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At least 1,153 records · Page 64Linked to original sources
PubMed2002

Crystallization and preliminary crystallographic analysis of a novel cytochrome P450 from Mycobacterium tuberculosis.

The product of the Rv2276 gene of Mycobacterium tuberculosis is a cytochrome P450 (P450 MT2, CYP121) which has been shown to bind tightly to a range of azole-based antifungal drugs (e.g. miconazole, clotrimazole). These drugs are potent inhibitors of mycobacterial growth, suggesting that P450 MT2 (CYP121) may be a potential drug target. The enzyme has been overexpressed in Escherichia coli and crystallized by the hanging-drop method. Crystals of P450 MT2 (CYP121) belong to the hexagonal space group P6(1)22 or P6(5)22, with unit-cell parameters a = b = 78.3, c = 265.6 A. Native data have been collected to 1.6 A resolution and Hg-derivative data to 2.5 A resolution using a synchrotron-radiation source.

Crystallization↗
PubMed1990

Low-resolution models for ribosomal particles reconstructed from electron micrographs of tilted two-dimensional sheets.

Models of the whole ribosome (70S) and its large subunit (50S) were obtained at low resolution (47 and 28 A respectively) by three-dimensional image reconstruction using diffraction data collected from electron micrographs of two-dimensional ordered arrays. The comparison of the various reconstructed images, using interactive computer graphics, enabled the assessment of the reliability of the method, the derivation of the shape of the small subunit (30S) and the assignment of several functional features such as the probable path taken by the nascent protein chain, the presumed site for the process of biosynthesis of proteins, and a feasible mode for tRNA binding. The reconstructed models of the various ribosomal particles may be used for phasing of X-ray diffraction data at low resolution.

Chemical Phenomena↗
PubMed1987

[Simultaneous determination of disintegration and dissolution times of solid drug forms in a rotating flask dissolution tester. "Apparent" and "intrinsic" disintegration time].

'Disintegration' and 'dissolution' of solid drug dosage forms are considered as partial processes of drug liberation. Besides the (apparent) disintegration time that is determined in the official disintegration tester, there is a second (intrinsic) disintegration time which can be deduced from the experimental dissolution data, but shows only limited correlation with the former. Various methods for the graphical resolution of dissolution data and the calculation of the intrinsic disintegration time therefrom are discussed. For the simultaneous determination of disintegration and dissolution, the approved rotating flask method is recommended.

Chemistry, Pharmaceutical↗
PubMed2004

Optimisation of high-performance liquid chromatography with diode array detection using an automatic peak tracking procedure based on augmented iterative target transformation factor analysis.

An automated method for the optimisation of high-performance liquid chromatography is developed. First of all, the sample of interest is analysed with various eluent compositions. All obtained data are combined into one augmented data matrix. Subsequently, augmented iterative target transformation factor analysis performs the integrated tasks of curve resolution and peak tracking. Since this type of curve resolution processes all data at once, it can deal with strong peak overlap and reveal the correspondence of compounds between runs, i.e. peak tracking. The retention time and peak width at half height for each component of the sample are determined for every eluent composition. Next, models are built for the retention time and the peak width at half height. These models are used to predict the resolution and the analysis time for each point in factor space. Finally, a multi-criterion decision-making method, Pareto optimality, is used to find the optimum. The method completes all calculations within a few minutes and without user intervention. By means of this procedure, a mixture of three benzodiazepines is successfully separated using a ternary mobile phase. There are two requirements for the automated optimisation method to work correctly. Firstly, all components of the sample must have sufficiently different spectra. Secondly, each compound should have the same spectrum under all experimental conditions.

Benzodiazepines↗
PubMed2003

Analysis of three crystal structure determinations of a 5-methyl-6-N-methylanilino pyridopyrimidine antifolate complex with human dihydrofolate reductase.

