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At least 289 records · Page 16Linked to original sources
PubMed1977

Mechanism of cholesterol side-chain cleavage. II. The enzymic hydroperoxide-glycol rearrangement of the epimeric 20-hydroperxycholesterols in 18O-enriched water.

Incubation of 20 alpha-hydroperoxycholesterol (I) and its 20 beta-isomer, 20 beta-hydroperoxy-20 isocholesterol (II) with adrenocortical mitochondrial preparations in the absence of molecular oxygen, in normal and 18O-enriched water, gave 20 alpha, 22R-dihydroxycholesterol (III) from I and 20 beta,21-dihydroxy-20-iso-cholesterol (IV) from II. Mass spectral analysis of the persilylated glycol products III and IV showed no uptake of 18O, indicating that the oxygen atoms of the C20-, C22- and C21-hydroxyl groups originated from the 20-hydroperoxy atomic oxygen complex is the intermediate in the enzymic oxidative reactions of cholesterol side-chain cleavage.

Adrenal Cortex↗
PubMed2005

Determination of total phthalates in urine by isotope-dilution liquid chromatography-tandem mass spectrometry.

Diesters of 1,2-benzenedicarboxylic acid are a family of industrial compounds called "phthalates." The physical and chemical properties of these diesters, and therefore their potential uses, depend on the structure of the dialkyl or alkyl/aryl side chain. The urinary concentrations of phthalate monoesters, which are metabolites, have been used as biomarkers of human exposure to specific phthalates. However, several phthalates, particularly those with side chains of eight or more carbon atoms, are complex mixtures of isomers. For these, the phthalate metabolites to be used as biomarkers of exposure have not been unequivocally identified. We developed a method for assessing total exposure to phthalates, including the isomeric mixtures of high molecular weight phthalates, by measuring the concentration of phthalic acid (PA) in human urine after acid hydrolysis of the phthalate metabolites to PA. The present method accurately assesses total exposure to phthalates without noticeable contamination from the ubiquitous phthalates in the environment, but it gives no information about the parent phthalate.

Adult↗
PubMed1980

The structure of a DNA unwinding protein and its complexes with oligodeoxynucleotides by x-ray diffraction.

The structure of the gene 5 DNA unwinding protein from bacteriophage fd has been solved to 2.3 A resolution by x-ray diffraction techniques. The molecule contains an extensive cleft region that we have identified as the DNA binding site on the basis of the residues that comprise its surface. The interior of the groove has a rather large number of basic amino acid residues that serve to draw the polynucleotide backbone into the cleft. Arrayed along the external edges of the groove are a number of aromatic amino acid side groups that are in position to stack upon the bases of the DNA and fix it in place. The cleft then acts as an elongated pair of jaws that draws the DNA between them by charge interactions involving the phosphates with the interior lysines and arginines. The jaws then close on the DNA strand through small conformation changes and the rotation of aromatic side-chains into position to stack upon the purines and pyrimidines. Complexes of the gene 5 protein with a variety of oligodeoxynucleotides have been formed and crystallized for x-ray diffraction analysis. The crystallographic parameters of four different unit cells indicate that the fundamental unit of the complex is composed of six gene 5 protein dimers. We believe this aggregate has 622 point group symmetry and is a ring formed by end to end closure of a linear array of six dimers. From our results we have proposed a double helical model for the gene 5 protein-DNA complex in which the protein forms a spindle or core around which the DNA is spooled. 5.0-A x-ray diffraction data from one of the crystalline complexes is currently being analyzed by molecular replacement techniques to obtain what we believe will be the first direct visualization of a protein-deoxyribonucleic acid complex approaching atomic resolution.

Coliphages↗
PubMed2004

Mysteries of the transferrin-transferrin receptor 1 interaction uncovered.

How does the iron (Fe) binding protein, transferrin (Tf), bind to the transferrin receptor 1 (TfR1) to donate Fe to cells? In this issue of Cell, Cheng et al., describe the molecular structure of the human TfR1-Tf complex, This atomic model shows that Tf binds laterally to the TfR1 dimer and extends into the gap between the bottom of the receptor ectodomain and the membrane.

Animals↗
PubMed1979

Ionophore-mediated cation translocation in artificial systems. I. A23187-mediated calcium translocation.

