Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “data resolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17Linked to original sources
PubMed1983

Structure of human oxyhaemoglobin at 2.1 A resolution.

The structure of human oxyhaemoglobin was determined by single crystal X-ray analysis at 2.1 A resolution. Data were collected on an Arndt-Wonacott camera at -2 degrees C. The structure was refined to an R factor of 0.223 by the Jack-Levitt method, starting from Baldwin's model of human carbon monoxide haemoglobin. The active sites in the alpha and beta subunit are distinct. The iron atoms are 0.16(8) A and 0.00(8) A from the mean plane of the porphyrin carbons and nitrogens (0.12(8) A and -0.11(8) A from the mean plane of the porphyrin nitrogens) in the alpha and beta subunit, respectively, in correlation with the orientation of HisF8 relative to the porphyrin nitrogens. The haem group appears to be nearly planar in the alpha subunit but ruffled in the beta subunit. The Fe-O(1)-O(2) angles are 153(7) degrees and 159(12) degrees in the alpha and beta subunit, respectively. The oxygen molecule forms a hydrogen bond to N epsilon of HisE7 in the alpha, but either none or a weak one in the beta subunit. The following bond lengths were found: Fe-N epsilon (HisF8) = 1.94(9) A (alpha) and 2.07(9) A (beta); Fe-O(1) = 1.66(8) A (alpha) and 1.87(13) A (beta); Fe-Nporph (mean = 1.99(5) A (alpha) and 1.96(6) A (beta). These dimensions agree with the values obtained in oxymyoglobin and model compounds. The C-terminal residues, ArgHC3(141 alpha) and HisHC3(146 beta), are relatively delocalized, and their positions do not enable them to form the intersubunit salt bridges in which they are involved in deoxyhaemoglobin. The penultimate tyrosine residues, TyrHC2 140 alpha and 145 beta, are relatively localized and maintain the hydrogen bonds to the carbonyl oxygens of ValFG5 (93 alpha and 98 beta), with only minor variations compared to their geometry in deoxyhaemoglobin. TyrHC2(145 beta), however, alternates between a major and a minor site, in conjunction with CysF9(93 beta), both sharing the internal pocket between the F and H helices while in the major conformation. This suggests that the role of the penultimate tyrosines in the allosteric mechanism may differ from that previously proposed by Perutz. The overall quaternary structure of oxyhaemoglobin is identical, within experimental error, to that of carbon monoxide haemoglobin, and thus confirms the applicability of the allosteric mechanisms proposed by Perutz and Baldwin & Chothia to the process of oxygen binding.

Amino Acid Sequence↗
PubMed2000

Gas-phase mercury in the atmosphere over the southern Baltic Sea coast

Results of atmospheric total gaseous mercury (TGM) measurements performed at two Baltic Sea coastal stations, Peninsula Hel (Poland) and Preila (Lithuania), from June 16 to August 11, 1997, are presented. High time-resolution data were obtained by using automated atomic absorption mercury vapor analyzers (Model Gardis-1A). Analysis of TGM concentration data (directional distribution, correlation with meteorological parameters, diurnal variability) detected the Baltic sea, in particular its southern part and Gulf of Gdansk, as the main gaseous mercury source for the region during the summer months. The source seemed to be activated by solar radiation, air temperature, and, probably, wind.

Journal Article↗
PubMed2000

Education, outreach and the future of remote sensing in human health.

The human health community has been slow to adopt remote sensing technology for research, surveillance, or control activities. This chapter presents a brief history of the National Aeronautics and Space Administration's experiences in the use of remotely sensed data for health applications, and explores some of the obstacles, both real and perceived, that have slowed the transfer of this technology to the health community. These obstacles include the lack of awareness, which must be overcome through outreach and proper training in remote sensing, and inadequate spatial, spectral and temporal data resolutions, which are being addressed as new sensor systems are launched and currently overlooked (and underutilized) sensors are newly discovered by the health community. A basic training outline is presented, along with general considerations for selecting training candidates. The chapter concludes with a brief discussion of some current and future sensors that show promise for health applications.