Structural data are reported for the first example of the potent antifolate inhibitor 2,4-diamino-5-methyl-6-[(3',4',5'-trimethoxy-N-methylanilino)methyl]pyrido[2,3-d]pyrimidine (1) in complex with human dihydrofolate reductase (hDHFR) and NADPH. Small differences in crystallization conditions resulted in the growth of two different forms of a binary complex. The structure determination of an additional crystal of a ternary complex of hDHFR with NADPH and (1) grown under similar conditions is also reported. Diffraction data were collected to 2.1 A resolution for an R3 lattice from a hDHFR ternary complex with NADPH and (1) and to 2.2 A resolution from a binary complex. Data were also collected to 2.1 A resolution from a binary complex with hDHFR and (1) in the first example of a tetragonal P4(3)2(1)2 lattice. Comparison of the intermolecular contacts among these structures reveals differences in the backbone conformation (1.9-3.2 A) for flexible loop regions (residues 40-46, 77-83 and 103-107) that reflect differences in the packing environment between the rhombohedral and tetragonal space groups. Analysis of the packing environments shows that the tetragonal lattice is more tightly packed, as reflected in its smaller V(M) value and lower solvent content. The conformation of the inhibitor (1) is similar in all structures and is also similar to that observed for TMQ, the parent quinazoline compound. The activity profile for this series of 5-deaza N-substituted non-classical trimethoxybenzyl antifolates shows that the N10-CH(3) substituted (1) has the greatest potency and selectivity for Toxoplasma gondii DHFR (tgDHFR) compared with its N-H or N-CHO analogs. Models of the tgDHFR active site indicate preferential contacts with (1) that are not present in either the human or Pneumocystis carinii DHFR structures. Differences in the acidic residue (Glu30 versus Asp for tgDHFR) affect the precise positioning of the diaminopyridopyrimidine ring, while changes in other residues, particularly at positions 60 and 64 (Leu versus Met and Asn versus Phe), involve interactions with the trimethoxybenzyl substituents.

Binding Sites↗
PubMed2005

Techniques for efficient, real-time, 3D visualization of multi-modality cardiac data using consumer graphics hardware.

We exploit consumer graphics hardware to perform real-time processing and visualization of high-resolution, 4D cardiac data. We have implemented real-time, realistic volume rendering, interactive 4D motion segmentation of cardiac data, visualization of multi-modality cardiac data and 3D display of multiple series cardiac MRI. We show that an ATI Radeon 9700 Pro can render a 512x512x128 cardiac Computed Tomography (CT) study at 0.9 to 60 frames per second (fps) depending on rendering parameters and that 4D motion based segmentation can be performed in real-time. We conclude that real-time rendering and processing of cardiac data can be implemented on consumer graphics cards.

Algorithms↗
PubMed1992

Crystallization and preliminary X-ray structure analysis of pigeon egg-white lysozyme.

Calcium binding lysozyme from pigeon egg-white was crystallized by the hanging drop vapor diffusion technique using ammonium sulphate as a precipitant. The crystals belong to the orthorhombic system, space group P2(1)2(1)2(1), and have unit cell dimensions of a = 34.2 A, b = 34.8 A, and c = 99.4 A. One asymmetric unit contains one molecule of the pigeon lysozyme. The crystals diffract X-rays at least to 2.0 A resolution and are suitable for high resolution structure analysis. The diffraction data up to 3.0 A resolution were collected with a diffraction image processor, DIP100, using a Fuji imaging plate as an area detector. The structure was solved by the molecular replacement technique and refined to an R factor of 0.216. Least-squares fitting of the main-chains of pigeon egg-white lysozyme with those of chicken egg-white lysozyme and baboon alpha-lactalbumin showed that the main-chain folding of pigeon lysozyme is more similar to that of chicken lysozyme than that of alpha-lactalbumin. The largest differences between the pigeon and chicken lysozymes are in the surface loop regions.

Amino Acid Sequence↗
PubMed2002

Short-term light and leaf photosynthetic dynamics affect estimates of daily understory photosynthesis in four tree species.

