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PubMed1993

On the application of phase relationships to complex structures. XXXII. A small protein at low resolution.

The direct-methods program SAYTAN is applied to data at various restricted resolutions for a small protein. It is shown that useful sets of phases can be obtained even down to 3 A resolution. Conventional figures of merit are not very discriminating for the phase sets developed, but modified figures of merit seem capable of selecting the better phase sets, at least for those generated from 2 A or higher resolution data.

Journal Article↗
PubMed1983

Quantitative double-label radiography of two-dimensional protein gels using color negative film and computer analysis.

We have devised a method of data collection and computer analysis which allows utilization of the resolving power of two-dimensional gel electrophoresis of proteins, in conjunction with the versatility of using two different radionuclides simultaneously. Cultures of Escherichia coli growing with exponential growth rate constants (mu) of 0.32 and 1.43 were labeled with [3H]leucine and [14C]leucine, respectively; these samples were mixed, and cell protein was separated on a two-dimensional gel. Spacial and quantitative data for both radionuclides were recorded on color negative film by radiographic exposure. Data for 14C alone were then collected photographically from the red-light-sensitive layer of the film using a red filter, while data for 3H and spillover of 14C were collected photographically from the blue-light-sensitive layer using a blue filter. These two data sets were analyzed by CINT, a computer program for analysis of two-dimensional gels, and quantitative data for 3H were calculated after determination of spillover of 14C in a manner analogous to quantification of 3H and 14C by liquid scintillation counting. Quantitative data from over 1000 protein spots representing from 0.002% to 10% of the total 3H or 14C, respectively, are available in a matter of hours. We have used this method to analyze the effect of growth rate and medium composition on the relative levels of individual proteins in a pathogenic strain of E. coli which contains group 111 O-antigen. As expected, the relative levels of aminoacyl-tRNA synthetases, protein chain elongation factors, ribosomal proteins, and the alpha-subunit of RNA polymerase are all increased with increased growth rate; the magnitude of these changes agreed with previous data derived using other strains of E. coli. Alterations in the levels of other proteins identified on the two-dimensional gels could be interpreted in terms of changes in medium composition. When compared to manual data collection by excising radiolabeled proteins and quantifying 3H and 14C in a liquid scintillation counter following combustion to H2O and CO2, respectively, this new method of data collection and computer analysis increases the resolution of data collection and decreases the time involved from days to hours.

Bacterial Proteins↗
PubMed1992

[Paroxysmal atrial fibrillation in patients with chronic ischemic cardiopathy: a study of high-resolution atrial activation].

BACKGROUND: Patients with ischemic heart disease and episodes of paroxysmal atrial fibrillation are at major risk of stroke. In order to prevent such episodes, through the identification of patients prone to atrial fibrillation, we investigated the high-resolution atriogram of 65 patients with chronic ischemic heart disease, 54 male and 11 female, mean age 60.22 +/- 9.04 years. Based on previous documented episodes of atrial fibrillation, the patients were divided into two groups: group A, 45 males and 3 females, mean age 58.92 +/- 7.68 years, without atrial fibrillation; group B, 9 males and 8 females, mean age 63.88 +/- 11.6 years, with atrial fibrillation. RESULTS: High resolution atrial duration (100-300 Hz) in group B (with atrial fibrillation) was higher than in group A (without atrial fibrillation) (140.59 +/- 16.85 ms vs 121.77 +/- 11.27 ms, p < 0.001); Non filtered atrial duration (0-300 Hz) was not different between the two groups, A and B (118.54 +/- 10.96 ms vs 123.53 +/- 18.77 ms, p = NS); The prevalence of late atrial potentials was higher in group B than in group A (60.8% vs 7.1%, p < 0.001); No relation was observed between high resolution atriogram data and echocardiographic measurements; Sensibility was 82%, specificity 81%, and predictivity 60%. CONCLUSIONS: Data from our study show that high resolution electrocardiography is a valid tool for identifying patients prone to atrial fibrillation. Such patients can be identified by the presence of "late atrial potentials" that, like late ventricular potentials for ventricular tachycardia, are correlated with atrial fibrillation. Nevertheless, a larger cohort of patients is necessary to confirm these results.

Aged↗
PubMed1989

Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallographic data at 1.6-A resolution.