Communicable Disease Control↗
PubMed2001

A tunable diode laser system for ammonia flux measurements over multiple plots.

This paper reports on the field testing of a tunable diode laser trace gas analyzer system for micrometeorological monitoring of ammonia fluxes. This system uses infrared absorption spectroscopy to measure atmospheric ammonia concentrations and the fluxgradient method to relate the measured concentration gradient to a flux of ammonia. For the field tests, we monitored ammonia fuxes over three plots receiving different manure applications. Each plot was sampled for 15 or 30 min of each hour, producing a high-temporal resolution data set. Analysis of the system response showed that ammonia adsorption to the tubing walls was greatly reduced by the system design and did not interfere with the flux measurement.

Agriculture↗
PubMed1991

Optical performance of an aspheric multifocal intraocular lens.

A five zone, centrosymmetric, multifocal intraocular lens has been developed using a design analysis approach which assumes that the optical image strength (intensity) achieved by an optical zone is linearly proportional to its aperture. The advantages of including an aspheric zone are discussed, and the optical performance of this IOL is characterized interferometrically. Optical resolution data have been obtained according to the ANSI procedure, using standard Air Force targets. These experimental data are compared with theoretical models of optical performance of diffraction-limited circular, annular, and compound circular-annular lenses.

Lenses, Intraocular↗
PubMed1999

Clathrin: anatomy of a coat protein.

Clathrin is a vesicle coat protein involved in the assembly of membrane and cargo into transport vesicles at the plasma membrane and on certain intracellular organelles. Recently, crystal structures of two separate parts of the clathrin heavy chain, a fragment of the proximal leg and the N-terminal domain, have been analysed, providing the first high-resolution data for a vesicle coat protein. Viewing these structures in the context of a hexagonal barrel coat, recently determined to 21 A by cryo-electron microscopy, provides new insights into the assembly of clathrin coats.

Animals↗
PubMed2002

Detection, characterization, and prediction of tick-borne disease foci.

Tick-borne disease (TBD) transmission foci need to be characterized in space and time, and are often discontinuous on both scales. An active TBD focus is dependent on the fulfillment of three conditions: tick survival, pathogen survival and opportunities for human exposure. The essentials for tick survival include food sources, reproduction, and protection from environmental extremes. The pathogen survival kit includes sufficient densities of ticks and suitable reservoir hosts, and opportunities for transmission between them in order to maintain infection. Opportunities for human exposure depend on sufficient number of encounters between ticks and humans. Because tick foci need to be described on a range of spatial and temporal resolutions, data for such characterization include a variety of surveillance data, field and laboratory experimental data, as well as results of statistical and mathematical analysis and modeling. The application of new tools from molecular biology, geographic information systems (GIS), and satellite imagery, in conjunction with appropriate analytical methods allow for detection of unknown foci and prediction of new ones. A long-term multi-scale study of Ixodes scapularis and Lyme disease in the north-central U. S. is reviewed. Diverse surveillance methods of ticks, rodents, deer, canids and humans were coupled with environmental characterization in situ to create a habitat profile for Lyme disease ticks. Incorporating various digitized databases, a statistical model was used to develop a risk map for tick distribution in the region. The process of introduction and establishment of new tick foci along the Illinois River is described in relation to the known tick distribution and predictions of invasion based on the risk model.

Animals↗
PubMed2002

Latest developments in crystallography and structure-based design of protein kinase inhibitors as drug candidates.

Protein kinases have been identified as being implicated in many diseases, and the launch of the anti-cancer Bcr/Abl-kinase inhibitor Glivec has been a major advance in validating protein kinases as 'druggable' targets. High-resolution data exists for many classes of protein kinases and, in some cases, these structures are co-complexed with an inhibitor and/or substrate mimic. Coupled with the increasing reliability of computational predictions, structure-based design is now playing an increasingly important role in the discovery and optimisation of novel, potent and selective protein kinase inhibitors.

