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At least 91 records · Page 5Linked to original sources
PubMed2001

Saccharomyces cerevisiae leukotriene A4 hydrolase: formation of leukotriene B4 and identification of catalytic residues.

Leukotriene A(4) hydrolase in mammals is a bifunctional zinc metalloenzyme that catalyzes the hydrolysis of leukotriene A(4) into the proinflammatory mediator leukotriene B(4), and also possesses an aminopeptidase activity. Recently we cloned and characterized an leukotriene A(4) hydrolase from Saccharomyces cerevisiae as a leucyl aminopeptidase with an epoxide hydrolase activity. Here we show that S. cerevisiae leukotriene A(4) hydrolase is a metalloenzyme containing one zinc atom complexed to His-340, His-344, and Glu-363. Mutagenetic analysis indicates that the aminopeptidase activity follows a general base mechanism with Glu-341 and Tyr-429 as the base and proton donor, respectively. Furthermore, the yeast enzyme hydrolyzes leukotriene A(4) into three compounds, viz., 5S,6S-dihydroxy-7,9-trans-11,14-cis-eicosatetraenoic acid, leukotriene B(4), and Delta(6)-trans-Delta(8)-cis-leukotriene B(4), with a relative formation of 1:0.2:0.1. In addition, exposure of S. cerevisiae leukotriene A(4) hydrolase to leukotriene A(4) selectively inactivates the epoxide hydrolase activity with a simultaneous stimulation of the aminopeptidase activity. Moreover, kinetic analyses of wild-type and mutated S. cerevisiae leukotriene A(4) hydrolase suggest that leukotriene A(4) binds in one catalytic mode and one tight-binding, regulatory mode. Exchange of a Phe-424 in S. cerevisiae leukotriene A(4) hydrolase for a Tyr, the corresponding residue in human leukotriene A(4) hydrolase, results in a protein that converts leukotriene A(4) into leukotriene B(4) with an improved efficiency and specificity. Hence, by a single point mutation, we could make the active site better suited to bind and turn over the substrate leukotriene A(4), thus mimicking a distinct step in the molecular evolution of S. cerevisiae leukotriene A(4) hydrolase toward its mammalian counterparts.

Amino Acid Sequence↗
PubMed2001

Reactions of aluminum, gallium, and indium (M) atoms with phosphine: generation and characterization of the species M.PH3, HMPH2, and H2MPH.

Upon deposition of Al, Ga, or In atoms (M) together with phosphine in a solid argon matrix, metal atom complexes M.PH3 are formed. Photolysis of the matrices at lambda = 436 nm results in the tautomerization of the adduct species to the insertion products HMPH2 and H2MPH. In addition, PH is formed from the reactions with Ga and In, with HMPH2 being its most likely precursor. Further photolysis into the absorption maximum of HMPH2 near 550 nm results in decomposition of HMPH2 with partial re-formation of the adduct M.PH3 and further buildup of PH. H2MPH is photostable under these conditions but suffers decomposition under the action of UV light (200 < or = lambda < or = 400 nm). All the molecules have been identified by their IR spectra, the assignments being attested by the effects of deuteration and also by comparison either with the vibrational properties anticipated by density functional theory (DFT) calculations or with those of known, related molecules. The resulting analysis is elaborated for the light it sheds on the structures and properties of the new molecules and on the mechanisms of the reactions affording, or disposing of, them.

Journal Article↗
PubMed2004

Gas phase infrared spectroscopy of mono- and divanadium oxide cluster cations.

The vibrational spectroscopy of the mono- and divanadium oxide cluster cations VO(1-3)+ and V2O(2-6)+ is studied in the region from 600 to 1600 wave numbers by infrared photodissociation of the corresponding cluster cation-helium atom complexes. The comparison of the experimental depletion spectra with the results of density functional calculations on bare vanadium oxide cluster cations allows for an unambiguous identification of the cluster geometry in most cases and, for VO(1-3)+ and V2O(5,6)+, also of the electronic ground state. A common structural motif of all the studied divanadium cluster cations is a four-membered V-O-V-O ring, with three characteristic absorption bands in the 550-900 wave number region. For the V-O-V and V=O stretch modes the relationship between vibrational frequencies and V-O bond distances follows the Badger rule.

Journal Article↗
PubMed1981

Molecular engineering: An approach to the development of general capabilities for molecular manipulation.

Development of the ability to design protein molecules will open a path to the fabrication of devices to complex atomic specifications, thus sidestepping obstacles facing conventional microtechnology. This path will involve construction of molecular machinery able to position reactive groups to atomic precision. It could lead to great advances in computational devices and in the ability to manipulate biological materials. The existence of this path has implications for the present.