Carp parvalbumin coordinates calcium through one carbonyl oxygen atom and the oxygen-containing side chains of 5 amino acid residues, or 4 residues and a water molecule, in a helix-loop-helix structural motif. Other calcium-binding proteins, including calmodulin and troponin C, also possess this unique calcium-binding design, which is designated EF-hand or calmodulin fold. Parvalbumin has two such sites, labeled CD and EF. Each of the calcium-binding sites of refined structures of proteins belonging to this group has a 7-oxygen coordination sphere except those of the structure of parvalbumin as it was reported in 1975. This structure had been refined at 1.9 A using difference Fourier techniques on film data. The CD site appeared to be 6-coordinate and the EF site 8-coordinate. Results of NMR experiments using 113Cd-substituted parvalbumin, however, indicate that the sites are similar to one another with coordination number greater than 6. To resolve the inconsistency between crystallographic and NMR results, 1.6 A area detector data was collected for native and cadmium-substituted parvalbumin; the structures have been refined to R factors of 18.7% and 16.4%, respectively, with acceptable geometry and low errors in atomic coordinates. Differences between the parvalbumin structure described in 1975 and the present structure are addressed, including the discovery of 7-coordination for both the CD and EF sites.

Animals↗
PubMed1993

[Mitochondrial morphogenesis in insects during meiosis and spermatogenesis: a comparative study between modern high resolution microscopy and historical data].

Spermatogenesis in cysts isolated from testes of Drosophila and morphogenesis of male germ cell mitochondria were observed in vitro and compared with their first description in the literature. Since Drosophila started to be used for laboratory research only at the beginning of the 20th century, publications dealing with other insects have been consulted for earlier periods. Formerly, results were usually obtained from squashed preparations. This technique causes many artifacts and only occasionally can intact cysts be observed. It was only after tissue culture technique and microscopes improved that in vitro observation of differentiating cysts became possible. However, thanks to acute observational skills and careful reasoning, former researchers already had a correct picture of the early development of male germ cell mitochondria. Modern high resolution microscopy confirmed their results.

Animals↗
PubMed1999

Crystallization and preliminary X-ray analysis of alpha-D-glucuronidase from Bacillus stearothermophilus T-6.

alpha-D-Glucuronidases cleave the alpha-1,2-glycosidic bond of the 4-O-methyl-alpha-D-glucuronic acid side chain in xylan. Of the xylan-debranching hydrolases, these enzymes are the least studied and characterized. The alpha-glucuronidase gene (aguA) from Bacillus stearothermophilus T-6 has been cloned, sequenced and overproduced in Escherichia coli. The gene encodes for a protein of 679 amino acids with a calculated molecular weight of 78480 and a pI of 5.42. alpha-Glucuronidase T-6 shows high homology to the alpha-glucuronidases of Thermotoga maritima (60% identity) and of Tri-choderma reesei (44% identity). Based on the amino-acid sequence similarity, it is likely that these enzymes represent a new class of glycosyl hydrolases. Crystallographic studies of alpha-glucuronidase T-6 were initiated to study the mechanism of catalysis, as well as to provide a structural basis for rational introduction of enhanced thermostability by site-specific mutagenesis. In this report, the crystallization and preliminary crystallographic characterization of the native alpha-glucuronidase T-6 enzyme is described. Two crystal forms were found suitable for detailed crystal structure analysis. The T1 form was obtained by the vapour-diffusion method using PEG 4000 as a precipitant and 2-propanol as an organic additive. The crystals belong to a primitive tetragonal crystal system (space group P41212 or P43212) with unit-cell dimensions a = b = 76.1 and c = 331.2 A. These crystals are mechanically strong, are stable in the X--ray beam and diffract X-rays to better than 2.4 A resolution. A full 3.0 A resolution diffraction data set (97.3% completeness, Rmerge 9.8%) has recently been collected on one crystal at room temperature using a rotating-anode X-ray source and an R-AXIS IIc imaging-plate detector. The M1 form was obtained and characterized by similar techniques. The best crystallization occurred at a slightly lower pH and a lower concentration of 2-propanol. The crystals belong to a primitive monoclinic crystal system (space group P21) with unit-cell dimensions a = 65.8, b = 127.4, c = 96.6 A and beta = 97.9 degrees. These crystals are also quite strong and stable, and diffract to better than 2.8 A resolution. A full 2.8 A resolution diffraction data set (96.2% completeness, Rmerge 7.6%) has recently been collected on one crystal at room temperature using the same R-AXIS IIc setup. Both forms are currently being used to obtain crystallographic phasing via isomorphous heavy-atom derivatives and selenomethionine MAD experiments.