Amino Acid Sequence↗
PubMed2005

Characterization of high-molecular-weight sulfur-containing aromatics in vacuum residues using Fourier transform ion cyclotron resonance mass spectrometry.

Millions of tons of vacuum residues are produced in refineries every year and could be a potentially valuable resource for generating electricity and has possible application as heating and marine fuel. In this work, the polycyclic aromatic sulfur compounds (PASHs) from the aromatic fraction of vacuum residue before and after partial hydrodesulfurization (HDS) were derivatized by methylation to the methylsulfonium salts. Fourier transform ion cyclotron resonance mass spectrometry provided high-resolution data on these high-molecular-weight sulfur compounds. Compounds containing one and two S atoms were found to dominate, with masses up to ca. 900 Da. Classification according to hydrogen deficiency and the number of heteroatoms showed extensive series of homologues for double bond equivalents from 5 to 20. The sulfur-containing aromatics were separated using a palladium(II) complex as a liquid chromatographic phase into two compound groups: one containing compounds with an unconjugated thiophene ring and another with a condensed thiophene ring. This, combined with the mass spectrometry (MS) data, allows for the identification of several parent structures. Partial HDS removed primarily compounds with one S atom, whereas those with two S atoms were largely unaffected.

Journal Article↗
PubMed2006

Determination of carbon monoxide concentration and total pressure in gas cavities in the silica glass body of light bulbs by FT-IR spectrometry.

Fourier transform infrared (FT-IR) spectroscopy has been adapted to control the quality of light bulbs made from silica glass. Such light bulbs contain a molybdenum accessory which, if contaminated with carbon, during the melting procedure of bulb fabrication, can cause the production of carbon monoxide. This CO can be trapped in small gas cavities in the silica glass body of the bulb. A method has been developed for the detection of CO and the total pressure within these gas cavities by traditional FT-IR spectrometry using a spectral resolution of 0.5 cm(-1). The concentration of CO was determined by using a classical least-squares (CLS) method, and the accuracy of concentration determination is reported for the case with sample and reference spectra recorded at different pressures. The total pressure in the cavities was established by two different methods: either by CLS fitting of reference spectra to sample spectra or fitting a Voigt line shape function to the spectral lines within the CO fundamental stretching band. In the latter method, the width of the lines was determined and pressure-broadening coefficients are given and compared with high-resolution data from the literature. According to the measurements, 0.55-0.80 atm total pressure and 0.8-4.0% (v/v) CO was determined in the gas cavities. This method can also be applied to determine the total pressure in similar enclosed spaces in which an appropriate indicator gas component exists.

Journal Article↗
PubMed2000

Catalytic cysteine of thymidylate synthase is activated upon substrate binding.

