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PubMed1988

Crystallization of a ternary complex of lactate dehydrogenase from Bacillus stearothermophilus.

Bacillus stearothermophilus lactate dehydrogenase was purified from an overexpressing Escherichia coli cell line. The enzyme has been crystallized in several different forms. All of these crystal forms were grown in the presence of NADH, sodium oxamate and fructose 1,6-bisphosphate. Three crystal forms have been characterized, an orthorhombic P2(1)2(1)2 (type III, a = 86 A, b = 105 A, c = 136 A) and two monoclinic P21 forms (type IV, a = 85 A, b = 118 A, c = 136 A, beta = 96 degrees; type V, a = 112 A, b = 85 A, c = 136 A, beta = 91 degrees). Precession photographs from these crystal forms are very alike, suggesting the molecular packing to be similar in all three forms. The P21 type IV crystals diffract to beyond 2 A spacing and are stable to irradiation with X-rays. A complete medium-resolution (4.7 A) dataset has been collected from a single crystal using synchrotron radiation. Rotation function studies with these data show the two tetramers of the asymmetric unit to be in very similar orientations. Higher-resolution data are being collected.

Cell Line↗

PubMed1994

The crystal structure of affinity-matured human growth hormone at 2 A resolution.

A variant of human growth hormone (hGH), in which 15 mutations were introduced with phage display mutagenesis to improve receptor binding affinity by 400-fold, yielded two related crystal forms diffracting to high resolution. The structure of this variant was determined in both crystal forms, one at 2.0 A resolution and one at 2.4 A resolution, using molecular replacement with wild-type hGH taken from the receptor complex structure as a search model. Crystallographic refinement of the 2 A structure gave an R-value R-value of 18.5% for data in the resolution range 8 to 2 A. The final model consists of residues 1 to 128 and 155 to 191, with three side-chains modeled in alternative conformations, together with 77 water molecules. Comparison of the structure with wild-type hGH shows that most of the secondary structural elements are unchanged. The exception is the first turn of the third helix in the four-helix bundle core, which is unraveled in the present variant. Analysis of the two related packing environments suggests that this change is caused by crystal packing forces. A large change in the orientation of a short segment of helix found in the connection between the first two core helices is interpreted as evidence for rigid-body variability of this helical segment. Analysis of the mutations in light of the structure of the wild-type hGH/receptor complex shows that six of the mutations are buried in the hormone, whereas the remaining nine involve residues that interact with the receptor in the complex.

Amino Acid Sequence↗

PubMed2006

Phylogeny of the Schisandraceae based on cpDNA mat-K and rpL16 intron data.

The chloroplast mat-K region and rpL16 intron region were sequenced for 14 species of Schisandraceae, representing both genera Kadsura Kaempf. ex Juss. and Schisandra Michx, to discuss the phylogeny of this family. Analyses were performed both in separate and combined sequence data sets (including the rbc-L sequence), with Illicium angustispealum A. C. Smith as the out-group. The results showed that the Schisandraceae are monophyletic. In all the analyses, Schisandra propinqua var. chinensis Oliva and Schisandra plena A. C. Smith were nested within Kadsura, which implies that the genera Kadsura and Schisandra are closely related. They might have originated from a common ancestor, but then evolved via different routes. The result inferred from the combined data showed a greater resolution within Schisandra than those from the two separate data sets. High bootstrap values supported the monophyly of most subgenera according to Law's system (1996). A combination of morphological, anatomical, and chemical analyses indicates that S. chinensis and S. rubriflora may be the primitive taxa in Schisandra.

DNA, Chloroplast↗

PubMed1993

A self-consistent method for the analysis of protein secondary structure from circular dichroism.

