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At least 955 records · Page 53Linked to original sources
PubMed2002

GC/MS evaluation of thyme (Thymus vulgaris L.) oil composition and variations during the vegetative cycle.

Capillary GC/MS analysis based on polar and non-polar columns has been applied to evaluation of the volatile oils hydrodistilled from thyme (Thymus vulgaris L.) plants. The adopted methodology has been used to monitor seasonal variations in the composition of the oil obtained from thyme herbs harvested at different periods during the plant vegetative and life cycles. Oils from thyme plants of young (2 years) and old (5 years) cultivations have been evaluated from four and two collections, respectively, effected throughout May/December growth period. Generally, the oil was found to be rich in the active monoterpene phenols (thymol and carvacrol) and their corresponding monoterpene hydrocarbon (HC) precursors (p-cymene and gamma-terpinene), which collectively showed synchronized patterns of variation during the different collection periods and in different seasons. The oil from old plant collected in May/June period (0.15% v/w) was characterized by significantly lower levels of monoterpene HCs (mainly gamma-terpinene) and the highest levels of the oxygenated monoterpenes (linalool and borneol), monoterpene phenols (mainly thymol) and their derivatives (mainly carvacrol methyl ether), sesquiterpenes (mainly beta-caryophyllene) and their oxygenated derivatives (e.g. caryophyllene oxide) in comparison with all other samples. A characteristic presence of camphor and thymodihydroquinone was also observed in the old plant oils. On the other hand, the young plant, collected in June/July just before the end of the vegetative cycle, provided the best oil yield (1.2%) with also the highest % content of the monoterpene phenols (thymol: 51.2% and carvacrol: 4%). This latter growth period can represent the best harvest time of young thyme plants in order to obtain an essential oil with better quality and quantity.

Gas Chromatography-Mass Spectrometry↗
PubMed2000

Toxicity of cinnamomin--a new type II ribosome-inactivating protein to bollworm and mosquito.

The toxicity of cinnamomin, a new type II ribosome-inactivating protein purified from the seeds of camphor tree (Cinnamomum camphora), to bollworm (Helicoverpa armigera) and mosquito (Culex pipines pallens) during larval stage was tested. The LC50 of cinnamomin to bollworm larvae fed on diet containing cinnamomin was 1839 ppm and the LC50 to larvae of mosquito was 168 ppm. The gut extract of bollworm larvae could apparently hydrolyze cinnamomin. The inhibition of protein synthesis by cinnamomin was tested in in vitro translation system of bollworm larvae, and its LC50 was determined to be approx. 14 nM. Bollworm larvae ribosome treated with cinnamomin produced a specific RNA fragment (R-fragment) characterized on urea-denatured polyacrylamide gel. Evidence was provided that hidden breaks exist in the largest ribosomal RNA of bollworm larvae.

Algal Proteins↗
PubMed1997

The synthesis of (R)-(+)-lipoic acid using a monooxygenase-catalysed biotransformation as the key step.

2-(2-Acetoxyethyl)cyclohexanone (4) was converted into the lactone (-)-(5) regio- and enantioselectively using 2-oxo-delta 3-4,5,5-trimethylcyclopentenyl acetyl-CoA monooxygenase, an NADPH-dependent Baeyer-Villiger monooxygenase from camphor grown Pseudomonas putida NCIMB 10007. The lactone (-)-(5) was converted into (R)-(+)-lipoic acid in six steps. In contrast cyclopentanone monooxygenase, an NADPH-dependent Baeyer-Villiger monooxygenase from cyclopentanol-grown Pseudomonas sp. NCIMB 9872 selectively oxidized the (S)-enantiomer of the ketone (4) giving better access to optically enriched, naturally occurring lipoic acid.

Biotransformation↗
PubMed2004

Fungi in endodontic infections.