Bacterial Proteins↗
PubMed1998

Structure of the capsid of Pf3 filamentous phage determined from X-ray fibre diffraction data at 3.1 A resolution.

We have recorded X-ray diffraction patterns at 3.1 A resolution from magnetically aligned fibres of the Pf3 strain of filamentous bacteriophage (Inovirus). The patterns are similar to patterns from the higher-temperature form of the Pf1 strain, indicating that the Pf3 and Pf1 virions have the same helix symmetry and similar protein subunit shape. This is of particular interest, given that the primary structures of the two protein subunits are quite different; and the nucleotide/protein subunit ratio in the Pf3 virion is more than twice that in Pf1, indicating important differences in DNA packaging. We have built a molecular model of the Pf3 protein capsid based on the model of Pf1, and refined it against the diffraction data using simulated annealing. The refinement confirms that the two structures are similar, which may reflect a fundamental motif of alpha-helix packing. However, there are some differences between the structures: the Pf3 subunit appears to be completely alpha-helical, beginning at the N terminus, whereas the first few residues of the Pf1 subunit are not helical; and the structure of the C-terminal region of the Pf3 subunit at the inner surface of the tubular capsid indicates that DNA/protein interactions in this virion may involve both aromatic side-chains and positively charged side-chains, whereas those in the Pf1 virion involve predominantly only the latter. In the course of this work, we have developed new approaches to refinement and validation of helical structures with respect to continuous transform fibre diffraction data.

Amino Acid Sequence↗
PubMed2004

Increased identification of peptides by enhanced data processing of high-resolution MALDI TOF/TOF mass spectra prior to database searching.

This paper presents application of sequential enhanced data processing procedures to high-resolution tandem mass spectra for identification of peptides using the Mascot database search algorithm. A strategy for (1) selection of fragment ion peaks from MS/MS spectra, (2) utilization of improved mass accuracy of the precursor ions, and (3) wavelet denoising of the mass spectra prior to fragment ion selection have been developed. The number of peptide identifications obtained using the enhanced processing was then compared with that obtained using software provided by the instrument manufacturer. Approximately 9000 MS/MS spectra acquired by the Applied Biosystems 4700 TOF/TOF MS instrument were used as a model data set. After application of the new processing, an increase of 33% unique peptides and 22% protein identifications with at least two unique peptides were found. The influence of the processing on the percentage of false positives, estimated by searching against a randomized database, was estimated to increase false positive identifications from 2.7 to 3.9%, which was still below the 5% error rate specified in the Mascot search. These data processing approaches increase the amount of information that can be extracted from LC-MS analysis without the necessity of additional experiments.

Algorithms↗
PubMed1995

Criteria for the mode of binding of DNA binding agents.

A complete characterization of DNA binding agents requires that their mode of binding to DNA be established. In the absence of high resolution structural data, the mode of binding is, of necessity, usually inferred indirectly from various solution studies. The purpose of this study is to show that only certain methods can be used reliably to infer the DNA binding mode. Comparative fluorescence and hydrodynamic studies using the proven intercalator ethidium and the groove binder Hoechst 33258 are described. The results of our studies show that while fluorescence intensity, polarization, and quenching measurements can detect a binding interaction of the ligand with DNA, none are sensitive indicators of the binding mode. Fluorescence contact energy transfer studies can reliably indicate intercalation, as can viscosity measurements. Our results illustrate reliable criteria that may be used to distinguish intercalation from groove binding in the absence of high resolution structural data.

Animals↗
PubMed1997

Disproportion of cerebral surface areas and volumes in cerebral dysgenesis. MRI-based evidence for connectional abnormalities.

In the normal adult human brain, there are quantitative relationships between a surface area measure of the grey matter and the volume of hemispheric grey matter, the volume of the hemispheric subcortical matter and the cross-sectional area of the corpus callosum as revealed by analysis of high resolution MRI data. These relationships reflect structural order in, and biological features of, normal human cerebral hemispheres. Cerebral dysgenesis (CD) is associated with disruption of the normal organization of the hemispheres to a greater or lesser extent and is often manifest as refractory epilepsy. We have examined structural proportions and their disruption in the brains of patients with epilepsy and CD. We found that structural measures were abnormal in 60% of patients with CD, with abnormalities in 64% of hemispheres that, on visual inspection alone, appeared completely normal. We showed that the disruptions found are compatible with expected histopathology in cases where histopathology may be predictable, and that extensive abnormalities may be due to abnormal patterns of connections within the hemispheres. In some cases, it may be possible to predict histopathology on the basis of quantitative analyses of high resolution MRI data, when such prediction is not possible on visual inspection alone.

