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At least 1,117 records · Page 62Linked to original sources

S-SWAT (softer single-wavelength anomalous technique): potential in high-throughput protein crystallography.

The drive for yet higher output of protein crystal structures sustains an interest in streamlining data-collection protocols. Highly organized automated robotics attend to one aspect. The data-collection elapsed time also depends on the number of wavelengths used, the data redundancy and the desired diffraction resolution limit. Synchrotron-radiation beamlines offer a centralized data-collection approach with considerable flexibility of choice of wavelength(s) with high beam intensity and fine collimation. The arrival of automated IPs (imaging plates) and CCDs (charge-coupled devices) with sample freezing has widened the scope for ease of data collection and achieving a high redundancy, the latter at the cost of elapsed time per sample. This paper reports a single-wavelength approach where a large optimized f" signal involving the Xe L1-absorption edge is harnessed. Even with modest data redundancy (7), a high-quality electron-density map was obtained from that single data set when combined with phase improvement methods. Two phasing protocols are compared for the same data set. Resolution extension (to 1.4 A), in this test, was also done but via a second data set. In future, with a tilted detector geometry, full diffraction resolution will be collectable in one experiment on the one beamline. Moreover, careful minimization of beamline Be window thickness on the new Daresbury SRS Multipole Wiggler Beamline 10 will maximize the 2-3 A (softer) wavelength intensity performance specification. The work has application to the harnessing of iodine f" optimized signals and enhanced sulfur f", as well as xenon f", in protein crystallography. This approach, softer-SWAT, should 'swat' many protein structures when it comes online.

Crystallography, X-Ray↗

On the application of phase relationships to complex structures. XXXIII. The problems with large structures and low resolution.

A conventional direct method, using the Sayre equation as a basis, has been shown to be capable of solving a small protein with data of 3.0 A resolution or better. An analysis of the Sayre equation, with data of various resolutions and with different lower limits of |E| for the contributors in the summation, shows that its effectiveness for phasing is independent of structural complexity but does decline as the resolution becomes worse. It is suggested that a practicable lower limit for the application of conventional direct methods is about 3.5 A. For large macromolecular structures the number of contributors to the summation in the Sayre equation becomes too large to handle and it is suggested that real-space methods should be used instead.

Journal Article↗

On the role of data quality in experimental charge-density studies.

High-resolution X-ray diffraction data were collected at T = 19 K from two similar spherical crystals of the fungal metabolite citrinin, C(13)H(14)O(5). The two data sets were of markedly different quality, one data set (MQ, medium quality) comprising a single octant of the reciprocal lattice and including reflections with obviously peculiar intensity profiles while the second (HQ, high quality) comprised a hemisphere of reflections and showed no flawed profiles. Parallel multipolar refinements were carried out for both. While most of the resulting geometric parameters, including bond lengths and angles, were in close agreement (the standard uncertainties were approximately twice as large for the MQ data, reflecting the smaller number of observations), the agreement is noticeably worse for electronic properties such as electron densities and their Laplacians at the bond and ring critical points. These latter features are especially sensitive to the quality of the low-angle (and strong) intensities, which was not high for the MQ data. By contrast, the magnitudes of the molecular dipole moment from the two experiments are the same within 1 standard uncertainty, with an angle of about 13 degrees between the two vectors. It is concluded that only true high-quality data allow a fully significant and quantitative analysis of the details of the experimental electron density rho(exp), while high-resolution medium-quality data, measured at very low temperature and adequately processed, can still be used for a qualitative analysis, or for the derivation of overall electronic properties.

Citrinin↗

Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 A resolution.

The three-dimensional structure of the monomeric bifunctional enzyme N-(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from Escherichia coli has been refined at 2.0 A resolution, using oscillation film data obtained from synchrotron radiation. The model includes the complete protein (452 residues), two phosphate ions and 628 water molecules. The final R-factor is 17.3% for all observed data between 15 and 2 A resolution. The root-mean-square deviations from ideal bond lengths and bond angles are 0.010 A and 3.2 degrees, respectively. The structure of N-(5'-phosphoribosyl)anthranilate isomerase: indole-3-glycerol-phosphate synthase from E. coli comprises two beta/alpha-barrel domains that superimpose with a root-mean-square deviation of 2.03 A for 138 C alpha-pairs. The C-terminal domain (residues 256 to 452) catalyses the PRAI reaction and the N-terminal domain (residues 1 to 255) catalyses the IGPS reaction, two sequential steps in tryptophan biosynthesis. The enzyme has the overall shape of a dumb-bell, resulting in a surface area that is considerably larger than normally observed for monomeric proteins of this size. The active sites of the PRAI and the IGPS domains, both located at the C-terminal side of the central beta-barrel, contain equivalent binding sites for the phosphate moieties of the substrates N-(5'-phosphoribosyl) anthranilate and 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate. These two phosphate binding sites are identical with respect to their positions within the tertiary structure of the beta/alpha-barrel, the conformation of the residues involved in phosphate binding and the hydrogen-bonding network between the phosphate ions and the protein. The active site cavities of both domains contain similar hydrophobic pockets that presumably bind the anthranilic acid moieties of the substrates. These similarities of the tertiary structures and the active sites of the two domains provide evidence that N-(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from E. coli results from a gene duplication event of a monomeric beta/alpha-barrel ancestor.