Fungi are chemoorganotroph eukaryotic microorganisms that can take part in endodontic infections and thereby may participate in the etiology of periradicular diseases. They possess virulence attributes--including adaptability to a variety of environmental conditions, adhesion to a variety of surfaces, the production of hydrolytic enzymes, morphologic transition, biofilm formation, and evasion and immunomodulation of the host defense--that may play a role in the pathogenesis of periradicular diseases. Fungi have occasionally been found in primary root canal infections, but they seem to occur more often in the root canals of obturated teeth in which treatment has failed. Candida albicans is by far the fungal species most commonly isolated from infected root canals, and this species has been considered a dentinophilic microorganism because of its invasive affinity to dentin. C albicans has also been discovered to be resistant to some intracanal medicaments, such as calcium hydroxide. Its ability to invade dentinal tubules and resistance to commonly used intracanal medicaments may help to explain why C albicans has been associated with cases of persistent root canal infections. Some medicaments, such as chlorhexidine digluconate, calcium hydroxide combinations (with camphorated paramonochlorophenol or chlorhexidine), and EDTA, have the potential to be used as effective intracanal medications for patients in whom fungal infection is suspected.

Candida albicans↗
PubMed2003

Cinnamomin: a multifunctional type II ribosome-inactivating protein.

Plant ribosome-inactivating proteins (RIPs) are a group of toxic proteins that can irreversibly inactivate ribosomes by specifically removing the conserved adenine base from the "Sarcin/Ricin domain" of the 28S RNA in ribosome. Cinnamomin is a novel type II RIP isolated in our laboratory from the mature seeds of camphor tree. Besides site-specific deadenylation of the A4324 in the Sarcin/Ricin domain of rat ribosome, this protein could also release the adenine base from DNA molecules at multiple sites and from AMP, ADP, dAMP and adenosine. Furthermore, cinnamomin displays cytotoxicity to carcinoma cells and insect larvae by modifying their ribosomal RNA. These functions possessed by cinnamomin shed a new light on the possible application of cinnamomin in the field of immunotoxin design and transgenic reagents. In this review, we introduce the major recent results on cinnamomin obtained in our laboratory, including purification of this protein, characterization of its enzymatic mechanism, structure and function, gene pattern, physiological role and its biological implications in cytotoxicity.

Algal Proteins↗
PubMed1999

Effective use of molecular recognition in gas sensing: results from acoustic wave and in situ FT-IR measurements.

To probe directly the analyte/film interactions that characterize molecular recognition in gas sensors, we recorded changes to the in situ surface vibrational spectra of specifically functionalized surface acoustic wave (SAW) devices concurrently with analyte exposure and SAW measurement of the extent of sorption. Fourier transform infrared external-reflectance spectra (FT-IR-ERS) were collected from operating 97-MHz SAW delay lines during exposure to a range of analytes as they interacted with thin-film coatings previously shown to be selective: cyclodextrins for chiral recognition, nickel camphorates for Lewis bases such as pyridine or organophosphonates, and phthalocyanines for aromatic compounds. In most cases where specific chemical interactions--metal coordination, "cage" compound inclusion, or pi-stacking--were expected, analyte dosing caused distinctive changes in the IR spectra, together with anomalously large SAW sensor responses. In contrast, control experiments involving the physisorption of the same analytes by conventional organic polymers did not cause similar changes in the IR spectra, and the SAW responses were smaller. For a given conventional polymer, the partition coefficients (or SAW sensor signals) roughly followed the analyte fraction of saturation vapor pressure. These SAW/FT-IR results support earlier conclusions derived from thickness-shear mode resonator data.

Acoustics↗
PubMed1994

Kinetics and thermodynamics of CO binding to cytochrome P450nor.

