Biomedical subjects

M Archer

Publications and source records attributed to M Archer.

At least 19 recordsLinked to original sources

PubMed2006

Crystallization and preliminary structure determination of the membrane-bound complex cytochrome c nitrite reductase from Desulfovibrio vulgaris Hildenborough.

The cytochrome c nitrite reductase (cNiR) isolated from Desulfovibrio vulgaris Hildenborough is a membrane-bound complex formed of NrfA and NrfH subunits. The catalytic subunit NrfA is a soluble pentahaem cytochrome c that forms a physiological dimer of about 120 kDa. The electron-donor subunit NrfH is a membrane-anchored tetrahaem cytochrome c of about 18 kDa molecular weight and belongs to the NapC/NirT family of quinol dehydrogenases, for which no structures are known. Crystals of the native cNiR membrane complex, solubilized with dodecylmaltoside detergent (DDM), were obtained using PEG 4K as precipitant. Anomalous diffraction data were measured at the Swiss Light Source to 2.3 A resolution. Crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 79.5, b = 256.7, c = 578.2 A. Molecular-replacement and MAD methods were combined to solve the structure. The data presented reveal that D. vulgaris cNiR contains one NrfH subunit per NrfA dimer.

Cell Membrane↗

PubMed2006

Comparative study of ortho- and meta-nitrated inhibitors of catechol-O-methyltransferase: interactions with the active site and regioselectivity of O-methylation.

In this work, we present a comparative case study of "ortho-" and "meta-nitrated" catecholic inhibitors of catechol-O-methyltransferase (COMT), with regard to their interaction with the catalytic site of the enzyme and the in vitro regioselective formation of their mono-O-methyl ether metabolites. In particular, the effects of altering the attachment position of the inhibitors' side-chain substituent, within the classic nitrocatechol pharmacophore, were investigated. For this purpose, we compared two simple regioisomeric nitrocatechol-type inhibitors of COMT, BIA 3-228 and BIA 8-176, which contain the benzoyl substituent attached at the meta and ortho positions, respectively, relative to the nitro group. The two compounds were slowly O-methylated by COMT in vitro, but the particular substitution pattern of each compound was shown to have a profound impact on the regioselectivity of their O-methylation. To provide a plausible interpretation of these results, a comprehensive analysis of the protein-inhibitor interactions and of the relative chemical susceptibility to O-methylation of the catechol hydroxyl groups was performed by means of docking simulations and ab initio molecular orbital calculations. The major structural and chemical factors that determine the enzyme regioselectivity of O-methylation were identified, and the X-ray structure of the complex of COMT with S-adenosyl-l-methionine and BIA 8-176 is herein disclosed. This is the first reported structure of the soluble form of COMT complexed with a nitrocatecholic inhibitor having a bulky substituent group in adjacent position (ortho) to the nitro group. Structural and dynamic aspects of this complex are analyzed and discussed, in the context of the present study.

Animals↗

PubMed2004

Crystallization and preliminary X-ray diffraction studies of a catechol-O-methyltransferase/inhibitor complex.

Inhibitors of the enzyme catechol-O-methyltransferase (COMT) are used as co-adjuvants in the therapy of Parkinson's disease. A recombinant form of the soluble cytosolic COMT from rat has been co-crystallized with a new potent inhibitor, BIA 8-176 [(3,4-dihydroxy-2-nitrophenyl)phenylmethanone], by the vapour-diffusion method using PEG 6K as precipitant. Crystals diffract to 1.6 A resolution on a synchrotron-radiation source and belong to the monoclinic space group P2(1), with unit-cell parameters a = 52.77, b = 79.63, c = 61.54 A, beta = 91.14 degrees.

Animals↗

PubMed2004

Macroporous silicon electrical sensor for DNA hybridization detection.

Macroporous silicon (pore diameter 1-2 microm) was used in an electrical sensor for real time, label free detection of DNA hybridization. Electrical contacts were made exclusively on the back side of the substrate, which allowed complete exposure of the porous layer to DNA. Hybridization of a DNA probe with its complementary sequence produced a reduction in the impedance and a shift in the phase angle resulting from a change in dielectric constant inside the porous matrix and a modification of the depletion layer width in the crystalline silicon structure. The effect of the DNA charge on the response was corroborated using peptide nucleic acid (PNA), an uncharged analog of DNA. The sensitivity and selectivity of the device were characterized and the sensing properties of the porous layer alone were investigated using self-supporting macroporous silicon membranes.