A self-consistent procedure for estimating the secondary structure content from circular dichroism spectra of proteins is presented. In this method the spectrum of the protein to be analyzed is included in the basis set and an initial guess is made for the unknown structure as a first approximation. The resulting matrix equation is solved using the singular value decomposition algorithm and the initial guess is replaced by the solution. The process is repeated until self-consistency is attained. The best features of the variable selection and the locally linearized methods are incorporated in this procedure. We have applied this method to examine the inconsistencies in the CD data, to compare the predictions with different ranges and resolutions of the CD data, and to compare different assignments of secondary structures from X-ray structure analyses in the context of secondary structure predictions. The results are compared using the root mean square differences and correlation coefficients. The results obtained are as good as or better than the previous analyses. For most of the proteins considered the self-consistent solutions obtained with different initial guesses were similar. We find the Kabsch and Sander protein crystal structure analysis to be most suitable for our prediction method.

Circular Dichroism↗

PubMed2006

Comparison of the performance of tracer kinetic model-driven registration for dynamic contrast enhanced MRI using different models of contrast enhancement.

RATIONALE AND OBJECTIVES: The quantitative analysis of dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) data is subject to model fitting errors caused by motion during the time-series data acquisition. However, the time-varying features that occur as a result of contrast enhancement can confound motion correction techniques based on conventional registration similarity measures. We have therefore developed a heuristic, locally controlled tracer kinetic model-driven registration procedure, in which the model accounts for contrast enhancement, and applied it to the registration of abdominal DCE-MRI data at high temporal resolution. MATERIALS AND METHODS: Using severely motion-corrupted data sets that had been excluded from analysis in a clinical trial of an antiangiogenic agent, we compared the results obtained when using different models to drive the tracer kinetic model-driven registration with those obtained when using a conventional registration against the time series mean image volume. RESULTS: Using tracer kinetic model-driven registration, it was possible to improve model fitting by reducing the sum of squared errors but the improvement was only realized when using a model that adequately described the features of the time series data. The registration against the time series mean significantly distorted the time series data, as did tracer kinetic model-driven registration using a simpler model of contrast enhancement. CONCLUSION: When an appropriate model is used, tracer kinetic model-driven registration influences motion-corrupted model fit parameter estimates and provides significant improvements in localization in three-dimensional parameter maps. This has positive implications for the use of quantitative DCE-MRI for example in clinical trials of antiangiogenic or antivascular agents.

Abdominal Neoplasms↗

PubMed2004

Separation, bioactivity, and dissipation of enantiomers of the organophosphorus insecticide fenamiphos.

Most chiral pesticides are used as racemates despite the fact that the pesticidal activity of the given pesticide is usually the result of the preferential reactivity of only one enantiomer while the other enantiomers may have toxic effects against other nontarget organisms. Accordingly, the enantiomer of fenamiphos, an organophosphorus pesticide, was separated by high-performance liquid chromatography with reverse phase and normal phase on a Pirkle model chiral stationary phase column. It was found that n-hexane/isopropanol (95/5) was the best solvent system for enantiomer resolution of fenamiphos. Chromatographic data including capacity factor (k'), separation factor (alpha), and resolution (Rs) are presented. Inhibitory activity to enzyme butyrylcholinesterase and toxicity to Daphnia of enantiomers and racemic insecticide fenamiphos were also studied. In the toxicity tests of Daphnia, the lethal concentration (LC50) of (+)-fenamiphos, (-)-fenamiphos, and racemate were 0.0016, 0.0061, and 0.0019 microg/mL, respectively. No significant difference of LC50 values between (+)-fenamiphos and racemate were found, but (-)-fenamiphos showed significantly lower toxicity to Daphnia. The inhibitory concentration (IC50) to the cholinesterase were 0.008, 0.15, and 0.46 microg/mL for (+)-fenamiphos, (-)-fenamiphos, and racemate, respectively. Both enantiomers and the racemate showed significant difference in inhibiting the cholinesterase. However, (+)-fenamiphos proved to be about 20 times more toxic to Daphnia and only about four times more inhibitory activity to butyrylcholinesterase than (-)-fenamiphos. The dissipation of (+)-fenamiphos, (-)-fenamiphos, and racemate in selected soils and natural water samples were also studied. The half-life (t(1/2)) of (+)-, (-)-, and racemate in soils showed no related to the soil texture, pH, or organic carbon content. By comparing the residues of (+)-, (-)-, and racemate in the water, it was found that (+)-fenamiphos was degraded faster than the others after 21 days. Briefly, (+)-fenamiphos is more toxic than (-)-fenamiphos to a nontarget organism (Daphnia), but the environmental persistence of the two compounds showed no significant difference.