Journal Article↗
PubMed1998

Evaluating the risk of death via the hematopoietic syndrome mode for prolonged exposure of nuclear workers to radiation delivered at very low rates.

During a Phase-I effort, studies were planned to evaluate deterministic (nonstochastic) effects of chronic exposure of nuclear workers at the Mayak atomic complex in the former Soviet Union to relatively high levels (> 0.25 Gy) of ionizing radiation. The Mayak complex has been used, since the late 1940's, to produce plutonium for nuclear weapons. Workers at Site A of the complex were involved in plutonium breeding using nuclear reactors, and some were exposed to relatively large doses of gamma rays plus relatively small neutron doses. The Weibull normalized-dose model, which has been set up to evaluate the risk of specific deterministic effects of combined, continuous exposure of humans to alpha, beta, and gamma radiations, is here adapted for chronic exposure to gamma rays and neutrons during repeated 6-h work shifts--as occurred for some nuclear workers at Site A. Using the adapted model, key conclusions were reached that will facilitate a Phase-II study of deterministic effects among Mayak workers. These conclusions include the following: (1) neutron doses may be more important for Mayak workers than for Japanese A-bomb victims in Hiroshima and can be accounted for using an adjusted dose (which accounts for neutron relative biological effectiveness); (2) to account for dose-rate effects, normalized dose X (a dimensionless fraction of an LD50 or ED50) can be evaluated in terms of an adjusted dose; (3) nonlinear dose-response curves for the risk of death via the hematopoietic mode can be converted to linear dose-response curves (for low levels of risk) using a newly proposed dimensionless dose, D = X(V), in units of Oklad (where D is pronounced "deh"), and V is the shape parameter in the Weibull model; (4) for X < or = Xo, where Xo is the threshold normalized dose, D = 0; (5) unlike absorbed dose, the dose D can be averaged over different Mayak workers in order to calculate the average risk of death via the hematopoietic mode for the population exposed at Site A; and (6) the expected cases of death via the hematopoietic syndrome mode for Mayak workers chronically exposed during work shifts at Site A to gamma rays and neutrons can be predicted using ln(2)B M[D]; where B (pronounced "beh") is the number of workers at risk (criticality accident victims excluded); and M[D] is the average (mean) value of D (averaged over the worker population at risk, for Site A, for the time period considered). These results can be used to facilitate a Phase II study of deterministic radiation effects among Mayak workers chronically exposed to gamma rays and neutrons.

Chronic Disease↗
PubMed2001

Unconventional decay law for excited states in closed many-body systems.

We study the time evolution of an initially excited many-body state in a finite system of interacting Fermi particles in the situation when the interaction gives rise to the "chaotic" structure of compound states. This situation is generic for highly excited many-particle states in quantum systems such as heavy nuclei, complex atoms, quantum dots, spin systems, and quantum computers. For a strong interaction the leading term for the return probability W(t) has the form W(t) approximately exp(-Delta(2)(E)t(2)) with Delta(2)(E) as the variance of the strength function. The conventional exponential linear dependence W(t)=C exp(-Gammat) formally arises for a very larger time. However, the prefactor C turns out to be exponentially large, thus resulting in a strong difference from the conventional estimate for W(t).

Journal Article↗
PubMed2001

Lifetime measurements of metastable states in Fe+.

The lifetime of two metastable levels in Fe+ has been measured by laser probing of a stored ion beam. In the dense spectrum of Fe+, the metastable levels a (6)S(5/2) and b (4)D(7/2) were selected and their lifetimes were determined to be 230 +/- 30 and 530 +/- 30 ms, respectively. The lifetimes are compared with previous theoretical results. Metastable lifetime measurements of Fe+ are of great importance for interpretation of spectra from astronomical objects. The present experiment opens for the possibilities to investigate lifetimes of metastable states in complex atomic ions, which have, so far, been unexplored.

Journal Article↗
PubMed2003

Direct determination of strain and composition profiles in SiGe islands by anomalous x-Ray diffraction at high momentum transfer.

Anomalous x-ray scattering is employed for quantitative measurements of the Ge composition profile in islands on Si(001). The anomalous effect in SiGe is enhanced exploiting the dependence of the complex atomic form factors on the momentum transfer. Comparing the intensity ratios for x-ray energies below and close to the K edge of Ge at various Bragg reflections in the grazing incidence diffraction setup, the sensitivity for the Ge profile is considerably enhanced. The method is demonstrated for SiGe dome-shaped islands grown on Si(001). It is found that the composition inside the island changes rather abruptly, whereas the lattice parameter relaxes continuously.

Journal Article↗
PubMed2003

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics.