Absorption↗

PubMed2001

Crystallization and preliminary crystallographic characterization of catechol-O-methyltransferase in complex with its cosubstrate and an inhibitor.

Catechol-O-methyltransferase (COMT) is involved in the metabolism of catecholamines, catechol steroids and xenobiotic catechols. A precise knowledge of the enzyme-inhibitor structural interactions could help in the design of better inhibitors. Soluble rat COMT was expressed in Escherichia coli and the recombinant protein was crystallized with a new tight-binding inhibitor, BIA 3-335 [1-(3,4-dihydroxy-5-nitrophenyl)-3-(n-3'-trifluoromethylphenyl)piperazine-1-propanone dihydrochloride]. The crystals were obtained by the sitting-drop vapour-diffusion method using PEG 6K as a precipitant. These crystals diffracted to better than 1.9 A and belong to the trigonal space group P3(2)21. The unit-cell parameters for the crystal measured at room temperature were a = b = 51.5, c = 168.3 A; each shrank by about 1 A on freezing.

Animals↗

PubMed2001

p45(NFE2) is a negative regulator of erythroid proliferation which contributes to the progression of Friend virus-induced erythroleukemias.

In previous studies, we identified a common site of retroviral integration designated Fli-2 in Friend murine leukemia virus (F-MuLV)-induced erythroleukemia cell lines. Insertion of F-MuLV at the Fli-2 locus, which was associated with the loss of the second allele, resulted in the inactivation of the erythroid cell- and megakaryocyte-specific gene p45(NFE2). Frequent disruption of p45(NFE2) due to proviral insertion suggests a role for this transcription factor in the progression of Friend virus-induced erythroleukemias. To assess this possibility, erythroleukemia was induced by F-MuLV in p45(NFE2) mutant mice. Since p45(NFE2) homozygous mice mostly die at birth, erythroleukemia was induced in +/- and +/+ mice. We demonstrate that +/- mice succumb to the disease moderately but significantly faster than +/+ mice. In addition, the spleens of +/- mice were significantly larger than those of +/+ mice. Of the 37 tumors generated from the +/- and +/+ mice, 10 gave rise to cell lines, all of which were derived from +/- mice. Establishment in culture was associated with the loss of the remaining wild-type p45(NFE2) allele in 9 of 10 of these cell lines. The loss of a functional p45(NFE2) in these cell lines was associated with a marked reduction in globin gene expression. Expression of wild-type p45(NFE2) in the nonproducer erythroleukemic cells resulted in reduced cell growth and restored the expression of globin genes. Similarly, the expression of p45(NFE2) in these cells also slows tumor growth in vivo. These results indicate that p45(NFE2) functions as an inhibitor of erythroid cell growth and that perturbation of its expression contributes to the progression of Friend erythroleukemia.

Animals↗

PubMed2000

Biochemical/spectroscopic characterization and preliminary X-ray analysis of a new aldehyde oxidoreductase isolated from Desulfovibrio desulfuricans ATCC 27774.

Aldehyde oxidoreductase (AOR) activity has been found in different sulfate reducing organisms (Moura, J. J. G., and Barata, B. A. S. (1994) in Methods in Enzymology (Peck, H. D., Jr., and LeGall, J., Eds.), Vol. 243, Chap. 4. Academic Press; Romão, M. J., Knäblein, J., Huber, R., and Moura, J. J. G. (1997) Prog. Biophys. Mol. Biol. 68, 121-144). The enzyme was purified to homogeneity from extracts of Desulfovibrio desulfuricans (Dd) ATCC 27774, a sulfate reducer that can use sulfate or nitrate as terminal respiratory substrates. The protein (AORDd) is described as a homodimer (monomer, circa 100 kDa), contains a Mo-MCD pterin, 2 x [2Fe-2S] clusters, and lacks a flavin group. Visible and EPR spectroscopies indicate a close similarity with the AOR purified from Desulfovibrio gigas (Dg) (Barata, B. A. S., LeGall, J., and Moura, J. J. G. (1993) Biochemistry 32, 11559-11568). Activity and substrate specificity for different aldehydes were determined. EPR studies were performed in native and reduced states of the enzyme and after treatment with ethylene glycol and dithiothreitol. The AORDd was crystallized using ammonium sulfate as precipitant and the crystals belong to the space group P6(1)22, with unit cell dimensions a = b = 156.4 and c = 177.1 A. These crystals diffract to beyond 2.5 A resolution and a full data set was measured on a rotating anode generator. The data were used to solve the structure by Patterson Search methods, using the model of AORDg.

