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 1,171 records · Page 65Linked to original sources
PubMed1995

Comparison of different X-ray data-collection systems using the crystal structure of octreotide.

The octapeptide octreotide crystallizes with three peptide molecules and about 20% water in the asymmetric unit, and in many ways possesses diffraction properties similar to those of a 'mini-protein' consisting of 24 amino-acid residues. It diffracts to about 1.0 A but data in the range 1.4-1.0 A are weak. It provides a suitable test of different macromolecular X-ray data-collection techniques, especially of their ability to measure weak reflections accurately. In contrast to typical proteins it is possible to perform a full anisotropic refinement, that we believe provides a more objective test of the quality of the data than the internal consistency of equivalent reflections. We have collected a total of six data sets. The X-ray sources included synchrotron radiation, Cu Kalpha rotating anodes and Mo Kalpha sealed tubes; position-sensitive two-dimensional detectors from four manufacturers and a four-circle diffractometer with scintillation counter were employed. Two of the six data sets were collected at low temperature. Reasonable anisotropic refinement was possible with all area-detector data sets, although significant differences in the precision of the final model were observed. In addition we tested the ability of automated Patterson interpretation to solve the structure using the six independent data sets. The structure solution was only successful using the synchrotron or rotating-anode data sets, i.e. for the more intense sources. It appears that for structure solution the maximum resolution of the data is critical, whereas for refinement the accuracy of the data is more important.

Journal Article↗
PubMedDate not supplied

[The effect of fixed water molecules on fractal properties of globular protein surfaces].

On the base of the technique developed by the authors together with Schmidt the fractal properties of the 17 globular proteins have been analysed using the crystal structure data at high resolution. For all the proteins there are the coordinates of fixed water molecules in the protein data bank. For each protein the fractal dimension of its surface D has been calculated with and without taking into account the fixed water molecules located inside a 3-Angstrom hydrated layer. Small but systematic decrease of the DS values for the proteins with the fixed water molecules has been demonstrated. It means that the fixed water molecules tend to fill gaps on the protein surfaces and in that way to smooth the surfaces. The volumes and the molecular surfaces of the proteins have been also calculated on the base of the cube technique. The molecular surfaces of the proteins with the fixed water molecules prove to decrease. This fact can be considered as the indirect evidence that the protein surfaces become to be smoother.

Proteins↗
PubMed1998

Structure of human apolactoferrin at 2.0 A resolution. Refinement and analysis of ligand-induced conformational change.

The three-dimensional structure of a form of human apolactoferrin, in which one lobe (the N-lobe) has an open conformation and the other lobe (the C-lobe) is closed, has been refined at 2.0 A resolution. The refinement, by restrained least-squares methods, used synchrotron radiation X-ray diffraction data combined with a lower resolution diffractometer data set. The final refined model (5346 protein atoms from residues 1-691, two Cl- ions and 363 water molecules) gives a crystallographic R factor of 0.201 (Rfree = 0. 286) for all 51305 reflections in the resolution range 10.0-2.0 A. The conformational change in the N-lobe, which opens up the binding cleft, involves a 54 degrees rotation of the N2 domain relative to the N1 domain. This also results in a small reorientation of the two lobes relative to one another with a further approximately 730 A2 of surface area being buried as the N2 domain contacts the C-lobe and the inter-lobe helix. These new contacts also involve the C-terminal helix and provide a mechanism through which the conformational and iron-binding status of the N-lobe can be signalled to the C-lobe. Surface-area calculations indicate a fine balance between open and closed forms of lactoferrin, which both have essentially the same solvent-accessible surface. Chloride ions are bound in the anion-binding sites of both lobes, emphasizing the functional significance of these sites. The closed configuration of the C-lobe, attributed in part to weak stabilization by crystal packing interactions, has important implications for lactoferrin dynamics. It shows that a stable closed structure, essentially identical to that of the iron-bound form, can be formed in the absence of iron binding.

Apoproteins↗
PubMed2001

Preparation and crystallization of a Bacillus subtilis arsenate reductase.