The role of Ser 167 of Escherichia coli thymidylate synthase (TS) in catalysis has been characterized by kinetic and crystallographic studies. Position 167 variants including S167A, S167N, S167D, S167C, S167G, S167L, S167T, and S167V were generated by site-directed mutagenesis. Only S167A, S167G, S167T, and S167C complemented the growth of thymidine auxotrophs of E. coli in medium lacking thymidine. Steady-state kinetic analysis revealed that mutant enzymes exhibited k(cat) values 1.1-95-fold lower than that of the wild-type enzyme. Relative to wild-type TS, K(m) values of the mutant enzymes for 2'-deoxyuridylate (dUMP) were 5-90 times higher, while K(m) values for 5,10-methylenetetrahydrofolate (CH(2)H(4)folate) were 1.5-16-fold higher. The rate of dehalogenation of 5-bromo-2'-deoxyuridine 5'-monophosphate (BrdUMP), a reaction catalyzed by TS that does not require CH(2)H(4)folate as cosubstrate, by mutant TSs was analyzed and showed that only S167A and S167G catalyzed the dehalogenation reaction and values of k(cat)/K(m) for the mutant enzymes were decreased by 10- and 3000-fold, respectively. Analysis of pre-steady-state kinetics of ternary complex formation revealed that the productive binding of CH(2)H(4)folate is weaker to mutant TSs than to the wild-type enzyme. Chemical transformation constants (k(chem)) for the mutant enzymes were lower by 1.1-6.0-fold relative to the wild-type enzyme. S167A, S167T, and S167C crystallized in the I2(1)3 space group and scattered X-rays to either 1.7 A (S167A and S167T) or 2.6 A (S167C). The high-resolution data sets were refined to a R(crys) of 19.9%. In the crystals some cysteine residues were derivatized with 2-mercaptoethanol to form S,S-(2-hydroxyethyl)thiocysteine. The pattern of derivatization indicates that in the absence of bound substrate the catalytic cysteine is not more reactive than other cysteines. It is proposed that the catalytic cysteine is activated by substrate binding by a proton-transfer mechanism in which the phosphate group of the nucleotide neutralizes the charge of Arg 126', facilitating the transfer of a proton from the catalytic cysteine to a His 207-Asp 205 diad via a system of ordered water molecules.

Binding Sites↗
PubMed2002

Anisotropic motion and molecular dynamics of cholesterol, lanosterol, and ergosterol in lecithin bilayers studied by quasi-elastic neutron scattering.

Quasi-elastic neutron scattering (QENS) was employed to study the molecular dynamics of three structurally related sterols, namely, cholesterol, lanosterol, and ergosterol. Oriented bilayers of dipalmitoylphosphatidylcholine (DPPC) were investigated at 40 mol % sterol content and at three temperatures (20, 36, and 50 degrees C) for two energy resolutions. Data analysis was concentrated on a direct comparison of the out-of-plane and the in-plane high-frequency motions of the three sterols in terms of their rates and amplitudes. The (spatially restricted) diffusive motion of the three sterols in the two directions was characterized by diffusion constants in the range of (5-30) x 10(-12) x m(2) x s(-1), with a significantly faster rate of diffusion along the membrane normal, resulting in a diffusional anisotropy, D(a). At low temperature (20 degrees C), cholesterol showed the highest value (D(a) = 4.5), while lanosterol gave the lowest one (D(a) = 2.0). At high temperature (50 degrees C), ergosterol diffusion had the highest diffusion anisotropy (D(a) = 2.0) compared to lanosterol (D(a) = 1.8) and cholesterol (D(a) = 1.6). Most interestingly, cholesterol showed at all three temperatures an amplitude of its out-of-plane-motion of 1.0-1.1 nm, more than a factor of 3 higher than measured for the other two sterols. This finding suggests that the short alkyl chain of the cholesterol molecule may cross at high frequency the bilayer midplane, while the other two sterols remain confined within the geometrical limits of each monolayer leaflet. The results provide an example of how slight structural alterations of sterols can affect their molecular dynamics in bilayers, which in turn may be relevant to the membrane micromechanical properties.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2004

Crystal structures of RIalpha subunit of cyclic adenosine 5'-monophosphate (cAMP)-dependent protein kinase complexed with (Rp)-adenosine 3',5'-cyclic monophosphothioate and (Sp)-adenosine 3',5'-cyclic monophosphothioate, the phosphothioate analogues of cAMP.

