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PubMedDate not supplied

A selective inversion recovery method for the improvement of 23Na NMR spectral resolution in isolated perfused rat hearts.

Shift-reagent-aided 23Na NMR spectroscopy allows differentiation of the intracellular (Na(i)) and extracellular sodium (Na(o)) signals. The goal of the present study has been to develop a 23Na NMR spectroscopic method to minimize the intensity of the shift-reagent-shifted Na(o) signal and thus increase Na(i) resolution. This is achieved by a selective inversion recovery (SIR) method which enhances the resolution between the Na(i) and Na(o) peaks in shift-reagent-aided 23Na NMR spectroscopy. The application of SIR with Dy(TTHA), Tm(DOTP), or with low concentrations of Dy(PPP)2 results in both good spectral resolution and physiologically acceptable contractile function in the isolated, perfused rat heart model.

Animals↗

PubMed2004

High resolution mass spectrometric alveolar proteomics: identification of surfactant protein SP-A and SP-D modifications in proteinosis and cystic fibrosis patients.

In the present study, one- and two-dimensional gel electrophoresis combined with high resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) have been applied as powerful approaches for the proteome analysis of surfactant proteins SP-A and SP-D, including identification of structurally modified and truncation forms, in bronchoalveolar lavage fluid from patients with cystic fibrosis, chronic bronchitis and pulmonary alveolar proteinosis. Highly sensitive micropreparation techniques were developed for matrix-assisted laser desorption/ionization (MALDI) FT-ICR MS analysis which provided the identification of surfactant proteins at very low levels. Owing to the high resolution, FT-ICR MS was found to provide substantial advantages for the structural identification of surfactant proteins from complex biological matrices with high mass determination accuracy. Several protein bands corresponding to SP-A and SP-D were identified by MALDI-FT-ICR MS after electrophoretic separation by one- and two-dimensional gel electrophoresis, and provided the identification of structural modifications (hydroxy-proline) and degradation products. The high resolution mass spectrometric proteome analysis should facilitate the unequivocal identification of subunits, aggregations, modifications and degradation products of surfactant proteins and hence contribute to the understanding of the mechanistic basis of lung disease pathogenesis.

Bronchoalveolar Lavage Fluid↗

PubMed2006

Identification of glycoconjugates in the urine of a patient with congenital disorder of glycosylation by high-resolution mass spectrometry.

More than 150 molecular species were detected in a single glycoconjugate fraction obtained from urine of a congenital disorders of glycosylation (CDG) patient by use of high-resolution FT-ICR MS. With respect to its high-mass accuracy and resolving power, FT-ICR MS represents an ideal tool for analysis of single components in complex glycoconjugate mixtures obtained from body fluids. The presence of overlapping nearly isobaric ionic species in glycoconjugate mixtures obtained from CDG patient's urine was postulated from fragmentation data of several precursor ions obtained by nanoESI Q-TOF CID. Their existence was confirmed by high-resolution/high-mass accuracy FT-ICR MS detection. High-resolution FT-ICR mass spectra can, therefore, be generally considered for glycoscreening of complex mixture samples in a single stage. From the accurate molecular ion mass determinations the composition of glycoconjugate species can be identified. Particular enhancement of identification is offered by computer-assisted calculations in combination with monosaccharide building block analysis, which can be extended by considerations of non-carbohydrate modifications, such as amino acids, phosphates and sulfates. Taking advantage of this strategy, the number of compositions assigned to mass peaks was significantly increased in a fraction obtained from urine by size exclusion and anion exchange chromatography.

Congenital Disorders of Glycosylation↗

PubMed1995

Carbohydrate binding sites in a pancreatic alpha-amylase-substrate complex, derived from X-ray structure analysis at 2.1 A resolution.

The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase (PPA, EC 3.2.1.1.) that was soaked with the substrate maltopentaose showed electron density corresponding to two independent carbohydrate recognition sites on the surface of the molecule. Both binding sites are distinct from the active site described in detail in our previous high-resolution study of a complex between PPA and a carbohydrate inhibitor (Qian M, Buisson G, Duée E, Haser H, Payan F, 1994, Biochemistry 33:6284-6294). One of the binding sites previously identified in a 5-A-resolution electron density map, lies at a distance of 20 A from the active site cleft and can accommodate two glucose units. The second affinity site for sugar units is located close to the calcium binding site. The crystal structure of the maltopentaose complex was refined at 2.1 A resolution, to an R-factor of 17.5%, with an RMS deviation in bond distances of 0.007 A. The model includes all 496 residues of the enzyme, 1 calcium ion, 1 chloride ion, 425 water molecules, and 3 bound sugar rings. The binding sites are characterized and described in detail. The present complex structure provides the evidence of an increased stability of the structure upon interaction with the substrate and allows identification of an N-terminal pyrrolidonecarboxylic acid in PPA.