Arsenate reductase (AR) in B. subtilis is encoded by the chromosomal arsC gene. Together with arsB and arsR, arsC participates in detoxification processes for the arsenate and arsenite ions. Full-length arsenate reductase without any modification has been expressed in Escherichia coli and purified in a soluble form. The recombinant protein has been crystallized at 277 K using polyethyleneglycol (PEG) or poly(ethyleneglycol) methyl ether (PME) as the main precipitant. At least two forms of crystals large enough for data collection have been obtained from wild-type protein under different conditions. An orthorhombic crystal diffracted to beyond 2.2 A with space group P2(1)2(1)2(1) and unit-cell parameters a = 51.22, b = 91.62, c = 101.93 A. A near-complete data set has been collected to 2.5 A. The application of the flash-annealing technique was crucial for high resolution during the data collection. The SeMet-substituted AR has also been produced and crystallized under very similar conditions as the wild type, but the unit-cell parameters are very different. The crystals of the SeMet protein diffracted to higher resolution than those of the wild type.

Adenosine Triphosphatases↗
PubMed1998

Photon energy recovery: a method to improve the effective energy resolution of gamma cameras.

UNLABELLED: One of the major limitations of gamma cameras is their relatively poor energy resolution. The main practical consequence of this is that the detection of both scattered and unscattered photons in the photopeak energy window, affecting image contrast and resolution, makes the data inconsistent with the assumption of scatter-free projection data in reconstruction and attenuation correction algorithms. Here, we proposed a method to improve the effective energy resolution of scintigraphic acquisitions. This method is called photon energy recovery (PER). METHODS: Photon energy recovery is based on a spectral deconvolution analysis and uses iterative recurrent linear regressions. In practice, PER only required splitting the photopeak energy window into several subwindows and did not need list mode acquisitions. The method was fully automated. Photon energy recovery was quantitatively validated on 99mTc planar images using a Monte Carlo simulation and a real phantom and was illustrated by a bone study. RESULTS: The Monte Carlo simulation demonstrated that convergence was reached within relatively few (10-15) iterations. Photon energy recovery led to a considerable quantitative improvement because the mean error between the photopeak energy window image and the true unscattered image was equal to 8.72 s.d. (the mean error between one image and the true image was the mean of the differences between the two images; the difference is expressed as several s.d., where s.d. was the square root of the true value), whereas the mean error between the 140-keV PER image and the true unscattered image was only equal to 2.70. Moreover, the true and PER spectra were highly correlated. The real phantom data pointed out that the counts in the 140-keV PER image calculated from the images acquired "with scatter" were not very different from the true counts given by the "scatter-free" reference image. Planar pelvic bone scintigraphy demonstrated the advantages of PER because contrast increased when only unscattered photons were selected. CONCLUSION: Photon energy recovery is a stable and automated method that allows recovery of the correct value of the photon energy after a scintigraphic acquisition. Its ability to separate scattered from unscattered events has been quantitatively validated.

Algorithms↗
PubMed1994

Crystallization and preliminary X-ray investigation of holotryptophanases from Escherichia coli and Proteus vulgaris.

Crystals of Proteus vulgaris holotryptophanase have been grown by the hanging-drop technique using polyethylene glycol 4000 as precipitant in the presence of monovalent cations K+ or Cs+. Orthorhombic crystals (P2(1)2(1)2(1)) grown with Cs+ have unit cell parameters a = 115.0 A, b = 118.2 A and c = 153.7 A and diffract to 1.8 A. There are four subunits of the tetrameric molecule in the asymmetric unit. Native data have been collected to 2.5 A resolution. The 3.4 A data were collected from tetragonal crystals of Escherichia coli holotryptophanase grown under conditions described by Kawata et al. (1991). The molecular replacement solution for this crystal form has been found using tyrosine phenol-lyase coordinates. The correct enantiomorph is P4(3)2(1)2. There are two subunits in the asymmetric unit.

