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 199 records · Page 11Linked to original sources
PubMed1985

Quantification of endocytosis-derived membrane traffic.

The main data covered by this article have been summarized in Table I. A fairly uniform picture is obtained for endocytosis-derived membrane transfer and compartmentation. This may be due to the limited amount of information and the resulting low resolution. Data on mainly three cell types are presented: macrophages, fibroblasts and amoebae. The data vary as much for one cell type as between different cells. Therefore, no possible differences related to cell function emerge. More detailed data, for more cell types, may change the picture. The values for cell surface area, although significantly different in absolute terms (column S in Table I), are rather similar when related to cell diameter, all being about 3-fold in excess of the surface area of the smooth sphere of comparable volume (column xi in Table I). The rate of plasma membrane internalization for macrophages and amoebae both professional phagocytes, is about 2 cell surface area equivalents per h or more. This may be somewhat higher than for fibroblasts (column PM/h in Table I). The average residence time for membrane on the cell surface, therefore, is about 30 min. A most interesting finding seems to be the rather uniform values obtained for the average size (volume weighted) of primary pinosomes, being about 0.3 micron in diameter (column phi-Internalization in Table I). Due to their rapid increase in size as a result of fusion (cf. Fig. 2), it has not been feasible to directly measure the size of primary pinosomes by morphometric means. The values in Table I, give no information on the size distributions of primary pinosomes and on whether these consist of one or more size classes. The steady-state average diameter of pinosomes is noticeably larger than that of primary pinosomes (column phi-pinosomes in Table I; cf. Table II for Acanthamoebae). The corresponding decrease in surface-to-volume ratio can make about 50% of pinosomal membrane available for recycling directly from this membrane compartment. Membrane recycling from the pinosomal compartment occurs after an average residence time of about 3 min for macrophages and 4-6 min for fibroblasts (column tau-pinosomes in Table I). The relative pool size of intracellular membranes participating in shuttling to and from the cell surface is significantly different for animal cells and amoebae (column rho in Table I). For macrophages, fibroblasts, CHO cells, and mast cells, this intracellular membrane pool amounts to about 10-20% the plasma membrane area, compared to 150-200% in the case of amoebae.(ABSTRACT TRUNCATED AT 400 WORDS)

5'-Nucleotidase↗
PubMed1999

The use of CCD area detectors in charge-density research. Application to a mineral compound: the alpha-spodumene LiAl(SiO3)2.

X-ray diffraction data sets collected on both Nonius and Siemens (Bruker) goniometers equipped with charge-coupled device (CCD) area detectors have been tested for the electron-density determination of the aluminosilicate mineral compound alpha-spodumene LiAl(SiO(3))(2), aluminium lithium silicon oxide. Data collection strategies, reflection intensity peak integration methods and experimental error estimates are different for the two instruments. Therefore, the consistency and quality of the two types of CCD measurements have been carefully compared to each other and to high-resolution data collected on a conventional CAD-4 point-detector diffractometer. Multipole density model refinements were carried out against the CCD data and the statistical factors analysed in terms of experimental weighting schemes based on the standard uncertainties of the diffraction intensities derived by the Nonius and Siemens software programs. Consistent experimental electron-density features in the Si-O-Si and Si-O-Al bridges were found from both CCD data sets. The net atomic charges obtained from the kappa refinements against each CCD data set are also in good agreement and quite comparable with the results of the conventional CAD-4 experiment.

Journal Article↗
PubMed2000

Structures of oxidized and reduced azurin II from Alcaligenes xylosoxidans at 1.75 A resolution.

Crystallographic structures of oxidized and reduced forms of azurin II are reported at 1.75 A resolution. Data were collected using one crystal in each case and by translating the crystal after each oscillation range to minimize photoreduction. Very small differences are observed at the Cu site upon reduction and these cannot be determined with confidence at current resolution. A comparison with the three-dimensional EXAFS reveals a good correspondence for all the ligand distances except for Cu-His46, where a larger deviation of approximately 0.12-0.18 A is observed, indicating that this ligand is more tightly restrained in the crystallographic refinement at the current resolution.

