectable in samples containing an average of 1.1 apurinic sites per molecule with both species of the enzyme. These results indicate that either species of the BAL 31 nuclease can recognize and cleave in response to a single apurinic site in duplex DNA. The F nuclease appears to be approx. 2.5-times as efficient in cleaving DNA containing apurinic lesions as the S enzyme in extended incubations.

Apurinic Acid↗

PubMed1984

NMR spectroscopic identification of a hexacyanochromate(III) binding site on Pseudomonas azurin.

Studies of redox reactions between the blue copper protein azurin and inorganic reagents have suggested the formation of discrete complexes between the reaction partners prior to the actual electron-transfer step. To get an insight into the structural nature of the complexes formed, we have studied the interaction (i) between oxidized Pseudomonas aeruginosa azurin and the anion Fe(CN)6(3-) and (ii) between reduced azurin and Cr(CN)6(3-). At low ionic strengths, stoichiometric binding of one Fe(CN)6(3-) ion to the oxidized protein is observed. In the high-resolution proton magnetic resonance spectra of the reduced protein, specific broadening of the assigned residues is observed upon titration with the redox-inert Cr(CN)6(3-) ion. Analysis of this paramagnetic spectral broadening in terms of the three-dimensional structure of the protein has led to the proposal that the binding site of the anions lies approximately midway between lysine residues 85 and 92. Evidence in support of this conclusion is provided by parallel studies on Alcaligenes faecalis azurin, which lacks these lysine residues. A similar site on the surface of Pseudomonas azurin has recently been identified by affinity labeling with chromous ions as an electron-transfer locus [ Farver , O., & Pecht , I. (1981) Isr . J. Chem. 21, 13-17]. The results presented here suggest that this region on the protein surface also may be employed by anionic electron-transfer agents.

Alcaligenes↗

PubMed1984

Preparation and characterization of pentaammineruthenium-(histidine-83)azurin: thermodynamics of intramolecular electron transfer from ruthenium to copper.

The reaction between a5RuH2O2+ (a is NH3) and Pseudomonas aeruginosa azurin at pH 7, followed by oxidation, yields a5Ru(His-83)3+-azurin(Cu2+) as the major product. Spectroscopic measurements (UV-visible, CD, EPR, and resonance Raman) indicate that the native structure is maintained in the modified protein. The site of ruthenium binding (His-83) was identified by peptide mapping. The a5RuHis/Cu ratio in the modified protein, determined from the EPR spectrum, is 1:1, and the reduction potentials (vs. normal hydrogen electrode, pH 7.0, 25 degrees C) are blue copper (Cu2+/1+), 320 +/- 2 mV; a5Ru(His-83)3+/2+, 50 +/- 10 mV. From measurements of the reduction potentials at several temperatures in the 5-40 degrees C range, delta H degree for intramolecular Ru2+ ----Cu2+ electron transfer was estimated to be -12.4 kcal mol-1 (1 cal = 4.184 J). Analysis of kinetic data in light of the electron transfer exothermicity indicates that the reorganizational enthalpy of the blue copper site can be no larger than 7.1 kcal mol-1.

Azurin↗

PubMed1983

Heme-heme orientation and electron transfer kinetic behavior of multisite oxidation-reduction enzymes.

Analysis of the polarized single-crystal absorption spectra of cytochrome cd1 of Pseudomonas aeruginosa shows that the heme c and heme d1 groups in each subunit are oriented perpendicularly to each other in both oxidized and reduced forms of the enzyme. These results, together with those of previous kinetic studies, indicate that a perpendicular heme-heme orientation may be an important factor in specifying kinetically slow steps in a sequential series of electron transfer reactions.

Cytochrome c Group↗

PubMed1983

Isolation and comparison of two molecular species of the BAL 31 nuclease from Alteromonas espejiana with distinct kinetic properties.

The extracellular nuclease from Alteromonas espejiana sp. BAL 31 can be isolated as two distinct proteins, the "fast" (F) and "slow" (S) species, both of which have been purified to homogeneity. The F and S species of the nuclease have molecular weights, respectively, of 109 X 10(3) and 85 X 10(3), and both are single polypeptide chains with an isoelectric pH near 4.2. Both species catalyze the degradation of single-stranded and linear duplex DNAs to 5'-mononucleotides. The degradation of linear duplex DNA occurs through a terminally directed hydrolysis mechanism that results in the removal of nucleotides from both the 3' and 5' ends. Apparent Michaelis constants (Km) have been obtained for the exonuclease activities of both species and for the activity against single-stranded DNA of the S species. The Km for the hydrolysis of single-stranded DNA catalyzed by the F species has not been obtained because the reaction velocity was maximal even at the lowest substrate concentrations accessible in the photometric assay. The ratio of the turnover numbers for the exonuclease activities of the two species indicates that the F species will shorten linear duplex DNA at a rate 27 +/- 5 (S.D.) times faster than an equimolar concentration of the S species in the limit of high substrate concentration, while the corresponding ratio for the activities against single-stranded DNA (1.2 +/- 0.1) shows that the two species are similar with respect to hydrolysis of this substrate. In the limit of high substrate concentrations, the F and S species break phosphodiester bonds in single-stranded DNA at rates 1.3 +/- 0.3 and 33 +/- 2 times those for the exonucleolytic degradation of linear duplex DNA, respectively. It has not been established whether the two species are physically related.

Bacteria↗