Crystallization↗
PubMed2002

Overexpression, purification, crystallization and preliminary X-ray crystallographic analysis of Pseudomonas aeruginosa L-arginine deiminase.

Pseudomonas aeruginosa L-arginine deiminase, an enzyme catalyzing the irreversible catabolism of arginine to citrulline, has been produced in selenomethionyl form. The protein was purified and crystallized by the sitting-drop vapour-diffusion method using a precipitant solution consisting of 55% MPD, 100 mM cacodylate pH 6.5, 20 mM MgCl(2). Crystals display tetragonal symmetry (P4(1)2(1)2 or P4(3)2(1)2), with unit-cell parameters a = b = 106.0, c = 300.2 A, and diffract to 2.7 A resolution. A complete MAD data set was collected to 3.2 A resolution on beamline BM30 at ESRF.

Base Sequence↗
PubMed1997

A low-resolution low-temperature neutron diffraction study of myoglobin.

Diffraction data to 5 A resolution were collected on a myoglobin crystal at 80, 130, 180 and 240 K. The linear coefficient of thermal expansion for myoglobin was determined to be 45 x 10(-6) K(-1), based on the measured expansion of the unit-cell parameters. The nature of the hydration layers surrounding the protein in the crystal is described in terms of a shell solvent model, which was used to calculate the coefficient of thermal expansion in reasonable agreement with the measured value. Wilson statistics were calculated and discussed in terms of an averaged disorder model. [F(T(2)) - F(80 K) exp(-iphi)] Fourier maps were calculated where T(2) was taken as 130, 180 and 240 K, respectively. None of these difference maps showed any features above 2.0sigma in the protein region. The 130 and 240 K difference maps showed many small and widely distributed negative difference features and showed very few positive difference features above 2.5sigma in the solvent region. However, the 180 K difference map showed an extensive negative difference feature at the interface between symmetry-related molecules, occurring in the vicinity of residues 40-50 on one molecule and 76-80 on a symmetry-related molecule. These difference neutron Fourier maps indicate a concerted effect at 180 K, which is interpreted in terms of an onset of extended lattice disorder.

Journal Article↗
PubMed1996

The Solar Acoustic Spectrum and Eigenmode Parameters

The Global Oscillation Network Group (GONG) project estimates the frequencies, amplitudes, and linewidths of more than 250,000 acoustic resonances of the sun from data sets lasting 36 days. The frequency resolution of a single data set is 0.321 microhertz. For frequencies averaged over the azimuthal order m, the median formal error is 0.044 microhertz, and the associated median fractional error is 1.6 x 10(-5). For a 3-year data set, the fractional error is expected to be 3 x 10(-6). The GONG m-averaged frequency measurements differ from other helioseismic data sets by 0.03 to 0.08 microhertz. The differences arise from a combination of systematic errors, random errors, and possible changes in solar structure.

Journal Article↗
PubMed2004

In vivo 2D magnetic resonance spectroscopy of small animals.

Localized in vivo NMR spectroscopy, chemical shift imaging or multi-voxel spectroscopy are potentially useful tools in small animals that are complementary to MRI, adding biochemical information to the mainly anatomical data provided by imaging of water protons. However the contribution of such methods remains hampered by the low spectral resolution of the in vivo 1D spectra. Two-dimensional methods widely developed for in vitro studies have been proposed as suitable approaches to overcome these limitations in resolution. The different homonuclear and heteronuclear sequences adapted to in vivo studies are reviewed. Their specific contributions to the spectral resolution of spectroscopic data and their limitations for in vivo investigations are discussed. The applications to experimental models of pathological processes or pharmacological treatment in mainly brain and muscle are presented. According to their combined sensitivity, acquisition duration and spatial resolution, the heteronuclear 2D experiments, which are mainly used for 1H detected-13C spectroscopy after administration of 13C-labeled compounds, appear to be less efficient than 1H detected-13C 1D methods at high field. However, the applications of 2D proton homonuclear methods show that they remain the best tools for in vivo studies when an improved resolution is required.