Adult↗
PubMed1993

High-resolution refinement of the hexagonal A-DNA octamer d(GTGTACAC) at 1.4 A.

The hexagonal crystal form of the octamer d(GTGTACAC), grown in the presence of spermine, has unit-cell dimensions a = b = 32.18 and c = 78.51 A, space group P6(1)22, with one DNA strand in the asymmetric unit. The structure has been refined starting with the earlier lower resolution model and using high-resolution 1.4 A data collected on a Siemens-Xentronics area detector at 258 K. There were 4365 unique reflections greater than 2sigma(F) in the resolution range 5-1.4 A. The model was refitted into 3F(o) - 2F(c). Sim-weighted omit maps and difference maps were used to locate water molecules. The final model with 161 DNA atoms and 37 water molecules gave an R factor of 19.8%. Crystals of the same octamer were also grown in the presence of spermidine instead of spermine, and refinement using nominal 1.45 A resolution data, 3292 unique reflections, final R = 19.1%, gave virtually identical DNA parameters. No bound spermine or spermidine was detected in either of these structure analyses. The electron density was clear for the DNA and showed holes in the center of the six-membered rings of bases, and also in the center of some of the sugar rings. The high-resolution structure has provided more precise DNA parameters and confirmed the features observed in the earlier 2 A study including the packing-induced distortion in the A7 (A15) sugar pucker from C(3')-endo and C(2')-endo. This change causes the end base pairs to bend away from the helix axis while the rest of the duplex is nearly linear. The hydration patterns in the deep and shallow grooves have been characterized. Chains of water molecules were found, but no rings. The familiar intermolecular contact region between the end base pair and the minor groove of a symmetry-related duplex, involving four residues on one strand and two on the other, has been analyzed. One of these interactions is a hydrogen bond.

Journal Article↗
PubMed2001

Resolution of two-way data: theoretical background and practical problem-solving. Part 1: theoretical background and methodology.

This paper reviews recent progress in the resolution of two-way data obtained from hyphenated instruments. Special emphasis is placed on the solution of practical problems. Methods for estimating the number of chemical components both statistically and visually (the first step in solving the resolution problem) and methods for resolving the pure profiles (the second step in solving the resolution problem) are discussed in detail. To deal with real-world problems, pitfalls in the chemometric analysis of the two-way data from the instrumental measurements are also pointed out. Applications of methods for solving some difficult practical problems in environmental chemistry, pharmaceutical chemistry, and physical chemistry will be discussed in the second part of this paper.

Journal Article↗
PubMed2004

High temporal and spatial resolution 4D MRA using spiral data sampling and sliding window reconstruction.

Contrast-enhanced magnetic resonance angiography (CE-MRA) requires high spatial resolution to demonstrate detailed vasculature and high temporal resolution to capture the contrast bolus. Sparse bright voxels in MRA permit substantial undersampling in MRI data acquisition, allowing simultaneous high temporal and spatial resolution. We developed a time-resolved 3D MRA technique using the efficient spiral sampling trajectory, and performed off-resonance corrections using inhomogeneity field maps. View sharing and sliding window reconstruction were utilized to generate high temporal resolution. High-resolution 3D angiograms were generated at 1-2 s per frame, with a 5-8 ml gadolinium dose, in patients with vascular disease.

Arteriosclerosis↗
PubMed1998

Experiences in intraoperative computer-aided navigation in ENT sinus surgery with the Aesculap navigation system.

Five patients with chronic sinus pathology and an indication for sinus surgery were selected. For intraoperative navigation, we used Surgical Planning and Orientation Computer Systems (SPOCS) Aesculap navigation software (ISG Technologies, Mississauga, Ontario, Canada) and surgical instruments fitted with light-emitting diodes. Navigation procedures are described in detail in the article. The system's precision was measured by pointing at anatomical landmarks. The accuracy was measured as the distance in millimeters between the bony structures of the computed tomographic (CT) scan on screen and the cross-hair of the pointer tip displayed on the screen. Another parameter of the system's accuracy was calculated by the system itself as the root mean square error in millimeters between the markers' position as registered and their position in the CT data set. Axial 3/3/1-mm spiral CT provided sufficient resolution, and data transfer via optical disk was practicable. Positioning of the navigation equipment required some experience, and the registration of the patient's head position also needed attention, as the markers have to be pointed at precisely. During the operation, the position of the head-tracking system on the patient's head must remain unchanged to ensure a correct navigation display. The main advantage of the computed navigation system was the constant orientation provided during the sinus surgical procedure. Borders and critical anatomical structures could be identified in the corresponding CT data set, thus enabling the surgeon to decide on subsequent procedures. Use of the navigation system was found to increase the operation time by about 1 h, resulting in additional time under anesthesia. We found the SPOCS Aesculap computed navigation system to be an established technical aid, ready for use in ENT sinus surgery. In the cases reported here, a precision between 1 and 3 mm was obtained.