Animals↗

PubMed2002

1.3-A resolution structure of human glutathione S-transferase with S-hexyl glutathione bound reveals possible extended ligandin binding site.

Cytosolic glutathione S-transferases (GSTs) play a critical role in xenobiotic binding and metabolism, as well as in modulation of oxidative stress. Here, the high-resolution X-ray crystal structures of homodimeric human GSTA1-1 in the apo form and in complex with S-hexyl glutathione (two data sets) are reported at 1.8, 1.5, and 1.3A respectively. At this level of resolution, distinct conformations of the alkyl chain of S-hexyl glutathione are observed, reflecting the nonspecific nature of the hydrophobic substrate binding site (H-site). Also, an extensive network of ordered water, including 75 discrete solvent molecules, traverses the open subunit-subunit interface and connects the glutathione binding sites in each subunit. In the highest-resolution structure, three glycerol moieties lie within this network and directly connect the amino termini of the glutathione molecules. A search for ligand binding sites with the docking program Molecular Operating Environment identified the ordered water network binding site, lined mainly with hydrophobic residues, suggesting an extended ligand binding surface for nonsubstrate ligands, the so-called ligandin site. Finally, detailed comparison of the structures reported here with previously published X-ray structures reveal a possible reaction coordinate for ligand-dependent conformational changes in the active site and the C-terminus.

Apoenzymes↗

PubMed1994

Structural analysis of two crystal forms of lentil lectin at 1.8 A resolution.

The structures of two crystal forms of lentil lectin are determined and refined at high resolution. Orthorhombic lentil lectin is refined at 1.80 A resolution to an R-factor of 0.184 and monoclinic lentil lectin at 1.75 A resolution to an R-factor of 0.175. These two structures are compared to each other and to the other available legume lectin structures. The monosaccharide binding pocket of each lectin monomer contains a tightly bound phosphate ion. This phosphate makes hydrogen bonding contacts with Asp-81 beta, Gly-99 beta, and Asn-125 beta, three residues that are highly conserved in most of the known legume lectin sequences and essential for monosaccharide recognition in all legume lectin crystal structures described thus far. A detailed analysis of the composition and properties of the hydrophobic contact network and hydrophobic nuclei in lentil lectin is presented. Contact map calculations reveal that dense clusters of nonpolar as well as polar side chains play a major role in secondary structure packing. This is illustrated by a large cluster of 24 mainly hydrophobic amino acids that is responsible for the majority of packing interactions between the two beta-sheets. Another series of four smaller and less hydrophobic clusters is found to mediate the packing of a number of loop structures upon the front sheet. A very dense, but not very conserved cluster is found to stabilize the transition metal binding site. The highly conserved and invariant nonpolar residues are distributed asymmetrically over the protein.

Amino Acid Sequence↗

PubMed1995

Crystals of an antibody Fv fragment against an integral membrane protein diffracting to 1.28 A resolution.

The Fv fragment of a monoclonal antibody, 7E2 (IgG1, kappa, murine), which is directed against the integral membrane protein cytochrome c oxidase (EC 1.9.3.1) from Paracoccus denitrificans, was cloned and produced in Escherichia coli. Crystals suitable for high-resolution X-ray analysis were obtained by microdialysis under low salt conditions. The crystals belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions of a = 51.51 A, b = 56.15 A, c = 99.86 A (1 A = 0.1 nm) and contain one Fv fragment per asymmetric unit. Using synchrotron radiation diffraction data were collected up to 1.28 A resolution. This high resolution is very unusual for a heterodimeric protein. The crystals should open the way for refining not only the atomic positions, but also for obtaining information about internal dynamics.

Amino Acid Sequence↗

PubMed1992

Ion detection limitations to mass resolution in matrix-assisted laser desorption time-of-flight mass spectrometry.