Animals↗

PubMed2001

Crystallization and preliminary X-ray analysis of a depressant insect toxin from the scorpion Buthus martensii Karsch.

Depressant insect toxins are a distinct group of scorpion neurotoxins for which no three-dimensional structures are yet available. A depressant insect toxin named BmK dITAP3 from the scorpion Buthus martensii Karsch (BmK) has been purified and crystallized. Single crystals of dITAP3 grew in the presence of the detergent CYMAL-6 using the hanging-drop vapour-diffusion method with ammonium sulfate as precipitant. A set of diffraction data to 2.6 A resolution has been collected. Preliminary analysis of the diffraction data indicated that the crystal belonged to space group R3, with unit-cell parameters a = b = 73.29, c = 68.90 A, alpha = beta = 90, gamma = 120 degrees. Assuming two molecules in the asymmetric unit, the estimated solvent content is 53.4%.

Animals↗

PubMed2006

Structure of the orthorhombic form of human inosine triphosphate pyrophosphatase.

The structure of human inosine triphosphate pyrophosphohydrolase (ITPA) has been determined using diffraction data to 1.6 A resolution. ITPA contributes to the accurate replication of DNA by cleansing cellular dNTP pools of mutagenic nucleotide purine analogs such as dITP or dXTP. A similar high-resolution unpublished structure has been deposited in the Protein Data Bank from a monoclinic and pseudo-merohedrally twinned crystal. Here, cocrystallization of ITPA with a molar ratio of XTP appears to have improved the crystals by eliminating twinning and resulted in an orthorhombic space group. However, there was no evidence for bound XTP in the structure. Comparison with substrate-bound NTPase from a thermophilic organism predicts the movement of residues within helix alpha1, the loop before alpha6 and helix alpha7 to cap off the active site when substrate is bound.

Crystallography, X-Ray↗

PubMed2005

Preliminary crystallographic analysis of the Escherichia coli YeaZ protein using the anomalous signal of a gadolinium derivative.

The Escherichia coli yeaZ gene encodes a 231-residue protein (Mr = 25,180) that belongs to a family of proteins that are conserved in various bacterial genomes. This protein of unknown function is predicted to be a hypothetical protease. The YeaZ protein was overexpressed in E. coli and crystallized at 298 K by the hanging-drop vapour-diffusion method. A MAD data set was collected using a gadolinium-derivative crystal that had been soaked with 0.1 M Gd-DOTMA. The data set contained data collected to a resolution of 2.7 A at two wavelengths at the L(III) absorption edge of gadolinium, while remote data were collected to a resolution of 2.28 A. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 76.3, b = 97.6, c = 141.9 A. Phasing using the MAD method confirmed there to be four monomers in the asymmetric unit related by two twofold axes as identified by the self-rotation function search.

Amino Acid Sequence↗

PubMed1994

Possible changes in luminal surface charge densities of small intestine membrane in the 4-7.4 pH range exhibit varied influence on the absorption rate constants of the ionized and un-ionized species of sulfadiazine in rats.

