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Query: UNIPROT:P06889 (Mol)
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Semiempirical molecular orbital calculations (by modified neglect of diatomic overlap method) were performed on diol epoxide metabolites of five polycyclic aromatic hydrocarbons (PAHs)--benzene, naphthalene, phenanthrene, chrysene, and benzo[a]pyrene (BP)--to gain insight into the various carcinogenic potencies of these compounds. Opening of the epoxide rings of the diol epoxides was calculated to be exothermic for all of the PAHs investigated. The bay-region diol epoxides of BP were calculated to open spontaneously to the triol carbonium ion upon protonation. For the bay-region trans- and cis-diequatorial diol epoxides of 5-methylchrysene the methyl group destabilized the epoxide. These results suggest that the conformation of the saturated, angular benzo-ring is important in determining bay-region epoxide stability. Conformational flexibility of the aromatic ring system is offered as one reason for partial stabilizing of bay-region epoxides. These results also suggest that the existence and potentiation of PAH carcinogenicity is correlated with the lack of stability of the bay-region epoxide ring. Considerations of thermochemical stability have value in predictions of carcinogenic potency.
Mol Pharmacol 1982 Sep
PMID:Molecular orbital studies of epoxide stability of carcinogenic polycyclic aromatic hydrocarbon diol epoxides. 714 38

We propose a new model for the segmental flexibility of immunoglobulin G (IgG). The flexibility of native and mildly reduced anti-5-(dimethylamino)naphthalene-1-sulfonyl (anti-dansyl) antibody was reexamined by nanosecond fluorescence spectroscopy using deconvolution and lamp-shift corrections. The rabbit antibodies used for this study were purified of dimers and other aggregates. The original results indicated that the decay of fluorescence anisotropy involved two rotational correlation times. It was suggested that the short rotational correlation time, phi s, represented a flexible Fab arm motion over a restricted angle and that the long correlation time, phi L, represented global tumbling of the molecule [Yguerabide, J., Epstein, H. F., & Stryer, L. (1970) J. Mol. Biol. 51, 573--590]. Our new data indicate that the long correlation time primarily represents motions of the Fab segments and not global tumbling of the entire molecule. This interpretation implies a more flexible model for IgG. Thus, in solution the antibody arms appear to move over a wide angle and are not restricted to 33 degrees as was suggested in the earlier model. Simple diffusion calculations and other evidence suggest that phi s may represent V-module flexibility about the switch peptides or Fab twisting around its long axis, whereas phi L may represent wagging or wobbling motions of the Fab arms about the hinge region. The faster motions appear to occur over small angles whereas the slower wagging or wobbling motions responsible for most of the decay of anisotropy appear to be much less restricted. The biological function of IgG and anisotropy changes resulting from hinge disulfide cleavage are interpreted in terms of the proposed model. We also demonstrate a useful method for comparison of time-dependent and steady-state fluorescence polarization data.
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PMID:Segmental flexibility of immunoglobulin G antibody molecules in solution: a new interpretation. 731 58

In the present study we have utilized comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship paradigm, to explore the physico-chemical requirements for binding to the Ah (dioxin) receptor. Recent developments by Gillner et al. [(1993) Mol. Pharmacol. 44, 336-345] prompted us to review and revise our previous CoMFA/QSAR model [Waller, C. L., and McKinney, J. D. (1992) J. Med. Chem. 36, 3660-3666] to include a structurally-diverse training set of Ah receptor ligands ranging in size from naphthalene to indolo[3,2-b]carbazole nuclei. An exhaustive validation process utilizing external test sets and hierarchical cluster analysis routines was employed during model construction and is discussed herein. The limitations of the approach presented herein are discussed with respect to predictive ability of the CoMFA/QSAR models, which is demonstrated to be dependent on a balance between structural diversity and redundancy in the molecules comprising the training set. The results of our modified CoMFA/QSAR model are consistent with and unify all previously established structure-activity relationships established for less structurally-diverse training sets of Ah receptor ligands. As a result of the more complete nature of the series of molecules under examination in the present study, the CoMFA/QSAR steric and electrostatic field contour plots as well as the essential and excluded volume plots provide for a more detailed characterization of the molecular binding domain of the Ah receptor. The implications of the CoMFA/QSAR model presented herein are explored with respect to quantitative hazard identification of potential toxicants.
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PMID:Three-dimensional quantitative structure-activity relationships of dioxins and dioxin-like compounds: model validation and Ah receptor characterization. 749 34