Aldehyde Oxidoreductases↗

PubMed2000

Crystallization and preliminary x-ray diffraction analysis of beta-cinnamomin, an elicitin secreted by the phytopathogenic fungus Phytophthora cinnamomin.

Cinnamomin (CIN) belongs to a family of 10 kDa proteins designated as elicitins. Some of these proteins induce a hypersensitive response in diverse plant species, leading to resistance against fungal and bacterial plant pathogens. CIN was crystallized by the vapour-diffusion method using either ammonium sulfate or polyethyleneglycol (PEG) as precipitants in solutions buffered at around pH 7. These crystals are isomorphous and belong to the triclinic space group, with unit-cell parameters a = 31.69, b = 36. 99, c = 44.09 A, alpha = 76.86, beta = 84.41, gamma = 80.26 degrees. A frozen crystal diffracted X-rays beyond 1.45 A resolution on a synchrotron-radiation source.

Algal Proteins↗

PubMed2000

Visual system in a diurnal marsupial, the numbat (Myrmecobius fasciatus): retinal organization, visual acuity and visual fields.

The visual system of the numbat (Myrmecobius fasciatus), a highly endangered diurnal marsupial, has been investigated both anatomically and behaviorally. The ganglion cell layer, examined in cresyl-violet stained wholemounts, contained 832,800 ganglion cells; the number of ganglion cells corresponded to optic axon counts. An area centralis was located in the mid-temporal retina, where cells formed a bilayer, but there was no evidence of a visual streak. Visual acuity, estimated from counts of peak ganglion cell density (8,100/mm(2)) and measurements of posterior nodal distance (7.84 mm), was found to be 6.3 cycles per degree. The value was similar to that of 5.2 cycles per degree estimated by behavioral tests. Sectioned material revealed the presence of numerous oil-droplets in a cone-dominated retina. A rich retinal vasculature of the end-artery type of paired arteries and veins formed beds in the ganglion cell and inner nuclear layers. Measurements of visual fields revealed a binocular overlap of 80 degrees in the horizontal plane, and a total field of view approaching 240 degrees of visual angle. Monitoring of pupillary responses with an infrared video camera showed that the numbat possesses a remarkably wide, static pupil. Our results are discussed in relation to the ecology of the species and its phylogeny.

Animals↗

PubMed1999

The cell-surface proteoglycan Dally regulates Wingless signalling in Drosophila.

Wingless (Wg) is a member of the Wnt family of growth factors, secreted proteins that control proliferation and differentiation during development. Studies in Drosophila have shown that responses to Wg require cell-surface heparan sulphate, a glycosaminoglycan component of proteoglycans. These findings suggest that a cell-surface proteoglycan is a component of a Wg/Wnt receptor complex. We demonstrate here that the protein encoded by the division abnormally delayed (dally) gene is a cell-surface, heparan-sulphate-modified proteoglycan. dally partial loss-of-function mutations compromise Wg-directed events, and disruption of dally function with RNA interference produces phenotypes comparable to those found with RNA interference of wg or frizzled (fz)/Dfz2. Ectopic expression of Dally potentiates Wg signalling without altering levels of Wg and can rescue a wg partial loss-of-function mutant. We also show that dally, a regulator of Decapentaplegic (Dpp) signalling during post-embryonic development, has tissue-specific effects on Wg and Dpp signalling. Dally can therefore differentially influence signalling mediated by two growth factors, and may form a regulatory component of both Wg and Dpp receptor complexes.

Animals↗

PubMed1999

Structural studies by X-ray diffraction on metal substituted desulforedoxin, a rubredoxin-type protein.