The ion detection process in a discrete-dynode electron multiplier can result in significant mass resolution losses in time-of-flight mass spectrometry (TOF-MS) for higher mass-to-charge (m/z) ion species. This resolution loss is attributed to propagation time delays and signal broadening in the ion detector. This is presumed to be due to the generation of a distribution of secondary ion species produced initially upon impact of a primary ion with the first dynode surface of the ion detector. Comparisons are made between the signals produced by a standard discrete dynode ion detector (which amplifies the negatively charged species produced by impact of a primary ion) and a detector modified to respond to only the positively charged secondary ion species produced by a primary ion impact. Ion signals for higher m/z ions with the standard detector geometry are seen to be due to a narrow signal component, most likely due to the generation of secondary electrons and/or very low mass secondary ions (H-), and a broad signal component, apparently due to secondary ions which take significant amounts of time to traverse the low potential fields between the first and second detector dynode. This results in ion signal tailing for higher m/z ion species. Numerical subtraction of the ion signal obtained with the standard and modified detector geometries (singly protonated molecular ion species of equine myoglobin) results in an improvement in mass resolution, such that a new adduct ion species (from trifluoroacetic acid) can be resolved.

Animals↗

PubMed1995

High resolution electrospray mass spectrometry with a magnetic sector instrument: accurate mass measurement and peptide sequencing.

The accurate molecular weights for a series of 37 unknown synthetic peptides, used in research studies involving synthetic vaccines, antibacterial peptides or the de novo design of helical peptides and proteins, were determined with a magnetic sector instrument. All data were obtained with external calibration over a wide mass range during magnetic scanning. Errors between observed and theoretical monoisotopic molecular weights were typically in the 5-60 ppm range for the unknowns at sector resolutions between 2500 and 9000 (10% valley). Isotopic clusters for charge states up to 10+ were resolved through the use of high resolution. Collisionally activated dissociation (CAD) in the electrospray interface resulted in product ions that enabled either full or partial sequencing of most unknown peptides of molecular weights below 2000 Da. The complete primary sequence for one peptide was determined and the importance of high resolution was demonstrated by the differentiation of lysine from glutamine, two amino acids differing in residue mass by only 0.0364 Da. Two other peptides, with identical monoisotopic masses, but different primary sequences, were differentiated based on CAD-MS data.

Amino Acid Sequence↗

PubMed2003

Comparison of conventional and enhanced mass resolution triple-quadrupole mass spectrometers for discovery bioanalytical applications.

A new triple-quadrupole mass spectrometry (MS) system with enhanced resolution capabilities has recently become available. In order to evaluate the performance of this new instrument for drug discovery assays, both the linearity and the limit of detection were compared in the positive electrospray ionization (ESI) mode with those of a conventional triple-quadrupole instrument supplied by the same manufacturer. For these studies, spiked mouse plasma standard samples were split and assayed by each instrument, which allowed for a direct comparison of the two systems. In the unit mass resolution mode, the new mass spectrometer was found to be at least ten-fold more sensitive than the conventional instrument. The sensitivity of the new mass spectrometer under the enhanced mass resolution mode was found to be even better by another factor of two. For the test compound, the linear dynamic range was found to be 0.05-5000 ng/mL for the new instrument as compared with 2.5-5000 ng/mL for the conventional mass spectrometer.

Animals↗

PubMed2000

High-resolution scanning electron microscopy study of sputtered nanolaminated Ti/TiN multilayers

This work presents the morphologic and structural study of nanolaminated Ti/TiN multilayers using high-resolution scanning electron microscopy (HR-SEM), coupled to x-ray reflectometry (XRR). The multilayers have been deposited by reactive rf-sputtering on silicon substrates. For large period thickness (lambda=40 nm, 10 periods), in XRR, the low number of interfaces makes the interference less structured. An experimental pattern with broad and weakly intense Braggs peaks is obtained, but is difficult to simulate. On the other hand, HR-SEM observation of cross sections gives excellent pictures of the multilayer, so that precise measurements of the thickness can be achieved: a 42 nm thick period is observed, formed with 17 nm of Ti and with 25 nm of TiN. For small (Ti+TiN) period thickness (lambda=2.5 nm, 120 periods), the XRR pattern exhibits intense and narrow Bragg peaks: the number of interfaces is sufficient to structure the interference and an intense signal is obtained. The best fit of simulation is obtained for a 2.6 nm thin period, made of 0.9 nm of Ti and 1.7 nm of TiN. No laminated structure has been observed by cross-section HR-SEM observation because its resolution (around 2 nm at 10 kV) is larger than the layer thickness in a period. High-resolution SEM and XRR are thus two complementary techniques for the routine characterization of multilayers.

Journal Article↗

PubMedDate not supplied

Correlative high-resolution morphologic analysis of the three-dimensional organization of human chromosomes.