Alcaligenes↗
PubMed1996

Crystallization and preliminary crystallographic analysis of the DNA gyrase B protein from B. stearothermophilus.

DNA gyrase B (GyrB) from B. stearothermophilus has been crystallized in the presence of the non-hydrolyzable ATP analogue, 5'-adenylyl-beta-gamma-imidodiphosphate (ADPNP), by the dialysis method. A complete native data set to 3.7 A has been collected from crystals which belonged to the cubic space group I23 with unit-cell dimension a = 250.6 A. Self-rotation function analysis indicates the position of a molecular twofold axis. Low-resolution data sets of a thimerosal and a selenomethionine derivative have also been analysed. The heavy-atom positions are consistent with one dimer in the asymmetric unit.

Journal Article↗
PubMed1999

[Pharmacokinetic-pharmacodynamic modeling in phase II of drug development. A comparative study with young and old volunteers with benzdiazepine as an example].

Especially for medical disciplines like anesthesiology, which represent only a small economic market, drug development is a cost intensive and with respect to financial aspects a high risk task. This situation requires methods, which in the early stages of the drug development process of an interesting compound allow the establishment of a reliable and valid data set, in order to make decisions on the continuation or discontinuation of a project. Given a compound out of the group of benzodiazepines as an example this paper represents todays methods of integrated pharmacokinetic-pharmacodynamic modelling as well as the special computer aided strategies of drug dosing as powerful tools in the anaesthetic drug development process. It is shown that one can generate data concerning differences in drug requirement and drug duration in the therapeutic dose range between different groups of possible patients, e.g. young and elderly, as early as the early phase II. It is concluded that these clinical pharmacological tools and the high resolution data generated by them facilitate the Go/No-Go decision to proceed to phase III and enhance the likelihood of passing phase III successfully.

Adolescent↗
PubMed1996

Large structures at high resolution: the 1.6 A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from spinach is a hexadecamer (L8S8, Mr = 550,000) consisting of eight large (L, 475 residues) and eight small subunits (S, 123 residues). High-resolution data collection on crystals with large unit cells is not a trivial task due to the effect of radiation damage and the large number of overlapping reflections when conventional data collection methods are used. In order to minimise these effects, data on rubisco were collected with a giant Weissenberg camera at long crystal to image-plate distances at the synchrotron of the Photon Factory, Japan. Relative to conventional data sets, this experimental arrangement allowed a 20 to 30-fold reduction of the X-ray dose/exposure time for data collection. This paper describes the refined 1.6 A crystal structure of activated rubisco complexed with a transition state analogue, 2-carboxyarabinitol-bisphosphate. The crystallographic asymmetric unit contains an L4S4 unit, representing half of the molecule. The structure presented here is currently the highest resolution structure for any protein of comparable size. Refinement of the model was carried out by restrained least squares techniques without non-crystallographic symmetry averaging. The results show that all L and S subunits have identical three-dimensional structures, and their arrangement within the hexadecamer has no intrinsic asymmetry. A detailed analysis of the high-resolution maps identified 30 differences in the sequence of the small subunit, indicating a larger than usual heterogeneity for this nuclear encoded protein in spinach. No such differences were found in the sequence of the chloroplast encoded large subunit. The transition state analogue is in the cis conformation at the active site suggesting a key role for the carbamate of Lys201 in catalysis. Analysis of the active site around the catalytically essential magnesium ion further indicates that residues in the second liganding sphere of the metal play a role in fine-tuning the acid-base character and the position of the residues directly liganded to the metal.

Amino Acid Sequence↗
PubMed2006

Free-breathing whole-heart coronary MR angiography on a clinical scanner in four minutes.