The octopine synthase (ocs or ocs-like) element has been previously reported to be responsive to the plant hormones, auxin, salicylic acid, and methyl jasmonate. Using transient assays with carrot protoplasts, we have demonstrated that an ocs element from the soybean auxin-inducible GH2/4 promoter is not only activated by strong auxins (i.e., 2,4-dichlorophenoxyacetic acid, 2,4,5-trichlorophenoxyacetic acid, alpha-naphthalene acetic acid) and salicylic acid, but also by weak auxin analogues (beta-naphthalene acetic acid), inactive auxin analogs (i.e., 2,3-dichlorophenoxyacetic acid, 2,4,6-trichlorophenoxyacetic acid), and inactive salicylic acid analogs (3-hydroxybenzoic acid and 4-hydroxybenzoic acid). Our results indicate that the ocs element in the GH2/4 promoter is not selectively induced by plant hormones and might function similarly to tandem AP-1 sites in some animal glutathione S-transferase (GST) genes. The ocs element, like the AP-1 sites in animal GST promoters, may be induced not only by certain hormones but also by some non-hormonal stress-inducing or electrophilic agents.
Plant Mol Biol 1994 Nov
PMID:The ocs element in the soybean GH2/4 promoter is activated by both active and inactive auxin and salicylic acid analogues. 781 65

Parenteral administration of naphthalene produces a dose-dependent and tissue-, species-, and cell-selective lesion of murine Clara cells. The rate and stereoselectivity of naphthalene metabolism by microsomal preparations correlate with tissue and species differences in cytotoxicity. Because earlier studies used microsomes obtained from whole tissue, differences in susceptibility of proximal and distal airways could not be related to differences in the metabolic activation or detoxication of naphthalene. Specific subcompartments of the respiratory system, obtained by microdissection, have been used to study the cytochrome P450-dependent metabolism of naphthalene and the epoxide hydrolase/glutathione transferase-dependent metabolism of naphthalene oxide. The rates of naphthalene metabolism were substantially higher in mouse airways than in comparable airways of hamsters or rats. Rates of metabolism were higher in distal airways than in the trachea of all species studied. Metabolism in mouse airways was highly stereoselective, whereas that in hamster and rat tissues was not. Nonciliated cells at all airway levels in mice were heavily labeled with an antibody to cytochrome P450 2F2; little labeling was observed in any portion of rat and hamster lungs. Postmitochondrial supernatants prepared from mouse and hamster airways metabolized racemic naphthalene oxide to diol and glutathione adducts at substantially higher rates than did comparable preparations from rats. Although glutathione levels varied 2-4-fold at different airway levels in the three species studied, levels at the most susceptible site (mouse distal bronchioles) were as high as or higher than those at other, less susceptible, sites. These studies support the view that the rate and stereoselectivity of naphthalene metabolism to naphthalene 1R,2S-oxide catalyzed by cytochrome P450 2F2 are critical determinants in the species-specific and region-selective cytotoxicity of naphthalene in mice. The lack of major differences in the catalytic activity or enantioselectivity of putative detoxication enzymes (epoxide hydrolase or glutathione transferases) between mouse and hamster tissue, combined with data showing that the differences in the metabolic fate of naphthalene oxide in proximal versus distal airways are not dramatic, suggests that the initial epoxidation of naphthalene is an important factor in site-selective toxicity. These studies support the need to use tissue from defined airway levels for studies on the relationship of biochemical and metabolic factors important in cellular injury by lung toxicants, such as naphthalene, where there are dramatic regional differences in susceptibility to injury within the respiratory system.
Mol Pharmacol 1995 Jan
PMID:Relationship of cytochrome P450 activity to Clara cell cytotoxicity. IV. Metabolism of naphthalene and naphthalene oxide in microdissected airways from mice, rats, and hamsters. 783 35