Cyclic adenosine 5'-monophosphate (cAMP) is an ancient signaling molecule, and in vertebrates, a primary target for cAMP is cAMP-dependent protein kinase (PKA). (R(p))-adenosine 3',5'-cyclic monophosphothioate ((R(p))-cAMPS) and its analogues are the only known competitive inhibitors and antagonists for cAMP activation of PKA, while (S(p))-adenosine 3',5'-cyclic monophosphothioate ((S(p))-cAMPS) functions as an agonist. The crystal structures of a Delta(1-91) deletion mutant of the RIalpha regulatory subunit of PKA bound to (R(p))-cAMPS and (S(p))-cAMPS were determined at 2.4 and 2.3 A resolution, respectively. While the structures are similar to each other and to the crystal structure of RIalpha bound to cAMP, differences in the dynamical properties of the protein when (R(p))-cAMPS is bound are apparent. The structures highlight the critical importance of the exocyclic oxygen's interaction with the invariant arginine in the phosphate binding cassette (PBC) and the importance of this interaction for the dynamical properties of the interactions that radiate out from the PBC. The conformations of the phosphate binding cassettes containing two invariant arginine residues (Arg209 on domain A, and Arg333 on domain B) are somewhat different due to the sulfur interacting with this arginine. Furthermore, the B-site ligand together with the entire domain B show significant differences in their overall dynamic properties in the crystal structure of Delta(1-91) RIalpha complexed with (R(p))-cAMPS phosphothioate analogue ((R(p))-RIalpha) compared to the cAMP- and (S(p))-cAMPS-bound type I and II regulatory subunits, based on the temperature factors. In all structures, two structural solvent molecules exist within the A-site ligand binding pocket; both mediate water-bridged interactions between the ligand and the protein. No structured waters are in the B-site pocket. Owing to the higher resolution data, the N-terminal segment (109-117) of the RIalpha subunit can also be traced. This strand forms an intermolecular antiparallel beta-sheet with the same strand in an adjacent molecule and implies that the RIalpha subunit can form a weak homodimer even in the absence of its dimerization domain.

Binding Sites↗
PubMed1997

Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate.

Dihydrodipicolinate reductase catalyzes the NAD(P)H-dependent reduction of the alpha,beta-unsaturated cyclic imine dihydrodipicolinate to form the cyclic imine tetrahydrodipicolinate. The enzyme is a component of the biosynthetic pathway that leads to diaminopimelate and lysine in bacteria and higher plants. Because these pathways are unique to microorganisms and plants, they may represent attractive targets for new antimicrobial or herbicidal compounds. The three-dimensional structure of the ternary complex of Escherichia coli dihydrodipicolinate reductase with NADH and the inhibitor 2,6-pyridinedicarboxylate has been solved using a combination of molecular replacement and noncrystallographic symmetry averaging procedures and refined against 2.6 A resolution data to a crystallographic R-factor of 21.4% (Rfree is 29.7%). The native enzyme is a 120 000 molecular weight tetramer of identical subunits. The refined crystallographic model contains a tetramer, three molecules of NADH, three molecules of inhibitor, one phosphate ion, and 186 water molecules per asymmetric unit. Each subunit consists of two domains connected by two flexible hinge regions. While three of the four subunits of the tetramer have a closed conformation, in which the nicotinamide ring of the cofactor bound to the N-terminal domain and the reducible carbon of the substrate bound to the substrate binding domain are about 3.5 A away, the fourth subunit is unliganded and shows an open conformation, suggesting that the enzyme undergoes a major conformational change upon binding of both substrates. The residues involved in binding of the inhibitor and the residues involved in catalysis have been identified on the basis of the three-dimensional structure. Site-directed mutants have been used to further characterize the role of these residues in binding and catalysis. A chemical mechanism for the enzyme, based on these and previously reported data, is proposed.

Binding Sites↗
PubMed1998

The B-DNA dodecamer at high resolution reveals a spine of water on sodium.