The CO-binding reaction of cytochrome P450nor isolated from denitrifying fungus, Fusarium oxysporum, has been studied by using a flash photolysis method in the millisecond time domain. We obtained the CO on- and off-rate constants in the bimolecular reaction, and determined the activation free energy, enthalpy, and entropy from the temperature dependence of these rate constants. To discuss the structural characteristics of P450nor, these parameters were compared with those of other cytochrome P450s, such as cytochrome P450cam from Pseudomonas putida and myoglobin. The on-rate constant (k(on)) for P450nor is larger than those of camphor-bound P450cam [P450cam(+)], suggesting that ligand entry to the heme pocket of P450nor is sterically less restricted than that of P450cam(+). In the P450norCO complex, the IR stretching band of the iron-bound CO is observed at 1942 cm-1, which is the same position as in P450cam(+)CO. This result suggests that the heme pocket immediate to the ligand-binding site is the same size in the two enzymes, in good agreement with the observation that the equilibrium constant (K = k(on)/k(off)) is identical in P450nor and P450cam(+). On the other hand, the entropy changes in the equilibrium and the off-activation processes are smaller in P450nor than in P450cam(+). This feature could reflect the lack of a bound substrate at the active site of P450nor. These structural characteristics of P450nor are discussed in relation to its unique catalytic property, rapid NO reduction to yield N2O.

Carbon Monoxide↗
PubMed1991

1H NMR identification of a beta-sheet structure and description of folding topology in putidaredoxin.

Putidaredoxin (Pdx), a 106-residue globular protein consisting of a single polypeptide chain and a [2Fe-2S] cluster, is the physiological reductant of P-450cam, which in turn catalyzes the monohydroxylation of camphor by molecular oxygen. No crystal structure has been obtained for Pdx or for any closely homologous protein. The application of two-dimensional 1H NMR methods to the problem of structure determination in Pdx is reported. A beta-sheet consisting of five short strands and one beta-turn has been identified from distinctive nuclear Overhauser effect patterns. All of the backbone resonances and a majority of the side-chain resonances corresponding to protons in the beta-sheet have been assigned sequence specifically. The sheet contains one parallel and three antiparallel strand orientations. Hydrophobic side chains in the beta-sheet face primarily toward the protein interior, except for a group of three valine side chains that are apparently solvent exposed. The potential significance of this "hydrophobic patch" in terms of biological activity is discussed. The folding topology, as determined by the constraints of the beta-sheet, is compared with that of other [2Fe-2S] proteins for which folding topologies are known.

Amino Acid Sequence↗
PubMed1983

Steroid 21-hydroxylase (cytochrome P-450) from porcine adrenocortical microsomes: microsequence analysis of cysteine-containing peptides.

The steroid 21-hydroxylase cytochrome P-450 from porcine adrenocortical microsomes was purified to homogeneity. The protein exhibited two NH2-terminal sequences, one of which was identical with the first but lacking the NH2-terminal methionine. The sequence was extremely hydrophobic but had little homology to the 17 alpha-hydroxylase/C17,20-lyase isolated from neonatal porcine testes or to rat or rabbit liver microsomal cytochromes P-450. The cysteine-containing fragments of the S-carboxymethylated protein were purified by high-performance liquid chromatography and sequenced. Three of the cysteine-containing peptides exhibited significant sequence homology with peptides from the major phenobarbital-induced rat liver cytochrome P-450 (P-450b) and two with peptides from cytochrome P-450cam (camphor methylene hydroxylase from Pseudomonas putida). The presence of conserved regions in the primary sequences of these proteins appears likely to provide clues to the nature of their heme-binding domains.

Adrenal Cortex↗
PubMed2001

Redox-dependent conformational selection in a Cys4Fe2S2 ferredoxin.