A correlative morphologic analysis was carried out on isolated metaphase chromosomes by means of field emission in-lens scanning electron microscopy (FEISEM) and atomic force microscopy (AFM). Whereas FEISEM provides ultra-high resolution power and allows the surface analysis of biological structures free of any conductive coating, the AFM allows imaging of biological specimens in ambient as well as in physiologic conditions. The analysis of the same samples was made possible by the use of electrical conductive and light transparent ITO glass as specimen holder. Further preparation of the specimen specific for the instrumentation was not required. Both techniques show a high correlation of the respective morphologic information, improving their reciprocal biological significance. In particular, the biological coat represents a barrier for surface morphologic analysis of chromosome spreads and it is sensitive to protease treatment. The chemical removal of this layer permits high-resolution imaging of the chromatid fibers but at the same time alters the chromosomal dimension after rehydration. The high-resolution level, necessary to obtain a precise physical mapping of the genome that the new instruments such as FEISEM and AFM could offer, requires homogeneously cleaned samples with a high grade of reproducibility. A correlative microscopical approach that utilizes completely different physical probes provides complementary useful information for the understanding of the biological, chemical, and physical characteristics of the samples and can be applied to optimize the chromosome preparations for further improvement of the knowledge about spatial genome organization.

Chromosomes, Human↗

PubMedDate not supplied

Resolution limit for electron beam-induced deposition on thick substrates.

Recently, the fabrication resolution in electron beam-induced deposition (EBID) has improved significantly. Dots with an average diameter of 1 nm have been made. These results were all obtained in transmission electron microscopes on thin samples. As one may think that such resolution can be achieved on thin samples only, it is the objective of this paper to show that this should also be possible on thick samples. For that purpose we use Monte Carlo simulations of the electron-sample interaction and determine the surface area where secondary electrons are emitted. Assuming that these electrons cause the deposition in EBID, a comparison can be made between deposition on a thin and a thick sample. The Monte Carlo code we developed will be described and applied to the deposition induced by a 200 keV primary electron beam on an ultra-thin (10 nm) and a bulk-like (1,000 nm) Cu sample. Near the point of incidence of the primary beam, the deposit size is independent of the substrate thickness, such that a 1-nm resolution should be possible to achieve on a thick substrate as well. Thicker substrates only affect the tails of the deposit distribution which contain more mass than thin substrate deposit tails.

Journal Article↗

PubMed1995

Crystal structure of human alpha-thrombin complexed with hirugen and p-amidinophenylpyruvate at 1.6 A resolution.

Crystals of human alpha-thrombin complexed with hirugen and the alpha-keto acid thrombin inhibitor APPA (p-amidinophenylpyruvate) that diffract to 1.6 A resolution were obtained by soaking an alpha-thrombin-hirugen crystal in a solution of APPA. The crystal structure was determined using the difference Fourier method and refined to an R factor of 18.7% at 1.6 A resolution. This structure is the highest resolution structure of the thrombin molecule that is currently available. With the exception of the region near Arg77A-Asn78, the structures of the thrombin and hirugen molecules in the ternary complex are similar to those reported for the thrombin-hirugen binary complex. As previously determined for the APPA-trypsin complex, the carbonyl carbon atom of APPA forms a covalent bond with O gamma of Ser195 of thrombin to yield a "transition-state" analog of the tetrahedral intermediate. Comparison of the specificity pocket of the APPA complexes of thrombin and trypsin reveals differences in hydrogen bonding and shows for the first time that the S1 site of thrombin is larger than that of trypsin and as a result thrombin may be able to accommodate a bulkier P1 group than trypsin.

Amino Acid Sequence↗

PubMed1996

A comparison of electrophoretic resolution for snapshot and finish-line imaging.

Finish-line imaging, in which DNA or other macromolecules are detected after electrophoresis for a constant distance, usually improves resolution compared to snapshot imaging, in which molecules are electrophoresed for a constant time in an apparatus of comparable dimensions. Resolving power, which is an objective measure of the ability of different separatory methods to detect closely spaced molecular species, can be used to compare directly the performance of systems employing both snapshot and finish-line imaging [E. A. Ribeiro and J. C. Sutherland, Anal. Biochem. 210, 378-388 (1993)]. Experimentally determined values of resolving power are influenced both by the method of imaging (snapshot vs finish-line) and by instrument-specific factors that affect resolution. Previous comparisons of the resolving power obtained with finish-line and snapshot imaging involved data sets acquired by different instruments with different instrumental resolutions. To reduce the influence of instrumental effects, we constructed a scanning laser fluorometer that can measure both snapshot and finish-line images of fluorochrome-labeled DNA. Snapshot and finish-line images of a DNA sample containing HaeII restriction fragments of the DNA from bacteriophage T7, which range in length from 474 to 6514 base pairs, were obtained under otherwise identical electrophoretic conditions. Snapshot and finish-line imaging give similar resolving powers for DNA molecules up to about 1.5 kbp long. For both imaging modes, maximum resolving power was achieved for DNA molecules between 2 and 3 kbp in length. For larger DNA molecules, finish-line imaging provided higher resolving power. The ratio of the resolving power of finish-line images to that of snapshot images increased monotonically as a function of DNA length. For the longest restriction fragments studied (6514 bp), the resolving power for finish-line images exceeded that of snapshot images by about 50%.