Humans↗
PubMed2005

High-resolution gas chromatography retention data as a basis for estimation of the octanol-water distribution coefficients (Kow) of PCB: the effect of experimental conditions.

The semi-experimental approach to approximating physicochemical data relevant to environmental distribution (vapor pressure and gas-octanol distribution) by correlation with gas chromatography (GC) retention data has been extended to the determination of Kow values. We estimated Kow values >10(4) for polychlorinated biphenyls (PCB), which are often derived by liquid chromatography, by correlation with gas chromatographic retention data. Selecting a set of reference compounds with known Kow values for relative retention time (RRT) correlation enables easy and accurate semi-empirical calculation of further Kow values for a given group of congeners. The RRT/log Kow correlation is validated in this paper with regard to the following gas chromatographic conditions: (1) isothermal versus temperature-programmed elution, (2) the possible effect of the polarity of the stationary phase, and (3) the effect of the format of the standardized GC retention data. The advantages of our Kow(GC) method can be summarized as follows: complex mixtures can be analyzed, only amounts in the nanogram-range or less are required, Kow values of isomers can be determined and the exact structure of compounds need not be known. Normalized GC retention data of persistent organic pollutants are readily available. The quality of the Kow values obtained by the GC method compares well with that for other Kow estimation methods. It depends mainly on the accuracy of the Kow data of the structurally correlated compounds used as standards for the correlation cohort. The Kow(GC) data for all 209 PCB congeners are given.

Chemical Phenomena↗
PubMed2006

Neutron Laue macromolecular crystallography.

Recent progress in neutron protein crystallography such as the use of the Laue technique and improved neutron optics and detector technologies have dramatically improved the speed and precision with which neutron protein structures can now be determined. These studies are providing unique and complementary insights on hydrogen and hydration in protein crystal structures that are not available from X-ray structures alone. Parallel improvements in modern molecular biology now allow fully (per)deuterated protein samples to be produced for neutron scattering that essentially eradicate the large-and ultimately limiting-hydrogen incoherent scattering background that has hampered such studies in the past. High quality neutron data can now be collected to near atomic resolution (approximately 2.0 A) for proteins of up to approximately 50 kDa molecular weight using crystals of volume approximately 0.1 mm3 on the Laue diffractometer at ILL. The ability to flash-cool and collect high resolution neutron data from protein crystals at cryogenic temperature (15 K) has opened the way for kinetic crystallography on freeze trapped systems. Current instrument developments now promise to reduce crystal volume requirements by a further order of magnitude, making neutron protein crystallography a more accessible and routine technique.

Crystallography↗
PubMed2003

High-resolution gas chromatography retention data as basis for the estimation of KOW values using PCB congeners as secondary standards.

We estimated KOW values that are usually derived by liquid chromatography solely from gas chromatographic (GC) data by selective correlation with PCB congeners as secondary standards. The GC method was established and validated with literature-known values obtained with other methods. Twenty-seven chlorinated diphenyl ethers (PCDE), 19 chlorinated naphthalenes (PCN), 4,4'-DDE, and three brominated diphenyl ethers (PBDE) were used for method validation. The advantages of our method are that only amounts in the nanogram range or less are needed, complex mixtures can be analyzed, KOW values of isomers can be determined, and even the exact structure of compounds does not have to be known. The quality of the KOW values obtained by the GC method mainly depends on the accuracy of the data of the compounds used as standards for the correlation. These data should be based on reliable experimental methods. Our semi-experimental approach in approximating physicochemical data relevant to the environmental distribution--vapor pressure of subcooled liquid and log KOW--can be extended to further classes of compounds because normalized GC retention data are easily available. We exemplified our approach with a bioaccumulating naturally occurring heptachlorinated 1-methyl-1',2-bipyrrole, which is highly abundant in fish from the South Atlantic among others.

Chromatography, Gas↗