Desulforedoxin (Dx), isolated from the sulfate reducing bacterium Desulfovibrio gigas, is a small homodimeric (2 x 36 amino acids) protein. Each subunit contains a high-spin iron atom tetrahedrally bound to four cysteinyl sulfur atoms, a metal center similar to that found in rubredoxin (Rd) type proteins. The simplicity of the active center in Dx and the possibility of replacing the iron by other metals make this protein an attractive case for the crystallographic analysis of metal-substituted derivatives. This study extends the relevance of Dx to the bioinorganic chemistry field and is important to obtain model compounds that can mimic the four sulfur coordination of metals in biology. Metal replacement experiments were carried out by reconstituting the apoprotein with In3+, Ga3+, Cd2+, Hg2+, and Ni2+ salts. The In3+ and Ga3+ derivatives are isomorphous with the iron native protein; whereas Cd2+, Hg2+, and Ni2+ substituted Dx crystallized under different experimental conditions, yielding two additional crystal morphologies; their structures were determined by the molecular replacement method. A comparison of the three-dimensional structures for all metal derivatives shows that the overall secondary and tertiary structures are maintained, while some differences in metal coordination geometry occur, namely, bond lengths and angles of the metal with the sulfur ligands. These data are discussed in terms of the entatic state theory.

Amino Acid Sequence↗

PubMed1998

New information about the skull and dentary of the Miocene platypus Obdurodon dicksoni, and a discussion of ornithorhynchid relationships.

A reconstruction of the skull, dentary and dentition of the middle Miocene ornithorhynchid Obdurodon dicksoni has been made possible by acquisition of nearly complete cranial and dental material. Access to new anatomical work on the living platypus, Ornithorhynchus anatinus, and the present comparative study of the cranial foramina of Ob. dicksoni and Or. anatinus have provided new insights into the evolution of the ornithorhynchid skull. The hypertrophied bill in Ob. dicksoni is seen here as possibly apomorphic, although evidence from ontogenetic studies of Or. anatinus suggests that the basic form of the bill in Ob. dicksoni (where the rostral crura meet at the midline) may be ancestral to the form of the bill in Or. anatinus (where the rostral crura meet at the midline in the embryonic platypus but diverge in the adult). Differences in the relative positions of cranial structures, and in the relationships of certain cranial foramina, indicate that the cranium may have become secondarily shortened in Or. anatinus, possibly evolving from a more elongate skull type such as that of Ob. dicksoni. The plesiomorphic dentary of Ob. dicksoni, with well-developed coronoid and angular processes, contrasts with the dentary of Or. anatinus, in which the processes are almost vestigial, as well as with the dentary of the late Oligocene, congeneric Ob. insignis, in which the angular process appears to be reduced (the coronoid process is missing). In this regard the dentary of Ob. insignis seems to be morphologically closer to Or. anatinus than is the dentary of the younger Ob. dicksoni. Phylogenetic conclusions differ from previous analyses in viewing the northern Australian Ob. dicksoni as possibly derived in possessing a hypertrophied bill and dorsoventrally flattened skull and dentary, perhaps being a specialized branch of the Obdurodon line rather than ancestral to species of Ornithorhynchus. The presence of functional teeth and the robust, flattened skull and dentary in Ob. dicksoni argue for differences in diet and lifestyle between this extinct ornithorhynchid and the living Ornithorhynchus.

Animals↗

PubMed1996

A structure-based catalytic mechanism for the xanthine oxidase family of molybdenum enzymes.

The crystal structure of the xanthine oxidase-related molybdenum-iron protein aldehyde oxido-reductase from the sulfate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas (Mop) was analyzed in its desulfo-, sulfo-, oxidized, reduced, and alcohol-bound forms at 1.8-A resolution. In the sulfo-form the molybdenum molybdopterin cytosine dinucleotide cofactor has a dithiolene-bound fac-[Mo, = O, = S, ---(OH2)] substructure. Bound inhibitory isopropanol in the inner compartment of the substrate binding tunnel is a model for the Michaelis complex of the reaction with aldehydes (H-C = O,-R). The reaction is proposed to proceed by transfer of the molybdenum-bound water molecule as OH- after proton transfer to Glu-869 to the carbonyl carbon of the substrate in concert with hydride transfer to the sulfido group to generate [MoIV, = O, -SH, ---(O-C = O, -R)). Dissociation of the carboxylic acid product may be facilitated by transient binding of Glu-869 to the molybdenum. The metal-bound water is replenished from a chain of internal water molecules. A second alcohol binding site in the spacious outer compartment may cause the strong substrate inhibition observed. This compartment is the putative binding site of large inhibitors of xanthine oxidase.