Aldose-Ketose Isomerases↗

Crystallization and preliminary X-ray diffraction analysis of a novel pectate lyase from Azospirillum irakense.

The PelA gene from the N(2)-fixing plant-associated bacterium Azospirillum irakense encodes a pectate lyase. Analysis of the corresponding amino-acid sequence revealed no homology to other bacterial, plant and fungal pectinases of known published structure, resulting in the classification of the enzyme in a new pectate lyase family. The A. irakense PelA has been crystallized using the hanging-drop vapour-diffusion method at 277 K. The crystals are hexagonal, with unit-cell parameters a = b = 85.55, c = 230.13 A, gamma = 120 degrees, and belong to space group P6(5)22 or P6(1)22, having one molecule per asymmetric unit. Diffraction data to a resolution of 1.97 A were collected at synchrotron facilities, as well as a three-wavelength MAD data set from an Hg-derivative crystal to a resolution of 2.6 A.

Azospirillum↗

Ability of navigated 3D ultrasound to delineate gliomas and metastases--comparison of image interpretations with histopathology.

BACKGROUND: The objective of the study was to test the ability of a 3D ultrasound (US) based intraoperative imaging and navigation system to delineate gliomas and metastases in a clinical setting. The 3D US data is displayed as reformatted 2D image slices. The quality of the displayed 3D data is affected both by the resolution of the acquired data and the reformatting process. In order to investigate whether or not 3D US could be used for reliable guidance in tumour surgery, a study was initiated to compare interpretations of imaged biopsy sites with histopathology. The system also enabled concomitant comparison of navigated preoperative MR with histopathology. METHOD: Eighty-five biopsies were sampled between 2-7 mm from the tumour border visible in the ultrasound images. Biopsies were collected from 28 operations (7 low-grade astrocytomas, 8 anaplastic astrocytomas, 7 glioblastomas and 6 metastases). Corresponding cross-sections of preoperative MR T1, MR T2 and intraoperative US were concomitantly displayed, steered by the biopsy forceps equipped with a positioning sensor. The surgeons' interpretation of the images at the electronically indicated biopsy sites were compared with the histopathology of the samples. FINDINGS: The ultrasound findings were in agreement with histopathology in 74% (n = 31) for low-grade astrocytomas, 83% (n = 18) for anaplastic astrocytomas, 77% (n = 26) for glioblastomas and 100% (n = 10) for metastases. Excluding irradiated patients, the results for glioblastomas improved to 80% concurrence (n = 20). As expected tumour cells were found in biopsies outside the US visible tumour border, especially in low-grade gliomas. Navigated 3D US have a significantly better agreement with histopathology than navigated MR T1 for low-grade astrocytomas. CONCLUSION: Reformatted images from 3D US volumes give a good delineation of metastases and the solid part of gliomas before starting the resection. Navigated 3D US is at least as reliable as navigated 3D MR to delineate gliomas and metastases.

Adult↗

Computer programs for the analysis of protein fluorescence quenching data.

Educational computer programs for analysis of fluorescence quenching studies of proteins have been developed. The program is written according to the classical Stern-Volmer equation and some modified Stern-Volmer equations. The static and dynamic quenching constants as well as the accessibility of the quencher molecules to the fluorescence groups are calculated. The experimental data are plotted on a high resolution graph. The calculated data or the graphs can be printed out to obtain a hard copy for filing.

Kinetics↗

High throughput assessment of cells and tissues: Bayesian classification of spectral metrics from infrared vibrational spectroscopic imaging data.