PURPOSE: To set up a robust and patient-friendly whole-heart protocol based on 32-receive-channel technology that will potentially allow a large part of the patient population to be addressed. MATERIALS AND METHODS: Ten volunteers were examined on a clinical 1.5 T scanner equipped with a 32-channel data acquisition system using an experimental 32-element coil array. A magnetization-prepared, navigator-gated and -tracked 3D Cartesian balanced FFE sequence was used for whole-heart coronary MR angiography (MRA). With the use of sensitivity encoding (SENSE) and partial Fourier encoding for scan acceleration, nearly isotropic high-resolution data sets were acquired during free breathing in four minutes. RESULTS: A high contrast and sufficient signal-to-noise ratio (SNR) were obtained, which allowed visualization of the major vessels up to the distal regions and detection of major branches. Phase encoding in the anterior-posterior (AP) direction was the most favorable SENSE configuration and allowed a reasonable scan time reduction with moderate SENSE factors. CONCLUSION: The employed 32-receive channel technology enabled a robust trade-off among SNR, spatial resolution, and scan time. In this study the most robust results were obtained using the smallest possible SENSE factors for a given voxel size and scan time.

Adult↗
PubMed1994

2.2 A resolution structure of the amino-terminal half of HIV-1 reverse transcriptase (fingers and palm subdomains).

BACKGROUND: HIV-1 reverse transcriptase (RT) catalyzes the transformation of single-stranded viral RNA into double-stranded DNA, which is integrated into host cell chromosomes. The molecule is a heterodimer of two subunits, p51 and p66. The amino acid sequence of p51 is identical to the sequence of the amino-terminal subdomains of p66. Earlier crystallographic studies indicate that the RT molecule is flexible, which may explain the difficulty in obtaining high-resolution data for the intact protein. We have therefore determined the structure of a fragment of RT (RT216), which contains only the amino-terminal half of the RT molecule ('finger' and 'palm' subdomains). RESULTS: The crystal structure of RT216 has been refined at 2.2 A resolution to a crystallographic R-value of 20.8%. The structure is very similar to that of the corresponding part of the p66 subunit in the p66/p51 heterodimer, although there is a small difference in the relative orientation of the two subdomains compared with the structure of an RT-DNA-antibody fragment complex. There are a large number of stabilizing contacts (mainly hydrogen bonds and hydrophobic interactions) between the subdomains. The locations of conserved amino acids and the position of some important drug-resistant mutations are described. CONCLUSIONS: The RT216 structure provides detailed three-dimensional information of one important part of HIV-1 RT (including the critical active site residues). We propose a model to explain the inhibitory effect of non-nucleoside inhibitors, which partially accounts for their effect in terms of conformational changes of active site residues.

Binding Sites↗
PubMed2006

Simulation studies of the fidelity of biomolecular structure ensemble recreation.

We examine the ability of Bayesian methods to recreate structural ensembles for partially folded molecules from averaged data. Specifically we test the ability of various algorithms to recreate different transition state ensembles for folding proteins using a multiple replica simulation algorithm using input from "gold standard" reference ensembles that were first generated with a Go-like Hamiltonian having nonpairwise additive terms. A set of low resolution data, which function as the "experimental" phi values, were first constructed from this reference ensemble. The resulting phi values were then treated as one would treat laboratory experimental data and were used as input in the replica reconstruction algorithm. The resulting ensembles of structures obtained by the replica algorithm were compared to the gold standard reference ensemble, from which those "data" were, in fact, obtained. It is found that for a unimodal transition state ensemble with a low barrier, the multiple replica algorithm does recreate the reference ensemble fairly successfully when no experimental error is assumed. The Kolmogorov-Smirnov test as well as principal component analysis show that the overlap of the recovered and reference ensembles is significantly enhanced when multiple replicas are used. Reduction of the multiple replica ensembles by clustering successfully yields subensembles with close similarity to the reference ensembles. On the other hand, for a high barrier transition state with two distinct transition state ensembles, the single replica algorithm only samples a few structures of one of the reference ensemble basins. This is due to the fact that the phi values are intrinsically ensemble averaged quantities. The replica algorithm with multiple copies does sample both reference ensemble basins. In contrast to the single replica case, the multiple replicas are constrained to reproduce the average phi values, but allow fluctuations in phi for each individual copy. These fluctuations facilitate a more faithful sampling of the reference ensemble basins. Finally, we test how robustly the reconstruction algorithm can function by introducing errors in phi comparable in magnitude to those suggested by some authors. In this circumstance we observe that the chances of ensemble recovery with the replica algorithm are poor using a single replica, but are improved when multiple copies are used. A multimodal transition state ensemble, however, turns out to be more sensitive to large errors in phi (if appropriately gauged) and attempts at successful recreation of the reference ensemble with simple replica algorithms can fall short.