The study of the temperature effect on the binding to the active site of human alpha-thrombin for ten different ligands, i.e. nine peptide substrates and the tight binding inhibitor N alpha -(naphthalene-sulphonyl-glycyl)-4-amidino-DL-phenyl-alanine-piperidine (alpha-NAPAP), showed that the enthalpy is constant over the temperature range spanning from 10 to 40 degrees C. It was found that the values of the binding enthalpy are linearly correlated to those of entropy, and that this correlation arises from a real phenomenon of chemical compensation. On the other hand, no compensatory chemical effect was found for the process of thrombin acylation. Additional experiments showed that binding to thrombin of two competitive thrombin inhibitors, i.e. proflavin and p-aminobenzamidine, is characterized by a change in the standard heat capacity change (delta Cp), approximately equal to -1 kcal/mol K. By analogy with model compound transfer studies and protein folding investigations, it is proposed that a burial of a large surface area of non-polar residues, roughly equal to 3000 A2, brings about the observed heat capacity change. Altogether, the observed phenomena of the chemical compensation and heat capacity change, although qualitatively different, are interpreted as expressions of the same property of the enzyme, i.e. the capacity to undergo conformational transitions upon ligation of the catalytic domain. These structural transitions are strictly ligand-linked and could play a central role for setting the rules which regulate the specificity of substrates and inhibitors binding to the catalytic groove of human alpha-thrombin.
J Mol Biol 1994 Jun 17
PMID:Thermodynamics of substrates and reversible inhibitors binding to the active site cleft of human alpha-thrombin. 800 69

The frequency of lateral root initiation in tomato (Lycopersicon esculentum Mill cv. VFN8) seedling roots is increased over eightfold in response to 1.6 microM alpha-naphthalene-acetic acid (NAA). To identify genes that are activated during lateral root initiation, a cDNA library was made with RNA from roots treated with auxin and differentially screened with radioactive probes made from RNA isolated from treated and untreated roots. A cDNA clone, TR132, was identified that hybridized to a transcript that was induced within 4 h of auxin treatment and increased tenfold by 72 h. A gene (RSI-1) corresponding to the TR132 cDNA was cloned and characterized with regard to its nucleotide sequence, transcription start site and chromosomal map position. Approximately 1 kb of the 5' flanking DNA was linked to the beta-glucuronidase (GUS) protein coding region and tested for expression in transgenic tomato seedlings. GUS activity was observed in both lateral and adventitious root initials, including very early initials, and persisted until shortly after the lateral emerged from the parent tissue. In roots from seedlings with high activity, GUS expression was also observed in the root cap and vascular tissue. The predicted RSI-1 protein is rich in cysteine, lysine and proline, and includes an N-terminal region with characteristics of a signal peptide. The putative mature protein exhibits 79% amino acid identity to a protein encoded by a gene (GAST1) that is induced by gibberellic acid in tomato shoots.
Mol Gen Genet 1994 Apr
PMID:A molecular marker for lateral root initiation: the RSI-1 gene of tomato (Lycopersicon esculentum Mill) is activated in early lateral root primordia. 817 11

Nonciliated bronchiolar epithelial (Clara) cells of mice are highly susceptible to toxicants that undergo metabolic activation, presumably because this cell type expresses high levels of cytochrome P450 monooxygenases. To establish the capability of these cells to metabolize an agent that causes Clara cell-selective toxicity in vivo, we evaluated the metabolism of naphthalene in isolated cells under two distinct conditions, i.e., in homogenized cell preparations supplemented with glutathione and glutathione S-transferases and in intact cells. In homogenized cell preparations naphthalene was metabolized to dihydrodiol (minor) and a single glutathione adduct (major) derived from the 1R,2S-epoxide. In intact cells the rate of formation of glutathione adduct was much lower and dihydrodiol predominated. Approximately 3-10% of racemic naphthalene oxide added to isolated homogenized cells was converted to glutathione adducts and dihydrodiol in 3-min incubations. At high concentrations of naphthalene oxide (0.25 and 0.5 mM), formation of the adduct derived from the 1R,2s-epoxide was favored. The intracellular glutathione concentration, measured by high performance liquid chromatography as the fluorescence of the monobromobimane-glutathione derivative, was 1.14 +/- 0.13 nmol/10(6) cells. To determine whether Clara cell injury results from cytotoxic metabolites of naphthalene, we assessed viability of intact cells in response to different concentrations of naphthalene and naphthalene metabolites. At high naphthalene concentrations (0.5 and 1.0 mM) cell viability decreased to 63% or less of control, whereas lower concentrations (0.1 or 0.05 mM) did not alter viability significantly. Naphthalene-induced decreases in cell viability were blocked by preincubation of Clara cells with the cytochrome P450 monooxygenase inhibitor piperonyl butoxide. The cytotoxicity of naphthalene metabolites varied. Incubation of cells with 0.5 mM dihydrodiol, 1-naphthol, or 1,2-naphthoquinone decreased cell viability to an extent similar to that produced by 0.5 mM naphthalene. In contrast, 0.5 mM naphthalene oxide and 1,4-naphthoquinone significantly decreased viability more than the parent compound. Preincubation of Clara cells with piperonyl butoxide did not affect the loss in cell viability associated with naphthalene oxide. We conclude that isolated Clara cells 1) are capable of metabolizing naphthalene, a Clara cell-specific cytotoxicant, to two major metabolites, 2) have a detectable intracellular glutathione pool, and 3) are more susceptible to specific naphthalene metabolites than to the parent compound naphthalene.
Mol Pharmacol 1994 Apr
PMID:Metabolism and cytotoxicity of naphthalene and its metabolites in isolated murine Clara cells. 818 45