Putidaredoxin (Pdx), a Cys4Fe2S2 ferredoxin from Pseudomonas putida, exhibits redox-dependent binding to its physiological redox partner, cytochrome P450(cam) (CYP101), with the reduced form of Pdx (Pdx(r)) binding with greater affinity to oxidized camphor-bound CYP101 than the oxidized form, Pdx(o). It has been previously shown that Pdx(o) is more dynamic than Pdx(r) on all accessible time scales, and it has been proposed that Pdx(r) samples only a fraction of the conformational substates populated by Pdx(o) on a time average. It is postulated that the ensemble subset populated by Pdx(r) is the same subset that binds CYP101, providing a mechanism for coupling the Pdx oxidation state to binding affinity for CYP101. Evidence from a variety of sources, including redox-dependent shifts of 15N and 13C resonances, indicates that the metal cluster binding loop of Pdx is the primary determinant of redox-dependent conformational selection. Patterns of paramagnetic effects suggest that the metal cluster binding loop contracts around the metal cluster upon reduction, possibly due to the strengthening of hydrogen bonds between the sulfur atoms of the metal cluster and the surrounding polypeptide NH and OH groups. Effects of this perturbation are then transmitted mechanically to other affected regions of the protein. A specific mutation has been introduced into the metal binding loop of Pdx, G40N, that slows conformational exchange sufficiently that the ensemble of conformational substates in Pdx(o) are directly observable as severe broadenings or splittings in affected NMR resonances. Many of the residues most affected by the mutation also show significant exchange contributions to 15N T(2) relaxation in wild-type Pdx(o). As predicted, G40N Pdx(r) shows a collapse of many of these multiplets and broadened lines to form much sharper resonances that are essentially identical to those observed in wild-type Pdx(r), indicating that Pdx(r) occupies fewer conformational substates than does Pdx(o). This is the first direct observation of such redox-dependent ensembles at slow exchange on the chemical shift time scale. These results confirm that conformational selection within the Fe2S2 cluster binding loop is the primary source of redox-dependent changes in protein dynamics in Pdx.

Amino Acid Sequence↗
PubMed1985

Tyrosine motions in relation to the ferric spin equilibrium of cytochrome P-450cam.

Second derivative spectroscopy was used to determine the percentage of tyrosine residues that are exposed to solvent in cytochrome P-450cam isolated from Pseudomonas putida. The ratio between two peak to trough second derivative absorbance differences has been shown to be dependent on the polarity of the microenvironment surrounding tyrosine residues [Ragone, R., Colonana, G., Balestrieri, C., Servillo, L., & Irace, G. (1984) Biochemistry 23, 1871]. With a number of camphor analogues that independently vary the spin equilibrium of the ferric cytochrome P-450 cam, experiments have demonstrated that the percentage of tyrosine residues exposed to solvent is linearly dependent on the percentage of ferric high-spin species present. This is not simply a function of the extent of substrate binding since in all cases the substrate concentration was sufficient to ensure saturation of the cytochrome. The local microenvironment of approximately one tyrosine residue appears to be linearly correlated with the percentage of ferric high-spin cytochrome. Structural studies of cytochrome P-450cam using small-angle X-ray scattering [Lewis, B. A., & Sligar, S. G. (1983) J. Biol. Chem. 258, 3599] and high-pressure difference spectroscopy [Fisher, M. T., Scarlata, S. F., & Sligar, S. G. (1985) Arch. Biochem. Biophys. 240, 456] imply that global conformational changes linked to the spin equilibria are small. Together with the data reported herein, these results suggest that one tyrosine residue is involved in a conformational change that is directly linked with the spin equilibrium.

Cytochrome P-450 Enzyme System↗
PubMed1986

Thermodynamic properties of oxidation-reduction reactions of bacterial, microsomal, and mitochondrial cytochromes P-450: an entropy-enthalpy compensation effect.

An optically transparent thin-layer electrode cell with a very small volume was used for determination of the formal reduction potentials of bacterial, microsomal, and mitochondrial cytochromes P-450. At an extrapolated zero concentration of dye, the bacterial cytochrome from Pseudomonas putida catalyzing the hydroxylation of camphor and the adrenal mitochondrial cytochrome catalyzing the cholesterol side-chain cleavage reaction had formal reduction potentials of -168 and -285 mV (pH 7.5 and 25 degrees C), respectively. The oxidation-reduction potentials for the rabbit liver microsomal cytochrome P-450 induced by 3-methylcholanthrene and the mitochondrial cytochrome for steroid 11 beta-hydroxylation were found as -360 and -286 mV, respectively. Potential measurements at different temperatures allowed documentation of the standard thermodynamic parameters for cytochrome P-450 reduction for the first time. All cytochromes tested were found to have a relatively large negative entropy change upon reduction. The extent of these changes is comparable to that observed for the ferric-ferrous couple of cytochrome c. An entropy-enthalpy compensation effect was observed among the four cytochromes P-450 examined although the correlation is weaker than that observed with cytochrome c isolated from various sources.