Algorithms↗
PubMed2003

Atomic resolution analysis of the catalytic site of an aspartic proteinase and an unexpected mode of binding by short peptides.

The X-ray structures of native endothiapepsin and a complex with a hydroxyethylene transition state analog inhibitor (H261) have been determined at atomic resolution. Unrestrained refinement of the carboxyl groups of the enzyme by using the atomic resolution data indicates that both catalytic aspartates in the native enzyme share a single negative charge equally; that is, in the crystal, one half of the active sites have Asp 32 ionized and the other half have Asp 215 ionized. The electron density map of the native enzyme refined at 0.9 A resolution demonstrates that there is a short peptide (probably Ser-Thr) bound noncovalently in the active site cleft. The N-terminal nitrogen of the dipeptide interacts with the aspartate diad of the enzyme by hydrogen bonds involving the carboxyl of Asp 215 and the catalytic water molecule. This is consistent with classical findings that the aspartic proteinases can be inhibited weakly by short peptides and that these enzymes can catalyze transpeptidation reactions. The dipeptide may originate from autolysis of the N-terminal Ser-Thr sequence of the enzyme during crystallization.

Aspartic Acid Endopeptidases↗
PubMed2004

Spatially adaptive high-resolution image reconstruction of DCT-based compressed images.

The problem of recovering a high-resolution image from a sequence of low-resolution DCT-based compressed observations is considered in this paper. The introduction of compression complicates the recovery problem. We analyze the DCT quantization noise and propose to model it in the spatial domain as a colored Gaussian process. This allows us to estimate the quantization noise at low bit-rates without explicit knowledge of the original image frame, and we propose a method that simultaneously estimates the quantization noise along with the high-resolution data. We also incorporate a nonstationary image prior model to address blocking and ringing artifacts while still preserving edges. To facilitate the simultaneous estimate, we employ a regularization functional to determine the regularization parameter without any prior knowledge of the reconstruction procedure. The smoothing functional to be minimized is then formulated to have a global minimizer in spite of its nonlinearity by enforcing convergence and convexity requirements. Experiments illustrate the benefit of the proposed method when compared to traditional high-resolution image reconstruction methods. Quantitative and qualitative comparisons are provided.

Algorithms↗
PubMed2002

Can fishes resolve temporal characteristics of sounds? New insights using auditory brainstem responses.

Numerous fish species produce broad-band pulsed sounds with a distinct temporal patterning which is thought to be important during intraspecific communication. In order to determine whether fishes are able to utilize temporal characteristics of acoustic signals, time resolution was determined in four species of otophysines and anabantoids by analyzing auditory brainstem responses (ABRs) to double-click stimuli with varying click periods. At click periods of 3.5 ms, two distinct ABRs were clearly detectable in all species. The minimum pulse period resolvable by the auditory system was below 1.5 ms in each species and slightly intensity-dependent. No differences were found between vocal and non-vocal species within each taxon. Comparisons of the time resolution data to the pulse periods of intraspecific sounds in the vocal species showed that the otophysine Platydoras costatus and the anabantoid Trichopsis vittata are likely to process each pulse within a series of intraspecific sounds. However, as non-vocal and vocal species have a similar minimum resolvable click period, the high temporal resolution capacities of the auditory system of fish might not represent special adaptations for intraspecific acoustic communication. Nonetheless, we suggest that temporal characteristics of naturally occurring conspecific and heterospecific sounds provide reliable information for acoustic communication.