Magnaporthe grisea are pathogenic, directly penetrating fungi which cause rice blast disease. Isolated, non-pathogenic mutant strains which are defective in the biosynthesis of dihydroxynapthalene-derived melanin fail to infect host plants and have been shown to lack certain key enzymes in melanin biosynthesis. One such enzyme is scytalone dehydratase that converts scytalone to 1,3,8-trihydroxy-naphthalene. Crystallization trials of scytalone dehydratase were undertaken with the expectation that structural information on this enzyme would facilitate design of high affinity inhibitors which might find use in the control of rice blast disease. We now report that recombinant scytalone dehydratase, complexed with a tight binding inhibitor, has been crystallized with PEG 4000 as a precipitant. The crystals are trigonal and belong to the space group P321 with the cell dimension: a = b = 75.5 A, c = 73.8 A. The observed diffraction extends to 2.5 A. Analysis of the packing in the cell suggests that scytalone dehydratase forms a symmetric trimer. These results are consistent with sedimentation equilibrium experiments indicating that the solution aggregation state of scytalone dehydratase was trimeric over a 24,000-fold concentration range.
J Mol Biol 1993 Aug 05
PMID:Preliminary crystallographic studies on scytalone dehydratase from Magnaporthe grisea. 835 86

TOL plasmid pWW0 from Pseudomonas putida mt-2 encodes catabolic enzymes required for the oxidation of toluene and xylenes. The structural genes for these catabolic enzymes are clustered into two operons, the xylCMABN operon, which encodes a set of enzymes required for the transformation of toluene/xylenes to benzoate/toluates, and the xylXYZLTEGFJQKIH operon, which encodes a set of enzymes required for the transformation of benzoate/toluates to Krebs cycle intermediates. The latter operon can be divided physically and functionally into two parts, the xylXYZL cluster, which is involved in the transformation of benzoate/toluates to (methyl)catechols, and the xylTEGFJQKIH cluster, which is involved in the transformation of (methyl)catechols to Krebs cycle intermediates. Genes isofunctional to xylXYZL are present in Acinetobacter calcoaceticus, and constitute a benzoate-degradative pathway, while xylTEGFJQKIH homologous encoding enzymes of a methylphenol-degradative pathway and a naphthalene-degradative pathway are present on plasmid pVI150 from P. putida CF600, and on plasmid NAH7 from P. putida PpG7, respectively. Comparison of the nucleotide sequences of the xylXYZLTEGFJQKIH genes with other isofunctional genes suggested that the xylTEGFJQKIH genes on the TOL plasmid diverged from these homologues 20 to 50 million years ago, while the xylXYZL genes diverged from the A. calcoaceticus homologues 100 to 200 million years ago. In codons where amino acids are not conserved, the substitutions rate in the third base was higher than that in synonymous codons. This result was interpreted as indicating that both single and multiple nucleotide substitutions contributed to the amino acid-substituting mutations, and hence to enzyme evolution. This observation seems to be general because mammalian globin genes exhibit the same tendency.
Mol Gen Genet 1993 May
PMID:Comparison of the nucleotide sequences of the meta-cleavage pathway genes of TOL plasmid pWW0 from Pseudomonas putida with other meta-cleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution. 851 Jun 67


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