The possibility of observing chemical reactions in ab initio molecular dynamics runs is severely hindered by the short simulation time accessible. We propose a new method for accelerating the reaction process, based on the ideas of the extended Lagrangian and coarse-grained non-Markovian metadynamics. We demonstrate that by this method it is possible to simulate reactions involving complex atomic rearrangements and very large energy barriers in runs of a few picoseconds.

Journal Article↗
PubMed1989

High-voltage electron diffraction from bacteriorhodopsin (purple membrane) is measurably dynamical.

Electron diffraction patterns of 45 A thick two-dimensional crystalline arrays of a cell membrane protein, bacteriorhodopsin, have been recorded at two electron voltages, namely 20 and 120 kV. Significant intensity differences are observed for Friedel mates at 20 kV, but deviations from Friedel symmetry are quite small at 120 kV. It does not seem likely that the measured Friedel differences can be accounted for by complex atomic structure factors, by curvature of the Ewald sphere, or by effects that might occur as a result of inelastic scattering (absorption). It is therefore concluded that dynamical diffraction within the single molecular layer of these crystals is responsible for the observed Friedel differences. The results are useful in estimating the maximum specimen thickness for which the kinematic approximation may be safely used in electron crystallography of biological macromolecules at the usual electron voltage of 100 kV, or even at higher voltages. The results show that the Friedel differences are independent of resolution and this opens up the possibility that dynamical effects occurring at lower voltages might be used to phase higher-voltage kinematic diffraction intensities.

Bacteriorhodopsins↗
PubMed2004

X-ray diffraction study of the ultrathin Al2O3 layer on NiAl110.

Ultrathin Al2O3 layers on alloys are used as templates for model catalysts, tunneling barriers in electronic devices, or corrosion-resistant layers. The complex atomic structure of well-ordered alumina overlayers on NiAl110 was solved by surface x-ray diffraction. The oxide layer is composed of a double layer of strongly distorted hexagonal oxygen ions that hosts aluminum ions on both octahedral and tetrahedral sites with equal probability. The alumina overlayer exhibits a domain structure that can be related to characteristic growth defects and is generated during the growth of a hexagonally ordered overlayer (Al2O3) on a body-centered cubic (110) substrate (NiAl).

Journal Article↗
PubMed1996

Biophysical aspects of Auger processes--A review.

Radionuclide decay by electron capture and/or internal conversion is accompanied by complex atomic vacancy cascades and emission of low-energy electrons, resulting in a highly charged daughter atom and a high density of electron irradiation in the immediate vicinity of the decay site. The molecular and cellular consequences of such decay events include DNA strand breaks, mutations, chromosome aberrations, malignant transformation, division delay, and cell death. Damage to cells depends largely on the intracellular location of the radionuclide. Decays outside the cell nucleus produce low-LET-type radiation effects (RBE approximately 1). In contrast, decays in DNA cause pronounced high-LET-type effects (RBE approximately 7-9). However, recent studies suggest that even for DNA-associated Auger emitters cell damage can be modified to resemble the pattern observed with low-LET radiations. These findings indicate that the molecular and cellular mechanism(s) responsible for the cytotoxic effects of Auger emitters remain obscure.

Biophysical Phenomena↗
PubMedDate not supplied

[Mg2+ cation initiates the conversion of nucleoside triphosphate to nucleoside monophospate through a radical mechanism. Quantum molecular dynamics simulation].

DFT:B3LYP (6-311G** basis set) quantum molecular dynamics simulation was used to study the conversion of guanosine triphosphate (GTP) to guanosine monophosphate upon the action of Mg2+. The computations were carried out at 310 K in a basin of 178 water molecules surrounding a Mg(2+)-GTP complex and imitating the behavior of the solvent. The cleavage of the Mg(2+)-GTP complex occurs over the 5-ps period and gives rise to two inorganic phosphates (Pi), a hydrated Mg2+ complex, atomic oxygen, and highly reactive GMP radical. The appearance of this radical is a result of action of the Mg2+ cation, which initiates the radical mechanism of GTP cleavage. At the very early step of interaction with GTP, Mg2+ is reduced to Mg+, thus producing an ion radical pair (+)Mg-GTP(3-). In the absence of Mg2+, a non-reactive form of GMP is formed rather than GMP; the process corresponds to hydrolytic cleavage of GTP through the ionic mechanism. The formation of GMP and its analogues with adenosine, cytidine, thymidine, and uridine is, seemingly, a key point in DNA and RNA synthesis.

Cations, Divalent↗
PubMed1983

Xenopus transcription factor A requires zinc for binding to the 5 S RNA gene.