Acoustic Stimulation↗
PubMed2002

Aspherical-atom scattering factors from molecular wave functions. 1. Transferability and conformation dependence of atomic electron densities of peptides within the multipole formalism.

In this study, the feasibility of building a database of theoretical atomic deformation density parameters applicable to the construction of the densities of biomacromolecules and to the interpretation of their X-ray diffraction data is discussed. The procedure described involves generation of valence-only structure factors of tripeptides calculated from theoretical densities at the B3LYP level and the refinement of multipole parameters against these simulated data. Our results so far indicate that the backbone pseudoatoms extracted in such a way are highly transferable and fairly invariant with respect to rotations around single bonds in the peptide framework. The ultimate goal is to use the aspherical-atom database for improved macromolecular refinements that are based on high-resolution data and for prediction of electrostatic properties of larger molecules.

Algorithms↗
PubMed2003

New techniques in macromolecular cryocrystallography: macromolecular crystal annealing and cryogenic helium.

Cryocrystallography is used today for almost all X-ray diffraction data collection at synchrotron beam lines, with rotating-anode generators, and micro X-ray sources. Despite the widespread use of flash-cooling to place macromolecular crystals in the cryogenic state, its use can ruin crystals, trips to the synchrotron, and sometimes even an entire project. Annealing of macromolecular crystals takes little time, requires no specialized equipment, and can save crystallographic projects that might otherwise end in failure. Annealing should be tried whenever initial flash-cooling causes an unacceptable increase in mosaicity, results in ice rings, fails to provide adequate diffraction quality, or causes a crystal to be positioned awkwardly. Overall, annealing improves the quality of data and overall success rate at synchrotron beam lines. Its use should be considered whenever problems arise with a flash-cooled crystal. Helium is a more efficient cryogen than nitrogen and will deliver lower temperatures. Experiments suggest that when crystals are cooled with He rather than N2, crystals maintain order and high-resolution data are less affected by increased radiation load. Individually or in combination, these two techniques can enhance the success of crystallographic data collection, and their use should be considered essential for high-throughput programs.

Cold Temperature↗
PubMedDate not supplied

A milestone in ribosomal crystallography: the construction of preliminary electron density maps at intermediate resolution.

Preliminary electron density maps of the large and the small ribosomal particles from halophilic and thermophilic sources, phased by the isomorphous replacement method, have been constructed at intermediate resolution. These maps contain features comparable in size with what is expected for the corresponding particles, and their packing arrangements are in accord with the schemes obtained by ab-initio procedures as well as with the motifs observed in thin sections of the crystals by electron microscopy. To phase higher resolution data, procedures are being developed for derivatization by specific labeling of the ribosomal particles at selected locations with rather small and dense clusters. Potential binding sites are being inserted either by site directed mutagenesis or by chemical modifications to facilitate cluster binding on the surface of the halophilic large and the thermophilic small ribosomal particles, which yield the crystals diffracting to highest resolution (2.9 and 7.3 A (1 A = 0.1 nm), respectively). For this purpose, the surface of these ribosomal particles is being characterized and procedures are being developed for quantitative detachment of selected ribosomal proteins and for their incorporation into core particles. The genes of these proteins are being cloned, sequenced, mutated to introduce reactive side groups, mainly cysteines, and overexpressed. In parallel, two in situ small and stable complexes were isolated from the halophilic ribosome. Procedures for their crystal production in large quantities are currently being developed. Models, reconstructed at low resolution from crystalline arrays of ribosomes and their large subunits, are being used for initial low-resolution phasing of the X-ray amplitudes. The interpretation of these models stimulated the design and the crystallization of complexes mimicking defined functional states of a higher quality than those obtained for isolated ribosomes. These models also inspired modelling experiments according to results of functional studies, performed elsewhere, focusing on the progression of nascent proteins.