Aldehyde Oxidoreductases↗

PubMed1995

Crystal structure of the xanthine oxidase-related aldehyde oxido-reductase from D. gigas.

The crystal structure of the aldehyde oxido-reductase (Mop) from the sulfate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas has been determined at 2.25 A resolution by multiple isomorphous replacement and refined. The protein, a homodimer of 907 amino acid residues subunits, is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different [2Fe-2S] centers. It is folded into four domains of which the first two bind the iron sulfur centers and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands.

Aldehyde Oxidoreductases↗

PubMed1995

Crystal structure of desulforedoxin from Desulfovibrio gigas determined at 1.8 A resolution: a novel non-heme iron protein structure.

The crystal structure of desulforedoxin from Desulfovibrio gigas, a new homo-dimeric (2 x 36 amino acids) non-heme iron protein, has been solved by the SIRAS method using the indium-substituted protein as the single derivative. The structure was refined to a crystallographic R-factor of 16.9% at 1.8 A resolution. Native desulforedoxin crystals were grown from either PEG 4K or lithium sulfate, with cell constants a = b = 42.18 A, c = 72.22 A (for crystals grown from PEG 4K), and they belong to space group P3(2)21. The indium-substituted protein crystallized isomorphously under the same conditions. The 2-fold symmetric dimer is firmly hydrogen bonded and folds as an incomplete beta-barrel with the two iron centers placed on opposite poles of the molecule. Each iron atom is coordinated to four cysteinyl residues in a distorted tetrahedral arrangement. Both iron atoms are 16 A apart but connected across the 2-fold axis by 14 covalent bonds along the polypeptide chain plus two hydrogen bonds. Desulforedoxin and rubredoxin share some structural features but show significant differences in terms of metal environment and water structure, which account for the known spectroscopic differences between rubredoxin and desulforedoxin.

Amino Acid Sequence↗

PubMed1995

Extraordinary diphyodonty-related change in dental function for a tooth of the extinct marsupial Ekaltadeta ima (Propleopinae, Hypsiprymnodontidae).

A time-dependent, fundamental change in function for a sectorial tooth in a group of extinct, propleopine kangaroos is reported. In juvenile Ekaltadeta ima (Marsupialia, Hypsiprymnodontidae, Propleopinae) the second premolar (P2) functions as a serrated blade at the anterior end of the cheek tooth row. In adults, this tooth drops far below the occlusal plane of the cheek tooth row where it assumes a completely different function, that of a buttress, anterolingual to the base of the crown of the much larger, newly erupted third premolar (P3). This pattern of diphyodonty-related change in dental function is unique within Mammalia. It also represents an extraordinary example of biological recycling of a normally discarded tooth.

Adaptation, Physiological↗

PubMed1993

Subunit composition, crystallization and preliminary crystallographic studies of the Desulfovibrio gigas aldehyde oxidoreductase containing molybdenum and [2Fe-2S] centers.

The Desulfovibrio gigas aldehyde oxidoreductase contains molybdenum bound to a pterin cofactor and [2Fe-2S] centers. The enzyme was characterized by SDS/PAGE, gel-filtration and analytical ultracentrifugation experiments. It was crystallized at 4 degrees C, pH 7.2, using isopropanol and MgCl2 as precipitants. The crystals diffract beyond 0.3-nm (3.0-A) resolution and belong to space group P6(1)22 or its enantiomorph, with cell dimensions a = b = 14.45 nm and c = 16.32 nm. There is one subunit/asymmetric unit which gives a packing density of 2.5 x 10(-3) nm3/Da (2.5 A3/Da), consistent with the experimental crystal density, rho = 1.14 g/cm3. One dimer (approximately 2 x 100 kDa) is located on a crystallographic twofold axis.

Aldehyde Oxidoreductases↗

PubMed1991

Bruxism.

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Bruxism↗