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 163 records · Page 9Linked to original sources
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↗
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↗
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↗
PubMed1994

Crystal structure of toxin II from the scorpion Androctonus australis Hector refined at 1.3 A resolution.

The crystal structure of toxin II from the scorpion Androctonus australis Hector has been refined at 1.3 A resolution using restrained least-squares methods. The final R-factor is 0.148 for the 13,619 reflections between 7.0 A and 1.3 A resolution with F > 2.5 sigma (F) and the bond length standard deviation from ideality is 0.017 A. Although minor changes have been introduced relative to the model previously refined at 1.8 A resolution, the use of higher-resolution data has allowed the modelling of some discrete disorder. Thus, three residues (including a disulphide bridge) have been built with multiple conformations. Occupancies were refined for the 106 solvent molecules included in the model, nine of them with explicit multiple sites. There is well-defined electron density for some of the protein hydrogen atoms in the final difference Fourier map. A detailed description of the toxin structure is presented, along with a comparison with the high-resolution structure of the related variant-3 scorpion toxin.

Amino Acid Sequence↗
PubMed1986

Effect of elastic bend distortions on electron diffraction data from thin protein microcrystals.

The effect of small elastic bend distortions in thin protein crystals on electron diffraction intensities is investigated using a model calculation for rubredoxin. The calculation, based on analytical expression derived by Cowley, has been shown previously to give an almost quantitative description of kinematical diffraction from linear chain systems. It is therefore shown that, unless the selected area used in the electron diffraction experiment is very small (or alternatively the incident beam has a small coherence length), the high resolution data may not be useful for structure determination, since they do not represent the total contents of the unit cell.

Chemical Phenomena↗
PubMed2001

Studies on the hydrolyzing mechanism for cyclodextrins of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structure of the mutant E354A complexed with beta-cyclodextrin, and kinetic analyses on cyclodextrins.

Crystals of the mutant E354A of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII) complexed with beta-cyclodextrin were prepared by a soaking method, and the diffraction data were collected at 100 K, using Synchrotron radiation (SPring-8). The crystals belong to an orthorhombic system with the space group P2(1)2(1)2(1) and cell dimensions a = 111.1 A, b = 117.7 A, c = 113.3 A, which is almost isomorphous with crystals of the wild-type TVAII, and the structure was refined to an R-factor = 0.208 (R(free) = 0.252) using 3.0 A resolution data. The refined structure shows that the interactions between Phe286 and two C6 atoms of beta-cyclodextrin at the hydrolyzing site are important for TVAII to recognize cyclodextrins as substrates. This observation from the X-ray structure was supported by kinetic analyses of cyclodextrins using the wild-type TVAII, the mutant F286A and F286L. These studies also suggested that the TVAII-hydrolyzing mechanism for cyclodextrins is slightly different from that for starch.

Amino Acid Substitution↗
PubMed1989

Improvements in MR angiography using phase-corrected data sets.

The objective of this work is refinement of an MR angiography technique via postprocessing removal of phase errors which inhibit static signal subtraction. Projective views of the object are obtained using interleaved flow-compensated and noncompensated gradient waveforms. Complex subtraction of data sets is required since a projection dephase pulse is used for static signal suppression. This renders the difference image susceptible to systematic phase errors which are modeled as a smoothly varying multiplicative phase function. The error function is estimated by comparison of heavily spatial filtered renditions of the object acquired without projection dephasing in order to minimize influence of flow. The phase correction is then applied to high-resolution data sets collected with projection dephasing to enhance flow sensitivity. The technique is demonstrated by improvement of MR angiograms of rats acquired on a 2-T, 31-cm-bore system.

Animals↗
PubMed2001

Improvement of SAS triple invariant estimates for macromolecular direct-methods phasing.

Single-wavelength anomalous dispersion (SAS) data can in principle be phased by direct methods since a priori estimates of the three-phase structure invariants can be computed from these data. The mean phase error of the most reliable triple estimates for a small protein, however, is typically no better than 60 degrees, and does not bode well for applications to larger structures. A procedure is described that can substantially lower the error in these estimates and introduce a larger number of useful triple invariants into the phasing process. The mean phase error of the most reliable triples for a 2.5 A resolution data set from a Pt derivative of a 115-residue protein was reduced from 55 to 25 degrees by this method. It was also possible to identify a significant number of the poorest triple estimates, those with mean phase errors approaching 90 degrees, such that they could be reliably down-weighted or excluded from the phasing process.

Crystallography, X-Ray↗
PubMed1998

End-of-life confusion in patients with cancer.

PURPOSE/OBJECTIVES: To review the literature on confusion at the end of life, provide accurate definitional and defining characteristics of confusion, and outline nursing strategies for its resolution. DATA SOURCES: Published articles, computerized databases, book chapters, reference lists from chapters and journal articles. DATA SYNTHESIS: As a major component of symptom distress in terminal care, confusion has not been defined clearly and therefore has not benefited from rigorous assessment and study as have other end-of-life symptoms. CONCLUSIONS: Increased knowledge about confusion that occurs in patients with widely metastatic cancer will assist in accurate symptom identification, early recognition, and timely management to reduce cognitive symptom distress at the end of life. Improved symptom resolution also can benefit family coping during terminal care. IMPLICATIONS FOR NURSING PRACTICE: Oncology nurses can devise management protocols for confused patients that include screening criteria, pharmacologic interventions, environmental support, and prophylactic safety measures.

Confusion↗
PubMed2005

The effect of delayed visual feedback on telerobotic surgery.

BACKGROUND: Telerobotic surgery is ideally suited for remote applications in which the instrument control console is stationed separately from the end-effectors at the patient's bedside. However, if the distance between the console and the patient is great enough, a lag effect or latency between end-effector manipulation and the depicted image leads to alterations in movement patterns. The purpose of this study was to determine the effect of visual delay on surgical task performance. METHODS: At an endoscopic skill station, an analogue delay device was interposed between the surgical field and monitor to delay the transmission of visual information, thus mimicking the distance effect of data transmission. Three surgeons with similar laparoscopic experience participated in the laparoscopic knot tying portion of the study, and seven residents participated in the accuracy and dexterity tasks. The time to complete a single throw was recorded in seconds after adding consecutively increasingly time delay in 50 ms increments. Similar time delay increments were added for the accuracy and dexterity tasks, which involved passing a needle through two adjacent circles and passing a small cylinder through a larger one to reproduce two-handed coordination and spatial resolution. Data were presented as the median time to complete each task. RESULTS: For all three tasks, an incremental increase in time delay was associated with a significant (p < 0.001) increase in the time to complete the task. For dexterity, a statistically significant (p <or= 0.05) delay was identified at 0.25 s of delay from control values without delay. A move-and-wait strategy was gradually adopted up to 0.4 s of visual delay. CONCLUSIONS: Compensation for visually delayed image perception occurs on several levels. Initial adaptations include slower end-effector manipulation; late adaptive changes include a move-and-wait strategy. Increased time to perform surgical maneuvers as well as diminished accuracy, diminished dexterity, and increasing fatigue represent additional performance encumbrances evoked by visual time delay. The nuances of both human and digital compensatory mechanisms for visual time delay must be defined and enhanced to maximize the potential for telerobotic surgical applications.

Adaptation, Physiological↗