Adrenal Cortex↗
PubMed2005

Redox-dependent structural differences in putidaredoxin derived from homologous structure refinement via residual dipolar couplings.

Structural differences in the [2Fe-2S] ferredoxin, putidaredoxin (Pdx), from the camphor hydroxylation pathway of Pseudomonas putida have been investigated as a function of oxidation state of the iron cluster. Pdx is involved in biological electron transfer to cytochrome P450(cam) (CYP101). Redox-dependent differences have been observed previously for Pdx in terms of binding affinities to CYP101, NMR spectral differences, and dynamic properties. To further characterize these differences, structure refinement of both oxidized and reduced Pdx has been carried out using a hybrid approach utilizing paramagnetic distance restraints and NMR orientational restraints in the form of backbone (15)N residual dipolar couplings. Use of these new restraints has improved the structure of oxidized Pdx considerably over the earlier solution NMR structure without RDC restraints, with the new structure now much closer in overall fold to the recently published X-ray crystal structures. We now observe better defined relative orientations of the major secondary structure elements as also of the conformation of the metal binding loop region. Extension of this approach to structure calculation of reduced Pdx has identified structural differences that are primarily localized for residues in the C-terminal interaction domain consisting of the functionally important residue Trp 106 and regions near the metal binding loop in Pdx. These redox-dependent structural differences in Pdx correlate to dynamic changes observed before and may be linked to differences in binding and electron transfer properties between oxidized and reduced Pdx.

Crystallography, X-Ray↗
PubMed1997

Flexibility of liver alcohol dehydrogenase in stereoselective binding of 3-butylthiolane 1-oxides.

Thiolane 1-oxides are analogs of the carbonyl substrates that bind to the alcohol dehydrogenase-NADH complex and are potent uncompetitive inhibitors against alcohol [Chadha, V. K., et al. (1985) J. Med. Chem. 28, 36-40]. The four stereoisomers of 3-butylthiolane 1-oxide (BTO) were separated by chiral phase chromatography. CD and 1H-NMR spectra identified the enantiomeric pairs. 1H-NMR chemical shifts were assigned on the basis of COSY spectra of both diastereoisomers and confirmed by HMQC spectra. Coupling constants were determined through one-dimensional decoupling experiments. NMR with chiral shift reagents, Eu(hfc)3 [europium tris [3-[(heptafluoropropyl)hydroxymethylene]-(+)-camphorate]] or (R)-(-)-N-(3,5-dinitrobenzoyl)-alpha-methylbenzylamine, determined that the most inhibitory isomer is either 1S,3R or 1R,3S. The chemical shifts of protons in the thiolane 1-oxide ring were influenced by the whole structure and were not correlated with the computed Mulliken charges. X-ray crystallography at 2.1 and 1.66 A resolution of the ternary enzyme complexes with NADH demonstrated that the absolute configuration of the most inhibitory (Kii = 0.31 microM) stereoisomer is 1S,3R and the next best inhibitor (Kii = 0.73 microM) is 1S,3S. The thiolane 1-oxide rings bind in the same position, in the substrate binding site, but the geometry of the complexes suggests that the sulfoxides are not transition state analogs. Significantly, the butyl groups of the two isomers are accommodated differently by flexible amino acid side chains adopting alternative rotameric conformations.

Alcohol Dehydrogenase↗
PubMed1999

A model for the solution structure of oxidized terpredoxin, a Fe2S2 ferredoxin from Pseudomonas.