We describe a very accurate addition (called structure X here) to the B-DNA dodecamer family of X-ray structures. Our results confirm the observation of Drew and Dickerson [(1981) J. Mol. Biol. 151, 535-556] that the spine of hydration in AT tract DNA is two layers deep. However, our results suggest that the primary spine is partially occupied by sodium ions. We suggest that many sequence-dependent features of DNA conformation are mediated by site specific binding of cations. For example, preferential localization of cations, as described here within the minor groove of structure X, is probably the structural origin of AT tract bending and groove narrowing. The secondary spine, which does not interact directly with the DNA, is as geometrically regular as the primary spine, providing a model for transmission of sequence information into solvent regions. A fully hydrated magnesium ion located in the major groove of structure X appears to pull cytosine bases partially out from the helical stack, exposing pi-systems to partial positive charges of the magnesium ion and its outer sphere. A partially ordered spermine molecule is located within the major groove of structure X. Dodecamer structures are derived from crystals of [d(CGCGAATTCGCG)]2 in space group P212121 (a = 25 A, b = 40 A, and c = 66 A). On average, those crystals diffracted to around 2.5 A resolution with 2500 unique reflections. Structure X, with the same space group, DNA sequence, and crystal form as the "Dickerson dodecamer", is refined against a complete, low-temperature, 1.4 A resolution data set, with over 11000 reflections. Structure X appears to be conformationally more ordered than previous structures, suggesting that at least a portion of the conformational heterogeneity previously attributed to DNA sequence in fact arises from experimental error.

Crystallization↗
PubMed2006

Laccase-catalyzed polymerization of two phenolic compounds studied by matrix-assisted laser desorption/ionization time-of-flight and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry with collision-induced dissociation experiments.

Enzymatic oxidation of two phenolic compounds [syringic acid (3,5-dimethoxy-4-hydroxybenzoic acid) and 2,6-dimethylphenol] was studied. The products of laccase- and laccase-mediator-catalyzed oxidation reactions were monitored by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and further analyzed by electrospray ionization Fourier transform ion cyclotron resonance (ESI-FTICR) MS with collision-induced dissociation (CID) experiments. For the oligomers of syringic acid, some variability was observed in MALDI-TOF analysis. However, the origin of this variability could not be resolved on the basis of MALDI-TOF spectra due to the poor resolution of the instrument in use. The strength of ESI-FTICR MS was the high-resolution data provided from oligomers of syringic acid. The CID experiments were extremely useful for structural studies of oligomers and verified that the variability of the products was due to the end groups; the phenolic hydroxyl group was modified during the oxidation.

Binding Sites↗
PubMed2003

A comparison of monocyclic and bicyclic phospholanes as acyl-transfer catalysts.

The synthesis and evaluation of chiral phosphines 11, 15a, 19a, 24a, and 28a as nucleophilic catalysts for anhydride activation and kinetic resolution of alcohols is described. The relative reactivity follows the order 11a > 11b > 15a > 1 in the monocyclic series, and 24a > 19a > 28ain the bicyclic series, with an overall rate advantage of ca. 2 orders of magnitude for the bicyclic phospholanes over the monocyclic analogues. The increased reactivity of the bicyclic phospholanes for the acylation of alcohols is attributed to conformational effects and ground-state destabilization in a highly associative mechanism. Kinetic resolution data demonstrate promising enantioselectivities for 24a.

Journal Article↗
PubMed1995

Tidal effects of disconnected hydrocarbon seas on Titan.

Thermodynamic and photochemical arguments suggest that Titan, the largest satellite of Saturn, has a deep ocean of liquid hydrocarbons. At visible wavelengths, Titan's surface is obscured by a thick stratospheric haze, but radar observations have revealed large regions of high surface reflectivity that are inconsistent with a global hydrocarbon ocean. Titan's surface has also been imaged at infrared wavelengths, and the highest-resolution data (obtained by the Hubble Space Telescope) show clear variations in surface albedo and/or topography. The natural interpretation of these observations is that Titan, like the Earth, has continents and oceans. But Titan's high orbital eccentricity poses a problem for this interpretation, as the effects of oceanic tidal friction would have circularized Titan's orbit for most configurations of oceans and continents. Here we argue that a more realistic topography, in which liquid hydrocarbons are confined to a number of disconnected seas or crater lakes, may satisfy both the dynamical and observational constraints.

Hydrocarbons↗