Transcription factor A from immature Xenopus oocytes is found associated with 5 S RNA in a 7 S nucleoprotein complex. Atomic absorption analysis of EDTA-dialyzed 7 S particles reveals 2 mol of zinc/mol of particle. Factor A obtained from EDTA-dialyzed particles binds specifically to the 5 S RNA gene as determined by DNase I footprinting. Factor A alone, obtained by RNase digestion of the 7 S particle, contains zinc when dialyzed in the absence of EDTA. However, the zinc bound to free factor A is removed by dialysis against a buffer containing EDTA. The apoprotein does not bind to the 5 S RNA gene. Inhibition of footprinting is also effected by addition of EDTA to factor A without prolonged dialysis. Under these conditions, specific DNA binding ability is restored following addition of zinc. 1,10-Phenanthroline also inhibits binding of factor A to the intragenic control region of the 5 S RNA gene. In addition, this reagent specifically inhibits factor A-dependent synthesis of 5 S RNA but not factor A-independent tRNA synthesis in a HeLa cell in vitro transcription system.

Animals↗
PubMed2004

Reduced basis set for the gold atom in cluster complexes.

To extend the metal cluster size used in interfacing between bulk metals and molecules in ab initio studies of molecular electronics and chemisorption, a reduced size atomic orbital basis set for the gold atom has been generated. Based on the SKBJ relativistic effective core potential set, the three component 5d Gaussian orbital basis set is completely contracted. Comparisons between the full and reduced basis set in Au atom clusters and cluster complexes for geometry, bond distances, dipole moments, atomic charges, spin, bond dissociation energies, lowest energy harmonic frequencies, electron affinities, ionization energies, and density of states distributions show the contracted set to be a viable replacement for the full basis set. This result is obtained using both the B3LYP and BPW91 exchange-correlation potentials in density functional theory.

Journal Article↗
PubMed2005

Three-dimensional computation of atom depth in complex molecular structures.

MOTIVATION: For a complex molecular system the delineation of atom-atom contacts, exposed surface and binding sites represents a fundamental step to predict its interaction with solvent, ligands and other molecules. Recently, atom depth has been also considered as an additional structural descriptor to correlate protein structure with folding and functional properties. The distance between an atom and the nearest water molecule or the closest surface dot has been proposed as a measure of the atom depth, but, in both cases, the 3D character of depth is largely lost. In the present study, a new approach is proposed to calculate atom depths in a way that the molecular shape can be taken into account. RESULTS: An algorithm has been developed to calculate intersections between the molecular volume and spheres centered on the atoms whose depth has to be quantified. Many proteins with different size and shape have been chosen to compare the results obtained from distance-based and volume-based depth calculations. From the wealth of experimental data available for hen egg white lysozyme, H/D exchange rates and TEMPOL induced paramagnetic perturbations have been analyzed both in terms of depth indexes and of atom distances to the solvent accessible surface. The algorithm here proposed yields better correlations between experimental data and atom depth, particularly for those atoms which are located near to the protein surface. AVAILABILITY: Instructions to obtain source code and the executable program are available either from http://sienabiografix.com or http://sadic.sourceforge.net CONTACT: niccolai@unisi.it SUPPLEMENTARY INFORMATION: http://www.Sienabiogzefix.com/publication.

Algorithms↗
PubMed2004

Metastable and stable states of xanthan polyelectrolyte complexes studied by atomic force microscopy.

The compaction of the semiflexible polysaccharide xanthan with selected multi- and polyvalent cations was studied. Polyelectrolyte complexes prepared at concentrations of 1-2 microg/ml were observed by tapping mode atomic force microscopy. High-molecular-weight xanthan compacted with chitosan yields a blend of mainly toroidal and metastable structures and a small fraction of rod-like species. Polyelectrolyte complexes of xanthan with polyethylenimine and trivalent chromium yielded similar structures or alternatively less well packed species. Racquet-type morphologies were identified as kinetically trapped states occurring on the folding path toward the energetically stable state of the toroids. Thermal annealing yielded a shift of the distribution of xanthan-chitosan morphologies toward this stable state. Ensembles of toroidal and rod-like morphologies of the xanthan-chitosan structures, collected using an asphericity index, were analyzed. The mean height of the toroids increased upon heating, with a selective increase in the height range above 2 nm. It is suggested that the observed metastable structures are formed from the high-molecular-weight fraction of xanthan and that these are driven toward the toroidal state, being a low-energy state, following annealing. Considered a model system for condensation of semiflexible polymers, the compaction of xanthan by chitosan captures the system at various stages in the folding toward a low-energy state and thus allows experimental analyses of these intermediates and their evolution.

Chitin↗