Algorithms↗
PubMed2005

Implementation of radiotelemetry in a lab-in-a-pill format.

A miniaturised lab-in-a-pill device has been produced incorporating a temperature and pH sensor with wireless communication using the 433.92 MHz ISM band. The device has been designed in order to enable real time in situ measurements in the gastrointestinal (GI) tract, and accordingly, issues concerning the resolution and accuracy of the data, and the lifetime of the device have been considered. The sensors, which will measure two key parameters reflecting the physiological environment in the GI (as indicators for disease) were both controlled by an application specific integrated circuit (ASIC). The data were sampled at 10-bit resolution prior to communication off chip as a single interleaved data stream. This incorporated a power saving serial bitstream data compression algorithm that was found to extend the service lifetime of the pill by 70%. An integrated on-off keying (OOK) radio transmitter was used to send the signal to a local receiver (base station), prior to acquisition on a computer. A permanent magnet was also incorporated in the device to enable non-visual tracking of the system. We report on the implementation of this device, together with an initial study sampling from within the porcine GI tract, showing that measurements from the lab-on-a-pill, in situ, was within 90% of literature values.

Animals↗
PubMed2002

Competitive interaction of the antitumor drug daunorubicin and the fluorescence probe ethidium bromide with DNA as studied by resolving trilinear fluorescence data: the use of PARAFAC and its modification.

The competitive interaction with DNA of daunorubicin (DR), being present in the clinical anti-tumor drug daunoblastina, and the fluorescence probe ethidium bromide (EB) has been studied by parallel-factor analysis (PARAFAC) and full-rank parallel-factor analysis (FRA-PARAFAC) of a fluorescence excitation-emission three-way data array. The PARAFAC algorithm can furnish stable resolution results for the data array studied, if the estimated number of chemical components is consistent with the real number. The FRA-PARAFAC algorithm is not sensitive to the estimated number of components of the fluorescence data array if the estimated number is not less than the real number. Both algorithms gave identical resolution for the three components concerned DR, EB, and the complex EB-DNA. Variations of the equilibrium concentrations of free DR, EB, and the complex EB-DNA were resolved by both algorithms. Experimental observation confirms the hypothesis that DR is an intercalator of DNA and that the binding interactions of DR and EB with DNA are a pair of parallel competitive intercalation reactions on same base sites of DNA. The method exemplified by this study provides a useful approach for studying competitive interactions of different drugs with DNA in the presence of interferents.

Algorithms↗
PubMed2006

Exploratory data analysis of DNA microarrays by multivariate curve resolution.

In this work, the application of a multivariate curve resolution procedure based on alternating least squares optimization (MCR-ALS) for the analysis of data from DNA microarrays is proposed. For this purpose, simulated and publicly available experimental data sets have been analyzed. Application of MCR-ALS, a method that operates without the use of any training set, has enabled the resolution of the relevant information about different cancer lines classification using a set of few components; each of these defined by a sample and a pure gene expression profile. From resolved sample profiles, a classification of samples according to their origin is proposed. From the resolved pure gene expression profiles, a set of over- or underexpressed genes that could be related to the development of cancer diseases has been selected. Advantages of the MCR-ALS procedure in relation to other previously proposed procedures such as principal component analysis are discussed.

Acute Disease↗
PubMed1999

31P MRS studies of exercising human muscle at high temporal resolution.

Methods for measuring mitochondrial activity from 31P magnetic resonance spectroscopy data collected during and after exercise were compared in controls, weight lifters, and peripheral vascular occlusive disease (PVOD) patients. There were trends toward increasing mitochondrial activity during exercise in order from PVOD patients, moderately active controls, highly active controls, to weight lifters. Results from PVOD patients show divergence of some measures due to 1) the non-exponential nature of phosphocreatine recovery, and 2) potential breakdown of [ADP] control of the mitochondria due to lack of oxygen (for Qmax calculation). These results demonstrate the utility of obtaining and directly analyzing high time resolution data rather than assuming monoexponential behavior of metabolite recovery.