The inophore A23187 stimulates the translocation of calcium from an aqueous Hepes buffer into an organic immiscible phase. At saturating calcium concentrations, 2 molecules of ionophore seem to complex each atom of calcium. Consistent with such a stoichiometric behaviour, the apparent ratio of calcium-ionophore association to dissociation rate constants increases as the concentration of ionophore is raised. As a result, at low calcium concentrations, the amount of translocated calcium increases as a power function of A23187 concentration. When allowance is made for such a phenomenon, the relation between calcium translocation and concentration is characterized by usual substrate-receptor binding kinetics.

Anti-Bacterial Agents↗
PubMed2003

Ten-electron coordination and reactivity of an arylphosphinidene ligand.

Photochemical decarbonylation of [Mo2Cp2(mu-PR*)(CO)4] (Cp = eta5-C5H5; R* = 2,4,6-C6H2tBu3) gives [Mo2Cp2(mu-kappa1:kappa1,eta6-PR*)(CO)2], which shows the first example of a remarkable 10-electron donor arylphosphinidene ligand which bridges two Mo atoms through its phosphorus atom while being pi-bonded to one Mo center through the six carbon atoms of the aryl ring. This causes a severe pyramidal distortion of the P-bound C atom. The complex adds CO to give [Mo2Cp2(mu-kappa1:kappa1,eta4-PR*)(CO)3], which has an 8-electron donor PR* ligand, and then the parent complex [Mo2Cp2(mu-PR*)(CO)4]. Protonation of [Mo2Cp2(mu-kappa1:kappa1,eta6-PR*)(CO)2] gives the hydride [Mo2Cp2(H)(mu-kappa1:kappa1,eta6-PR*)(CO)2]+, which undergoes P-C bond cleavage and hydride migration, affording the phosphido cation [Mo2Cp2(mu-P)(eta6-R*H)(CO)2]+.

Journal Article↗
PubMed1999

Highly Chemo- and Regioselective Thiocarbonylation of Conjugated Enynes with Thiols and Carbon Monoxide Catalyzed by Palladium Complexes: An Efficient and Atom-Economical Access to 2-(Phenylthiocarbonyl)-1,3-dienes.

The reaction of 1, 3-conjugated enynes bearing a terminal triple bond with thiols and carbon monoxide in the presence of catalytic quantities of Pd(OAc)(2) (3 mol %) and 1,3-bis(diphenylphosphino)propane (6 mol %) in THF at 110 degrees C gave 2-(phenylthiocarbonyl)-1,3-dienes in moderate to good yields. The thiocarbonylation takes place with high chemo- and regioselectivity, with the attack by the phenylthiocarbonyl group occurring exclusively at carbon-2 of the 1,3-conjugated enyne.

Journal Article↗
PubMed2003

The far-ultraviolet signature of the 'missing' baryons in the Local Group of galaxies.

The number of baryons detected in the low-redshift (z < 1) Universe is far smaller than the number detected in corresponding volumes at higher redshifts. Simulations of the formation of structure in the Universe show that up to two-thirds of the 'missing' baryons may have escaped detection because of their high temperature and low density. One of the few ways to detect this matter directly is to look for its signature in the form of ultraviolet absorption lines in the spectra of background sources such as quasars. Here we show that the amplitude of the average velocity vector of 'high velocity' O vi (O5+) absorption clouds detected in a survey of ultraviolet emission from active galactic nuclei decreases significantly when the vector is transformed to the frames of the Galactic Standard of Rest and the Local Group of galaxies. At least 82 per cent of these absorbers are not associated with any 'high velocity' atomic hydrogen complex in our Galaxy, and are therefore likely to result from a primordial warm-hot intergalactic medium pervading an extended corona around the Milky Way or the Local Group. The total mass of baryons in this medium is estimated to be up to approximately 10(12) solar masses, which is of the order of the mass required to dynamically stabilize the Local Group.

Journal Article↗
PubMed2005

Diffractive electron imaging of nanoparticles on a substrate.