Vibrational spectroscopy allows a visualization of tissue constituents based on intrinsic chemical composition and provides a potential route to obtaining diagnostic markers of diseases. Characterizations utilizing infrared vibrational spectroscopy, in particular, are conventionally low throughput in data acquisition, generally lacking in spatial resolution with the resulting data requiring intensive numerical computations to extract information. These factors impair the ability of infrared spectroscopic measurements to represent accurately the spatial heterogeneity in tissue, to incorporate robustly the diversity introduced by patient cohorts or preparative artifacts and to validate developed protocols in large population studies. In this manuscript, we demonstrate a combination of Fourier transform infrared (FTIR) spectroscopic imaging, tissue microarrays (TMAs) and fast numerical analysis as a paradigm for the rapid analysis, development and validation of high throughput spectroscopic characterization protocols. We provide an extended description of the data treatment algorithm and a discussion of various factors that may influence decision-making using this approach. Finally, a number of prostate tissue biopsies, arranged in an array modality, are employed to examine the efficacy of this approach in histologic recognition of epithelial cell polarization in patients displaying a variety of normal, malignant and hyperplastic conditions. An index of epithelial cell polarization, derived from a combined spectral and morphological analysis, is determined to be a potentially useful diagnostic marker.

Bayes Theorem↗

Determining global population distribution: methods, applications and data.

Evaluating the total numbers of people at risk from infectious disease in the world requires not just tabular population data, but data that are spatially explicit and global in extent at a moderate resolution. This review describes the basic methods for constructing estimates of global population distribution with attention to recent advances in improving both spatial and temporal resolution. To evaluate the optimal resolution for the study of disease, the native resolution of the data inputs as well as that of the resulting outputs are discussed. Assumptions used to produce different population data sets are also described, with their implications for the study of infectious disease. Lastly, the application of these population data sets in studies to assess disease distribution and health impacts is reviewed. The data described in this review are distributed in the accompanying DVD.

Communicable Diseases↗

Processing DOSY spectra using the regularized resolvent transform.

A new method for processing diffusion ordered spectroscopy (DOSY) data is presented. This method, the regularized resolvent transform (iRRT-the i denoting the adaptation of the method to evaluate the inverse Laplace transform), is better than conventional processing techniques for generating 2D DOSY spectra using data that has poor chemical shift resolution. From the same data, it is possible to use the iRRT to generate 1D subspectra corresponding to different components of the sample mixture; these subspectra compare favorably to 1D spectra of the pure substances. Both the 2D spectra and the 1D subspectra offer a vast improvement over results generated using a conventional processing technique (non-linear least-squares fitting). Consequently, we present the iRRT as a stable and reliable tool for solving the inverse Laplace transform problem present in experiments such as DOSY.

Acyclic Monoterpenes↗

Investigation of MALDI-TOF and FT-MS techniques for analysis of Escherichia coli whole cells.

Recently, it has been demonstrated that bacteria can be characterized using whole cells and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). However, identification of specific bacterial proteins usually requires analysis of cellular fractions or purified extracts. Here, the first application of Fourier transform mass spectrometry (FTMS) to analysis of bacterial proteins directly from whole cells is reported. It is shown that accurate mass MALDI-FTMS can be used to characterize specific ribosomal proteins directly from Escherichia coli cells. High-accuracy mass measurements and high-resolution isotope profile data confirm posttranslational modifications proposed previously on the basis of low-resolution mass measurements. Seven ribosomal proteins from E. coli whole cells were observed with errors of less than 27 ppm. This was accomplished directly from whole cells without fractionation, concentration, or overt overexpression of characteristic cellular proteins. MALDI-FTMS also provided information regarding E. coli lipids in the low-mass region. Although ions with m/z values below 1000 have been observed by FTMS of whole cells, this represents the first report of detection of ions in the 5000 to 10,000 m/z range by MALDI-FTMS using whole cells.

Escherichia coli↗

Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation.