Adenosine Diphosphate↗
PubMed1992

X-ray structure refinement and comparison of three forms of mitochondrial aspartate aminotransferase.

The X-ray crystal structures of three forms of the enzyme aspartate aminotransferase (EC 2.6.1.1) from chicken heart mitochondria have been refined by least-squares methods: holoenzyme with the co-factor pyridoxal-5'-phosphate bound at pH 7.5 (1.9 A resolution), holoenzyme with pyridoxal-5'-phosphate bound at pH 5.1 (2.3 A resolution) and holoenzyme with the co-factor pyridoxamine-5'-phosphate bound at pH 7.5 (2.2 A resolution). The crystallographic agreement factors [formula: see text] for the structures are 0.166, 0.130 and 0.131, respectively, for all data in the resolution range from 10.0 A to the limit of diffraction for each structure. The secondary, super-secondary and domain structures of the pyridoxal-phosphate holoenzyme at pH 7.5 are described in detail. The surface area of the interface between the monomer subunits of this dimeric alpha 2 protein is unusually large, indicating a very stable dimer. This is consistent with biochemical data. Both subunit and domain interfaces are relatively smooth compared with other proteins. The interactions of the protein with its co-factor are described and compared among the three structures. Observed changes in co-factor conformation may be related to spectral changes and the energetics of the catalytic reaction. Small but significant adjustments of the protein to changes in co-factor conformation are seen. These adjustments may be accommodated by small rigid-body shifts of secondary structural elements, and by packing defects in the protein core.

Aspartate Aminotransferases↗
PubMed2006

Purification, crystallization and preliminary crystallographic analysis of the putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3.

The putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3 has been overexpressed and purified. Crystallization was performed by the oil-microbatch method using 28%(v/v) 2-methyl-2,4-pentanediol as a precipitant at 291 K. A native X-ray diffraction data set at 1.9 A resolution and a single anomalous dispersion data set from a selenomethionine-derivative crystal at 2.1 A resolution were collected using synchrotron radiation at 100 K. The native crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 71.7, b = 71.2, c = 141.8 A.

Crystallization↗
PubMed2001

Solvation of acylium fragment ions in electrospray ionization quadrupole ion trap and Fourier transform ion cyclotron resonance mass spectrometry.

In electrospray ionization (ESI) quadrupole ion trap and Fourier transform ion cyclotron resonance mass spectrometry, certain fragment ions (e.g. acylium ions) generated either during the ion transportation process (in the source interface region) or in the ion trap are found to undergo ion--molecule reactions with ESI solvent molecules (water, acetonitrile and aliphatic alcohols) to form adduct species. These unexpected solvated fragment ions severely complicate the interpretation of mass spectrometic data. High-resolution accurate mass measurements are important in establishing the elemental compositions of these adduct species and preventing erroneous data interpretation.

Acetals↗
PubMed2005

Performance of the computer algorithm COMPLX for the detection of protein complexes in the mass spectra of simulated biological mixtures.

The performance of the algorithm COMPLX for detecting protein-ligand or other macromolecular complexes has been tested for highly complex data sets. These data contain m/z values for ions of proteins of the SWISS-PROT database within simulated biological mixtures where each component shares a similar molecular weight and/or isoelectric point (pI). As many as 1600 ion signals were entered to challenge the algorithm to identify ion signals associated with a single protein complex that has been ionised and detected within a mass spectrometer. Despite the complexity of such data sets, the algorithm is shown to be able to identify the presence of individual bimolecular complexes. The output data can be re-evaluated by the user as necessary in light of any additional information that is known concerning the nature of predicted associations, as well as the quality of the data-set in terms of errors in m/z values as a direct consequence of the mass calibration or resolution achieved. The data presented illustrates that the best results are obtained when output results are ranked according to the largest continuous series of ion pairs detected for a protein or macromolecule and its complex for which the ligand mass is assigned the lowest mass error.

Algorithms↗