The observation of the detailed atomic arrangement within nanostructures has previously required the use of an electron microscope for imaging. The development of diffractive (lensless) imaging in X-ray science and electron microscopy using ab initio phase retrieval provides a promising tool for nanostructural characterization. We show that it is possible experimentally to reconstruct the atomic-resolution complex image (exit-face wavefunction) of a small particle lying on a thin carbon substrate from its electron microdiffraction pattern alone. We use a modified iterative charge-flipping algorithm and an estimate of the complex substrate image is subtracted at each iteration. The diffraction pattern is recorded using a parallel beam with a diameter of approximately 50 nm, illuminating a gold nanoparticle of approximately 13.6 nm diameter. Prior knowledge of the boundary of the object is not required. The method has the advantage that the reconstructed exit-face wavefunction is free of the aberrations of the objective lens normally used in the microscope, whereas resolution is limited only by thermal vibration and noise.

Algorithms↗
PubMed1998

Oligomeric interaction of the PapB transcriptional regulator with the upstream activating region of pili adhesin gene promoters in Escherichia coli.

Transcriptional regulation of the pap genes, which encode fimbrial adhesins in uropathogenic Escherichia coli, depends on an upstream activating region. This region contains binding sites for a transcription factor, PapB, which is a member of a growing family of putative regulatory proteins found in several virulence-associated fimbrial gene systems. To assess the nature of the PapB binding sites, we studied different naturally occurring variants and a number of in vitro constructed mutant binding sites. DNase I footprinting analysis and visualization of the PapB-DNA complex by atomic force microscopy showed that the protein occupied a DNA region of more than 50 bp. Purified PapB protein was shown to recognize a motif including a 9 bp repeat sequence containing T/A triplets at a conserved position. PapB binding was affected by distamycin, and the results were consistent with the possibility that the binding to DNA occurred through minor groove interaction. From these analyses and estimation of the relative number of PapB proteins per binding site, we suggest that PapB binds the DNA in an oligomeric fashion and may function as an architectural factor in the transcriptional control of adhesin expression.

Adhesins, Bacterial↗
PubMed2005

Structure and energy difference of two isomers of He-CH3F.

The intermolecular potential surface of He-CH(3)F is investigated through ab initio calculations and microwave and millimeter-wave spectroscopies. The intermolecular potential is calculated at the fourth-order Møller-Plesset level with a large basis set including bond functions. Three minimums exist, the deepest of which is at the carbon end of the C-F axis and has a depth of 46.903 cm(-1), the second deepest is in a T-shaped position relative to the C-F axis with a depth of 44.790 cm(-1), and the shallowest is at the fluorine end of the C-F axis with a depth of 30.929 cm(-1). The barrier to internal rotation of the CH(3)F subunit about its C-F axis is very low, thus leading to essentially free internal rotation and two separate sets of bound states correlating to ortho-CH(3)F (|K| = 3n) for the ground, or A, internal rotor state upon which this study focuses, and to para-CH(3)F (|K| = 3n +/- 1) for the excited, or E, internal rotor state. Bound-state calculations of the A state performed using two different techniques show the lowest-energy state to have the helium localized in the T-shaped well with an energy of -11.460 cm(-1), while two excited configurations of the A state have the helium localized either in the well at the carbon end ("linear") with an energy of -7.468 cm(-1) or in the well at the fluorine end ("antilinear") with an energy of -4.805 cm(-1). Spectroscopic observations confirm the predicted energy-level structure of the ground and first excited states. Sixteen transitions between 12 distinct energy levels have been observed, including pure rotational transitions of both the T-shaped ground state and the linear excited state, as well as rovibrational transitions between the ground state and the linear excited state. The energy difference between the T-shaped state and the linear state is measured to be 132 374.081(16) MHz. There is significant Coriolis mixing of the ground state J(K(a)K(c)) = 2(20) and the linear J(K) = 2(0) levels which aided in the observation of the T to linear transitions. This mixing and the T to linear energy difference are sensitive probes of the relative well depths of the two lowest minimums and are well predicted by the ab initio potential. Improved agreement between experiment and theory is obtained by morphing the correlation energy of the potential. He-CH(3)F is one of just a few atom-molecule complexes for which the ground-state geometry does not coincide with the global potential minimum.

Algorithms↗
PubMed2005

Spectroscopy of Ar-SH and Ar-SD. II. Determination of the three-dimensional intermolecular potential-energy surface.