The overall apparent first-order rate constants (Kab) of small intestinal absorption of sulfadiazine were determined in rats in situ at various pHs (4.01-7.42) of the recirculation fluids at 32 degrees. The purpose of the study was to verify our hypothesis that the rate-determining step for the absorption of sulfonamides involves the formation of an "activated complex" consisting of a transient association of the sulfonamide molecules with the surface protein of the microvillus membrane. The Kab versus Fu (where Fu is the fraction of un-ionized sulfadiazine at a given pH) profile prepared according to the equation Kab = Ki+Fu(Ku-Ki), where Ki and Ku are the first-order rate constants of absorption of the ionized and un-ionized species, respectively, was clearly resolvable into two linear segments: one based on the data in the 4.01-6.43 pH range and the other based on the data in the 6.43-7.42 pH range. In view of the fact that the combined molar concentration of aspartic acid and glutamic acid in the microvillus membrane protein is about twice that of arginine and lysine, the resolution of the data into two linear segments suggested that the negative charge density of the microvillus surface membrane protein in the 6.43-7.42 pH range is greater than that in the 4.01-6.43 pH range. The Ku and Ki values of sulfadiazine were determined in each pH range. It was noted that Ku was greater than Ki in each pH range, and that Ki in the 4.01-6.43 pH range was greater than that in the 6.43-7.42 pH range.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1997

Structure of the calcium-binding echidna milk lysozyme at 1.9 A resolution.

A lysozyme isolated from the milk of a monotreme, the echidna, Tachyglossus aculeatus multiaculeatus, has been crystallized (space group P2(1), with unit-cell dimensions a = 37.1, b = 42.0, c = 38.1 A, beta = 91 degrees and Z = 2) and the structure refined to an R value of 0.167 for all measured data in the resolution range 7.0-1.9 A. It had previously been inferred from sequence homology with alpha-lactalbumins that echidna milk lysozyme (EML) would bind one calcium ion per molecule. This has been confirmed in the present study in which the largest peak in a difference Fourier synthesis is associated with a calcium ion. The calcium binding site of EML is very similar to that observed in baboon and human alpha-lactalbumins, and in a human lysozyme engineered to contain a calcium-binding site. The overall fold of the protein is similar to that of chick-type lysozymes. EML, like pigeon lysozyme, has only 125 residues terminating at a cysteine but in EML this forms a disulfide with a cysteine at residue 9 whereas the equivalent cysteine residue in all other lysozymes of known sequence occurs at position 6. These changes cause some minor structural rearrangements. The binding of calcium appears to have had little effect on the polypeptide backbone conformation and caused only small changes in the conformation of side chains coordinating the calcium ion. A homology modelling study [Acharya, Stuart, Phillips, McKenzie & Teahan (1994). J. Protein Chem. 13(6), 569-584] correctly predicted the overall structure of EML and the nature of its calcium binding site but generally failed to model some more subtle differences observed in the EML structure as evidenced by the fact that the homology model more closely resembles the starting structure from which the model was derived than it does the crystal structure.

Journal Article↗

PubMed2006

Pictorial review: electron beam computed tomography and multislice spiral computed tomography for cardiac imaging.

Electron beam computed tomography (EBCT) revolutionized cardiac imaging by combining a constant high temporal resolution with prospective ECG triggering. For years, EBCT was the primary technique for some non-invasive diagnostic cardiac procedures such as calcium scoring and non-invasive angiography of the coronary arteries. Multislice spiral computed tomography (MSCT) on the other hand significantly advanced cardiac imaging through high volume coverage, improved spatial resolution and retrospective ECG gating. This pictorial review will illustrate the basic differences between both modalities with special emphasis to their image quality. Several experimental and clinical examples demonstrate the strengths and limitations of both imaging modalities in an intraindividual comparison for a broad range of diagnostic applications such as coronary artery calcium scoring, coronary angiography including stent visualization as well as functional assessment of the cardiac ventricles and valves. In general, our examples indicate that EBCT suffers from a number of shortcomings such as limited spatial resolution and a low contrast-to-noise ratio. Thus, EBCT should now only be used in selected cases where a constant high temporal resolution is a crucial issue, such as dynamic (cine) imaging. Due to isotropic submillimeter spatial resolution and retrospective data selection MSCT seems to be the non-invasive method of choice for cardiac imaging in general, and for assessment of the coronary arteries in particular. However, technical developments are still needed to further improve the temporal resolution in MSCT and to reduce the substantial radiation exposure.