Bacteriophage T7↗

PubMed1996

Application of multivariate curve resolution to voltammetric data. II. Study of metal-binding properties of the peptides.

The complexation of Cd2+ by glutathione (GSH), in 0.13 m borate buffer at pH 9.5, was studied by differential pulse polarography (DPP) and multivariate curve resolution. The Cd-GSH system has been chosen as a model to check the possibilities of this new polarographic approach to the study of metal ion complexation by peptides. Experimental data obtained by DPP for different Cd2+-to-GSH concentration ratios have been analyzed by a procedure which consists of using several chemometrical techniques based on factor analysis: principal component analysis, evolving factor analysis, and multivariate curve resolution with alternating least-squares (ALS) optimization. The use of different constraints during the ALS optimization process, such as nonnegativity and unimodality constraints, yields the optimal sought solution from a chemical point of view. In the present work, a new constraint has been implemented during ALS optimization to take into account the expected peak-shaped signal of DPP. This data treatment allows us to detect simultaneously the formation of 1:1 and 1:2 Cd:GSH complexes which were very difficult to detect by univariate analysis of DPP data. It is concluded that the described multivariate curve resolution method could be a reliable tool for studying metal-binding properties of peptides.

Cadmium↗

PubMed2001

The spatial resolution of visual attention.

Two tasks were used to evaluate the grain of visual attention, the minimum spacing at which attention can select individual items. First, observers performed a tracking task at many viewing distances. When the display subtended less than 1 degrees in size, tracking was no longer possible even though observers could resolve the items and their motions: The items were visible but could not be individuated one from the other. The limiting size for selection was roughly the same whether tracking one or three targets, suggesting that the resolution limit acts independently of the capacity limit of attention. Second, the closest spacing that still allowed individuation of single items in dense, static displays was examined. This critical spacing was about 50% coarser in the radial direction compared to the tangential direction and was coarser in the upper as opposed to the lower visual field. The results suggest that no more than about 60 items can be arrayed in the central 30 degrees of the visual field while still allowing attentional access to each individually. Our data show that selection has a coarse grain, much coarser than visual resolution. These measures of the resolution of attention are based solely on the selection of location and are not confounded with preattentive feature interactions that may contribute to measures from flanker and crowding tasks. The results suggest that the parietal area is the most likely locus of this selection mechanism and that it acts by pointing to the spatial coordinates (or cortical coordinates) of items of interest rather than by holding a representation of the items themselves.

Adult↗

PubMed1993

High-resolution positron emission tomography of human ovarian cancer in nude rats using 124I-labeled monoclonal antibodies.

PET has inherently high resolution and excellent contrast imaging and accurately measures radioactivity concentrations in vivo. When combined with specific immunological targeting it might provide a highly specific and sensitive radioimmunoscintigraphic tool. To investigate this we injected 124I-labeled MAb MX35 or MAb MH99 monoclonal antibodies (doses 200-400 mu Ci) intravenously into nude rats bearing subcutaneous human ovarian cancer xenografts (SK-OV-7 and SK-OV-3 cell lines). A melanoma cell line (SK-MEL-30) was used as a control tumor. These murine monoclonal antibodies react with cell-surface antigens expressed by most ovarian cancer cells, including the ovarian cell line used. Imaging was performed at 1-6 days using a high-resolution positron emission tomograph (PCR-I) with a spatial resolution of 4.5 mm. The slice thicknesses were 0.5 and 1.0 cm. Forty to seventy thousand coincident pulses were obtained per frame. The PET results were compared with those of autopsy and histology. Samples of blood, tumor, and normal tissues were obtained at various time points. PET calculation of isotope uptake ratios demonstrated specific localization of the antibodies in tumor, with ratios of tumor to normal tissue uptake as high as 6:1. Subcutaneous ovarian cancer nodules as small as 7 mm were identified with PET imaging. The results corresponded well with tissue sampling. Our findings suggest that PET imaging of tumors with 124I-labeled monoclonal antibodies may be useful in human diagnostic and therapeutic applications in ovarian cancer as well as other diseases.

Animals↗