Terpredoxin (Tdx) is a 105-residue bacterial ferredoxin consisting of a single polypeptide chain and a single Fe2S2 prosthetic group. Tdx was first identified in a strain of Pseudomonas sp. capable of using alpha-terpineol as sole carbon source. The Tdx gene, previously cloned from the plasmid-encoded terp operon, that carries genes encoding for proteins involved in terpineol catabolism, has been subcloned and expressed as the holoprotein in E. coli. Physical characterization of the expressed Tdx has been performed, and a model for the solution structure of oxidized Tdx (Tdxo) has been determined. High-resolution homo- and heteronuclear NMR data have been used for structure determination in diamagnetic regions of the protein. The structure of the metal binding site (which cannot be determined directly by NMR methods due to paramagnetic broadening of resonances) was modeled using restraints obtained from a crystal structure of the homologous ferredoxin adrenodoxin (Adx) and loose restraints determined from paramagnetic broadening patterns in NMR spectra. Essentially complete 1H and 15N NMR resonance assignments have been made for the diamagnetic region of Tdxo (ca. 80% of the protein). A large five-stranded beta-sheet and a smaller two-stranded beta-sheet were identified, along with three alpha-helices. A high degree of structural homology was observed between Tdx and two other ferredoxins with sequence and functional homology to Tdx for which structures have been determined, Adx and putidaredoxin (Pdx), a homologous Pseudomonas protein. 1H/2H exchange rates for Tdx backbone NH groups were measured for both oxidation states and are rationalized in the context of the Tdx structure. In particular, an argument is made for the importance of the residue following the third ligand of the metal cluster (Arg49 in Tdx, His49 in Pdx, His56 in Adx) in modulating protein dynamics as a function of oxidation state. Some differences between Tdx and Pdx are detected by UV-visible spectroscopy, and structural differences at the C-terminal region were also observed. Tdx exhibits only 2% of the activity of Pdx in turnover assays performed using the reconstituted camphor hydroxylase system of which Pdx is the natural component.

Amino Acid Sequence↗
PubMedDate not supplied

The estimation of melting points and fusion enthalpies using experimental solubilities, estimated total phase change entropies, and mobile order and disorder theory.

Melting points and fusion enthalpies are predicted for a series of 81 compounds by combining experimental solubilities in a variety of solvents and analyzed according to the theory of mobile order and disorder (MOD) and using the total phase change entropy estimated by a group additivity method. The error associated in predicting melting points is dependent on the magnitude of the temperature predicted. An error of +/- 12 K (+/- 1 sigma) was obtained for compounds melting between ambient temperature and 350 K (24 entries). This error increased to +/- 23 K when the temperature range was expanded to 400 K (46 entries) and +/- 39 K for the temperature range 298-555 K (79 entries). Fusion enthalpies were predicted within +/- 2sigma of the experimental values (+/- 6.4 kJ mol(-1)) for 79 entries. The uncertainty in the fusion enthalpy did not appear dependent on the magnitude of the melting point. Two outliers, adamantane and camphor, have significant phase transitions that occur below room temperature. Estimates of melting temperature and fusion enthalpy for these compounds were characterized by significantly larger errors.

Journal Article↗
PubMed2006

Chiral magnetic metal-organic frameworks of dimetal subunits: magnetism tuning by mixed-metal compositions of the solid solutions.

The isostructural, chiral molecular magnetic materials with the formula [MxM'(2-x)(ca)2(1,4-dimb)]n [H2ca = D-(+)-camphoric acid, 1,4-dimb = 1,4-di-(1-imidazolyl-methyl)-benzene, M = Ni(II), M' = CoII, 0 < or = x < or = 2] consist of ca-bridged (4,4) layers with [M2(O2CR)4] as secondary building units that are pillared by the 1,4-dimb ligands into a unique 3D framework. The high-spin octahedral symmetry and the proportions of the mixed-metal ions were characterized by UV-vis spectroscopy. The compounds exhibit the onset of antiferromagnetic ordering at 7.5 approximately 23 K, as well as weak ferromagnetism, spin-flop, and glassy behavior that result from the randomness of the mixed-metal pairs, magnetic anisotropy of the metallic cations, and antisymmetric exchange. The composites should be regarded as molecular alloys of the pure Ni(II) and Co(II) compounds. The magnetic behavior of the solid solutions shows unambiguously that the organic bridges, bond angles, and bond distances greatly influence the effective interactions and bring about cooperative magnetic behavior in the chiral 3D frameworks.

Cobalt↗