Animals↗

PubMed2006

Reducing the missing wedge: High-resolution dual axis tomography of inorganic materials.

Electron tomography is a powerful technique that can probe the three-dimensional (3-D) structure of materials. Recently, this technique has been successfully applied to inorganic materials using Z-contrast imaging in a scanning transmission electron microscope to image nanomaterials in 3-D with a resolution of 1 nm in all three spatial dimensions. However, an artifact intrinsic to this technique limits the amount of information obtainable from any object, namely the missing wedge. One way to circumvent this problem is to acquire data from two perpendicular tilt axes, a technique called "dual axis tomography." This paper presents the first dual axis data at high resolution for inorganic materials, and by studying a CdTe tetrapod sample, demonstrates the increase in information obtained using this technique.

Journal Article↗

PubMed2004

Mg(1 + x)Ir(1 - x) (x = 0, 0.037 and 0.054), a binary intermetallic compound with a new orthorhombic structure type determined from powder and single-crystal X-ray diffraction.

The new binary compound Mg(1 + x)Ir(1 - x) (x = 0-0.054) was prepared by melting the elements in the Mg:Ir ratio 2:3 in a sealed tantalum tube under an argon atmosphere in an induction furnace (single crystals) or by annealing cold-pressed pellets of the starting composition Mg:Ir 1:1 in an autoclave under an argon atmosphere (powder sample). The structure was independently solved from high-resolution synchrotron powder and single-crystal X-ray data: Pearson symbol oC304, space group Cmca, lattice parameters from synchrotron powder data a = 18.46948 (6), b = 16.17450 (5), c = 16.82131 (5) A. Mg(1 + x)Ir(1 - x) is a topologically close-packed phase, containing 13 Ir and 12 Mg atoms in the asymmetric unit, and has a narrow homogeneity range. Nearly all the atoms have Frank-Kasper-related coordination polyhedra, with the exception of two Ir atoms, and this compound contains the shortest Ir-Ir distances ever observed. The solution of a rather complex crystal structure from powder diffraction, which was fully confirmed by the single-crystal method, shows the power of powder diffraction in combination with the high-resolution data and the global optimization method.

Alloys↗

PubMed1980

Direct quantitative analysis of indicine-N-oxide in cancer patient samples by gas chromatography using the internal standard heliotrine-N-oxide including a mass spectral comparison of their trimethylsilyl derivatives.

Indicine-N-oxide was analyzed quantitatively in biological samples using a direct partial purification method involving acetonitrite precipitation or methanol precipitation followed by ion exchange chromatography. Trimethylsilyl derivatization of the resultant provided either of two derivatives, depending on the reaction conditions used, both of which had good gas chromatographic qualities. Heliotrine-N-oxide was used as the internal standard for this work. Data are presented to show that this is a reliable and useful internal standard based on its behavior in the partial purification method and on the gas chromatographic characteristics of its two derivatives. In addition, both low and high resolution mass spectral data indicate that heliotrine-N-oxide produces two trimethylsilyl derivatives analogous to those produced by indicine-N-oxide under the same conditions. Application of this procedure to urine and blood samples from cancer patients in clinical trials indicates that over 95% of the drug is removed from the circulation and excreted in the urine over the course of 48 h.

Antineoplastic Agents, Phytogenic↗

PubMed2000

High-resolution magnetic resonance and volume rendering of the labyrinth.