A top-down approach based on sustained off-resonance irradiation collision-induced dissociation (SORI-CID) has been implemented on an electrospray ionization (ESI) Fourier transform mass spectrometer (FTMS) to characterize nucleic acid substrates modified by structural probes. Solvent accessibility reagents, such as dimethyl sulfate (DMS), 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT), and beta-ethoxy-alpha-ketobutyraldehyde (kethoxal, KT) are widely employed to reveal the position of single- vs double-stranded regions and obtain the footprint of bound proteins onto nucleic acids structures. Established methods require end-labeling of the nucleic acid constructs, probe-specific chemistry to produce strand cleavage at the modified nucleotides, and analysis by polyacrylamide gel electrophoresis to determine the position of the susceptible sites. However, these labor-intensive procedures can be avoided when mass spectrometry is used to identify the probe-induced modifications from their characteristic mass signatures. In particular, ESI-FTMS can be directly employed to monitor the conditions of probe application to avoid excessive alkylation, which could induce unwanted distortion or defolding of the substrate of interest. The sequence position of the covalent modifications can be subsequently obtained from classic tandem techniques, which allow for the analysis of individual target adducts present in complex reaction mixtures with no need for separation techniques. Selection and activation by SORI-CID has been employed to reveal the position of adducts in nucleic acid substrates in excess of 6 kDa. The stability of the different covalent modifications under SORI-CID conditions was investigated. Multiple stages of isolation and activation were employed in MS(n)() experiments to obtain the desired sequence information whenever the adduct stability was not particularly favorable, and SORI-CID induced the facile loss of the modified base. A new program called MS2Links was developed for the automated reduction and interpretation of fragmentation data obtained from modified nucleic acids. Based on an algorithm that searches for plausible isotopic patterns, the data reduction module is capable of discriminating legitimate signals from noise spikes of comparable intensity. The fragment identification module calculates the monoisotopic mass of ion products expected from a certain sequence and user-defined covalent modifications, which are finally matched with the signals selected by the data reduction program. Considering that MS2Links can generate similar fragment libraries for peptides and their covalent conjugates with other peptides or nucleic acids, this program provides an integrated platform for the structural investigation of protein-nucleic acid complexes based on cross-linking strategies and top-down ESI-FTMS.

Aldehydes↗

Value of volumetric data acquisition in expiratory high-resolution computed tomography of the lung.

OBJECTIVE: The purpose of this study is to determine the potential advantages of volumetric expiratory high-resolution computed tomography (HRCT) over noncontiguous expiratory HRCT in visualizing the airway conducting to the areas of air trapping and in providing additional significant information in patients with diffuse lung disease with small airway abnormalities. METHODS: Forty-one consecutive patients with suspected diffuse lung diseases with airway abnormalities who underwent volumetric expiratory HRCT scans from April to June 2003 were studied. Respiratory motion artifacts were evaluated at 3 anatomic levels (aortic arch, carina, and lung bases). The detectability of air trapping and its conducting airway were compared on contiguous versus noncontiguous (6 evenly spaced images per patient) end-expiratory HRCT images. Additional findings on contiguous HRCT images were also assessed regarding their diagnostic significance. RESULTS: The volumetric expiratory HRCT was diagnostically acceptable in 93% (38/41) of patients at arch level, 95% (39/41) at carina level, and 83% (34/41) at the lung bases, even with respiratory motion artifacts. In 35 patients with air trapping, the contiguous HRCT images enabled better identification of the conducting airway to the areas of air trapping and added diagnostically significant findings compared with noncontiguous images (P < 0.0001). CONCLUSION: Volumetric expiratory HRCT allows for better identification of the airway conducting to the areas of air trapping compared with noncontiguous images as well as additional findings of diagnostic significance.

Adult↗

Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.

The structure of a tetragonal crystal form of thiostrepton has been solved using the anomalous dispersive effects of five S atoms from high-redundancy data collected to 1.33 A resolution at the Cu Kalpha wavelength. Data measured to 1.02 A resolution with a synchrotron source were used for refinement. Details of the molecular structure, intramolecular and intermolecular interactions are given.

Anti-Bacterial Agents↗

Quantifying bone and liver alkaline phosphatase by the resolution of two-component inactivation data obtained with a centrifugal analyzer.

In this method we use a linear equation to resolve two-component decay data from the urea inactivation of mixtures of alkaline phosphatase (EC 3.1.3.1) of liver and bone origin. The specificity for the bone/liver isoenzyme is enhanced by including L-phenylalanine in the urea reaction to inhibit the intestinal and placental forms. Bone and liver fractions are each quantified from results of a single run on the centrifugal analyzer. Total activity and the L-phenylalanine-inhibited fraction are measured on separate runs. A simplification of this method has been used in our laboratory for 14 years in performing greater than 80,000 analyses of clinical specimens. Speed, accuracy, and precision are improved over previous methods by this mathematical solution. Data reduction is automated through the use of a personal computer interfaced to the analyzer. With such systems generally available, this method can now be suggested as suitable for routine use to separate these and perhaps other isoenzyme mixtures.

Alkaline Phosphatase↗