All the pure rotational transitions reported in the previous studies [J. Chem. Phys. 113, 10121 (2000); J. Mol. Spectrosc. 222, 22 (2003)] and newly observed rotation-vibration transitions, P = 1/2 <-- 3/2, for Ar-SH and Ar-SD [J. Chem. Phys. (2005), the preceding paper] have been simultaneously analyzed to determine a new intermolecular potential-energy surface of Ar-SH in the ground state. A Schrodinger equation considering the three-dimensional freedom of motion for an atom-diatom complex in the Jacobi coordinate, R, theta, and r, was numerically solved to obtain energies of the rovibrational levels using the discrete variable representation method. A three-dimensional potential-energy surface is determined by a least-squares fitting with initial values of the parameters for the potential obtained by ab initio calculations at the RCCSD(T)/aug-cc-pVTZ level of theory. The potential well reproduces all the observed data in the microwave and millimeter wave regions with parity doublings and hyperfine splittings. Several low-lying rovibrational energies are calculated using the new potential-energy surface. The dependence of the interaction energy between Ar and SH(2pi(i)) on the bond length of the SH monomer is discussed.

Journal Article↗
PubMed1981

Hydrogen bonding, overlap geometry, and sequence specificity in anthracycline antitumor antibiotic.DNA complexes in solution.

We have deduced structural aspects of the intercalation complex of the anthracycline antitumor antibiotic daunomycin and its analogs with the synthetic DNA poly(dA-dT) by 1H and 31P NMR in high-salt solution. We demonstrate that the base pairs are intact at the antibiotic binding site and that the anthracycline phenolic hydroxyls form intramolecular hydrogen bonds with the quinone carbonyls and are shielded from solvent in the intercalation complex. The complexation shifts of the exchangeable phenolic and nonexchangeable aromatic protons demonstrate that rings B and C of the anthracycline chromophore overlap with adjacent base pairs, while anthracycline ring D passes right through the intercalation site in the complex. We observe two resolved 31P resonances attributable to the dA-dT and dT-dA phosphodiester linkages in the phosphorus spectra of the neighbor-exclusion daunomycin.poly(dA-dT) complex. This suggests that the anthracycline antitumor antibiotic exhibits a sequence specificity in its intercalation complex with alternating purine-pyrimidine synthetic DNAs in solution. These conclusions on hydrogen bonding and overlap geometry at the intercalation site and sequence specificity for the daunomycin.poly(dA-dT) complex in solution are in agreement with the structure of the daunomycin.dC-dG-dT-dA-dC-dG hexanucleotide duplex crystalline complex at atomic resolution published recently [Quigley, G. J., Wang, A. H.-J., Ughetto, G., van der Marel, G., van Boom, J. H. & Rich, A. (1980) Proc. Natl. Acad. Sci. USA 77, 7204-7208].

Antibiotics, Antineoplastic↗
PubMed2000

Sequence-dependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)(2).

The solution structure of the dodecamer duplex d(CTTTTGCAAAAG)(2)and its 2:1 complex with the bis -benzimidazole Hoechst 33258 has been investigated by NMR and NOE-restrained molecular dynamics (rMD) simulations. Drug molecules are bound in each of the two A-tracts with the bulky N-methylpiperazine ring of each drug located close to the central TG (CA) step, binding essentially to the narrow minor groove of each A-tract. MD simulations over 1 ns, using an explicit solvation model, reveal time-averaged sequence-dependent narrowing of the minor groove from the 3'-end towards the 5'-end of each TTTT sequence. Distinct junctions at the TpG (CpA) steps, characterised by large positive roll, low helical and propeller twists and rapid AT base pair opening rates, add to the widening of the groove at these sites and appear to account for the bound orientation of the two drug molecules with the N-methylpiperazine ring binding in the wider part of the groove close to the junctions. Comparisons between the free DNA structure and the 2:1 complex (heavy atom RMSD 1.55 A) reveal that these sequence-dependent features persist in both structures. NMR studies of the sequence d(GAAAAGCTTTTC)(2), in which the A-tracts have been inverted with the elimination of the TpG junctions, results in loss of orientational specificity of Hoechst 33258 and formation of multiple bound species in solution, consistent with the drug binding in a number of different orientations.

Allosteric Regulation↗