Base Sequence↗
PubMed2002

Glycine receptors: lessons on topology and structural effects of the lipid bilayer.

The members of the superfamily of nicotinicoid receptors, sometimes referred to as the ligand-gated ion channel superfamily (LGICS), are essential mediators in the propagation of electrical signals between cells at neuronal and neuromuscular synapses. Given the significant sequence and proposed topological similarities between family members, the structural architecture of any one of these neuroreceptors is believed to be archetypic for the family of ligand-gated channels. We have focused our biophysical studies on the glycine receptor (GlyR) since homomeric expression of just the alpha1 chain of the receptor is sufficient to reconstitute native-like activity when expressed in heterologous cells, and we have successfully overexpressed and purified relatively large quantities of this receptor. Our CD data suggests that the historical four transmembrane helix topology model for nicotinicoid receptors may be erroneous. Proteolytic studies as well as chemical modification studies coupled with mass spectroscopy (MS) have provided additional evidence that this model may be inappropriate. While we suggest a novel topological model for the superfamily of nicotinicoid receptors, the absence of high resolution data for the transmembrane regions of these ion channels precludes further refinement of this model. In addition, we observe structural changes in the recombinant alpha1 GlyR as a function of bilayer composition, suggesting that these receptors may be dynamically modulated by cellular control over the properties of the plasma membrane.

Amino Acid Sequence↗
PubMed2004

Ab initio phasing based on topological restraints: automated determination of the space group and the number of molecules in the unit cell.

The connectivity-based phasing method has been demonstrated to be capable of finding molecular packing and envelopes even for difficult cases of structure determination, as well as of identifying, in favorable cases, secondary-structure elements of protein molecules in the crystal. This method uses a single set of structure factor magnitudes and general topological features of a crystallographic image of the macromolecule under study. This information is expressed through a number of parameters. Most of these parameters are easy to estimate, and the results of phasing are practically independent of these parameters when they are chosen within reasonable limits. By contrast, the correct choice for such parameters as the expected number of connected regions in the unit cell is sometimes ambiguous. To study these dependencies, numerous tests were performed with simulated data, experimental data and mixed data sets, where several reflections missed in the experiment were completed by computed data. This paper demonstrates that the procedure is able to control this choice automatically and helps in difficult cases to identify the correct number of molecules in the asymmetric unit. In addition, the procedure behaves abnormally if the space group is defined incorrectly and therefore may distinguish between the rotation and screw axes even when high-resolution data are not available.

Algorithms↗
PubMed2004

Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data.

Staphylococcal protein A (SpA) is a virulence factor from Staphylococcus aureus that is able to bind to immunoglobulins. The 3D structures of its immunoglobulin (Ig) binding domains have been extensively studied by NMR and X-ray crystallography, and are often used as model structures in developing de novo or ab initio strategies for predicting protein structure. These small three-helix-bundle structures, reported in free proteins or Ig-bound complexes, have been determined previously using medium- to high-resolution data. Although the location and relative orientation of the three helices in most of these published 3D domain structures are consistent, there are significant differences among the reported structures regarding the tilt angle of the first helix (helix 1). We have applied residual dipolar coupling data, together with nuclear Overhauser enhancement and scalar coupling data, in refining the NMR solution structure of an engineered IgG-binding domain (Z domain) of SpA. Our results demonstrate that the three helices are almost perfectly antiparallel in orientation, with the first helix tilting slightly away from the other two helices. We propose that this high-accuracy structure of the Z domain of SpA is a more suitable target for theoretical predictions of the free domain structure than previously published lower-accuracy structures of protein A domains.

Binding Sites↗