Our aim was to verify the feasibility of volume rendering (VR) of high-resolution magnetic resonance (HR-MR) data sets of the labyrinth. We retrospectively reviewed the HR-MR data sets of 16 consecutive patients with no MR evidence of labyrinthine pathology. High-resolution MR data sets were obtained by means of a 3D T2-weighted FSE sequence with the use of a 3-in. circular surface coil for signal reception, and processed with a high-end workstation. Two reviewers performed separately VR of the labyrinth by selecting the signal intensity interval for attribution of opacity and transparency. Concerning the time taken for definition of the volume of interest, the two observers needed, respectively, 28.9 and 33.1 min (SD +/- 8.7-9.5 min), whereas the time taken for VR was respectively, 26 and 33.2 min (SD +/- 8.8-8.9 min). Concerning the selection of the signal intensity interval, the two observers had, respectively, 86.4 and 88.7 mean lower threshold (SD +/- 34.5-33.5), 488.9 and 495.4 mean upper threshold (SD +/- 56.3-53.8). In our experience, we have found VR of HR-MR to offer a reliable and reproducible technique for producing 3D representations of the labyrinth. The VR algorithms use all data within the imaging volume and optimize the dynamic range ascribed to the object being visualized.

Adolescent↗

PubMed2005

Spatial and temporal trends of mercury and other metals in landlocked char from lakes in the Canadian Arctic archipelago.

Spatial and temporal trends of mercury (Hg) and 22 other elements were examined in landlocked Arctic char (Salvelinus alpinus) from six lakes in the Canadian Arctic (Char, Resolute and North Lakes, and Amituk Lake on Cornwallis Island, Sapphire Lake on Devon Island and Boomerang Lake on Somerset Island). The objectives of the study were to compare recent concentrations of Hg and other metals in char with older data from Amituk, Resolute and Char Lakes, in order to examine temporal trends as well as to investigate factors influencing spatial trends in contaminant levels such as lake characteristics, trophic position, size and age of the fish. Geometric mean Hg concentrations in dorsal muscle ranged from 0.147 microg/g wet weight (ww) in Resolute Lake to 1.52 microg/g ww in Amituk Lake for samples collected over the period 1999-2003. Char from Amituk Lake also had significantly higher selenium (Se). Mercury in char from Resolute Lake was strongly correlated with fish length, weight, and age, as well as with thallium, lead and Se. In 5 of 6 lakes, Hg concentrations were correlated with stable nitrogen isotope ratios (delta15N) and larger char were feeding at a higher trophic level presumably due to feeding on smaller char. Weight adjusted mean Hg concentrations in char from Amituk Lake, and unadjusted geometric means in Char Lake and Resolute Lakes, did not show any statistically significant increase from the early 1990s to 2003. However, small sample sizes from 1999-2003 for fish <1000 g limited the power of this comparison in Char and Amituk Lakes. In Resolute Lake char, manganese, strontium and zinc showed consistent decreases from 1997 or 1999 to 2003 while nickel generally increased over the 6 year period. Differences in char trophic level inferred from delta15N values best explained the higher concentrations of Hg in Amituk Lake compared to the other lakes.

Animals↗

PubMed2003

A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps.

Here, we report a new computational method, called sheetminer, for mining beta-sheets in the density maps at intermediate resolutions of 6 to 10A. The method employs a multi-step ad hoc morphological analysis of density maps to identify the unique characteristics of beta-sheets. It was tested on density maps from 12 protein crystal structures that were artificially blurred to intermediate resolutions. There are a total of 35 independent beta-sheets with a wide distribution of morphology. The method successfully located 34 of them and missed only one. The method was also applied to an experimental 9A electron cryomicroscopic structure and an 8A X-ray density map. In both cases, the sheet-searching results were found to agree very well with known high-resolution crystal structures. Collectively, these results demonstrate clearly the robustness of sheetminer in locating the regions belonging to beta-sheets in the intermediate-resolution density maps. Furthermore, sheetminer is completely complementary to all other existing computational methods, including helixhunter and threading algorithms. Their combined usage has the potential to significantly enhance the computational modeling capacity for a much more complete interpretation of structural data at intermediate resolutions, from which extraction of functional information would be more effective. This is particularly important in the field of structural genomics, in which the fast screening approach may not always yield crystals that diffract to atomic resolution. An exciting future application of sheetminer is as a valuable tool for revealing the structures of amyloid fibrils that are rich in beta-motifs.

Algorithms↗