Instantaneous measurements of photosynthesis are often implicitly or explicitly scaled to longer time frames to provide an understanding of plant performance in a given environment. For plants growing in a forest understory, results from photosynthetic light response curves in conjunction with diurnal light data are frequently extrapolated to daily photosynthesis (A(day)), ignoring dynamic photosynthetic responses to light. In this study, we evaluated the importance of two factors on A(day) estimates: dynamic physiological responses to photosynthetic photon flux density (PPFD); and time-resolution of the PPFD data used for modeling. We used a dynamic photosynthesis model to investigate how these factors interact with species-specific photosynthetic traits, forest type, and sky conditions to affect the accuracy of A(day) predictions. Increasing time-averaging of PPFD significantly increased the relative overestimation of A(day) similarly for all study species because of the nonlinear response of photosynthesis to PPFD (15% with 5-min PPFD means). Depending on the light environment characteristics and species-specific dynamic responses to PPFD, understory tree A(day) can be overestimated by 6-42% for the study species by ignoring these dynamics. Although these overestimates decrease under cloudy conditions where direct sunlight and consequently understory sunfleck radiation is reduced, they are still significant. Within a species, overestimation of A(day) as a result of ignoring dynamic responses was highly dependent on daily sunfleck PPFD and the frequency and irradiance of sunflecks. Overall, large overestimates of A(day) in understory trees may cause misleading inferences concerning species growth and competition in forest understories with < 2% full sunlight. We conclude that comparisons of A(day) among co-occurring understory species in deep shade will be enhanced by consideration of sunflecks by using high-resolution PPFD data and understanding the physiological responses to sunfleck variation.

Acer↗
PubMed1999

Crystallization of a macromolecular ring assembly of tubulin liganded with the anti-mitotic drug podophyllotoxin.

The interaction of the anti-cancer drug podophyllotoxin with a high-molecular-weight assembly of tubulin has been employed to produce three-dimensional crystals from avian erythrocyte tubulin as well as from pig brain tubulin. Avian erythrocyte tubulin crystals belong to the space group C2 with unit cell dimensions a = 740 A, b = 330 A, c = 460 A, beta = 128 degrees. The basis of these crystals is ring oligomers with a molecular mass of approximately 6 x 10(6) Da. So far, the crystals diffract to 8-A resolution and a first complete data set to 12-A resolution has been collected under cryogenic conditions. The crystals grew from conventionally purified tubulin consisting of multiple isoforms and different posttranslational modifications. Thus, the use of highly homogeneous tubulin preparations should improve the diffraction quality of these crystals.

Animals↗
PubMed2003

Preferential integration of human papillomavirus type 18 near the c-myc locus in cervical carcinoma.

The development of cervical cancer is highly associated with human papillomavirus (HPV) infection. Greater than 99% of all cervical tumors contain HPV DNA. Integration of high-risk HPV has been temporally associated with the acquisition of a malignant phenotype. Recent work from our lab has shown that HPV16, the most common high-risk HPV associated with cervical carcinoma, preferentially integrates at loci containing human common fragile sites (CFSs). CFSs are regions of genomic instability that have also been associated with deletions, translocations, and gene amplification during cancer development. The current work shows that HPV18, the second most prevalent high-risk HPV type found in cervical tumors, preferentially targets the CFSs. We identified 27 unique HPV18 integrations in cervical tumors, of which 63% (P<0.001) occur in CFSs. However, the distribution of HPV18 integrations found were profoundly different from those found for HPV16. Specifically, 30% of all HPV18 integrations occurred within the chromosomal band 8q24 near the c-myc proto-oncogene. None of the HPV16 integrations occurred in this region. Previous low-resolution mapping suggested that c-myc may be a target of HPV integration. Our data at nucleotide resolution confirm that in HPV18-positive cervical tumors, the region surrounding c-myc is indeed a hot spot of viral integration. These results demonstrate that CFSs are preferred sites of integration for HPV18 in cervical tumors. In addition, we have identified multiple cellular genes that have been disrupted by HPV18 integration in cervical tumors. Our results suggest that the sites of HPV18 integration are nonrandom and may play an important role in the development of cervical tumors.

Chromosome Mapping↗
PubMed1993

Deconvolution of disoriented fiber diffraction data using iterative convolution and local regression.

Computationally efficient procedures are described for the deconvolution of disoriented fiber diffraction data to the resolution limit of measurable intensity in the patterns. The methods can be applied to diffraction data from imperfectly parallel arrays of one-dimensionally periodic rods or two-dimensionally periodic sheets, randomly rotated about their unique axes, to derive a representation of the intensity distribution corresponding to perfectly parallel orientation. With use of angular convolution and local angular regression, a set of uniform cylindrically averaged squared structure factors are iteratively adjusted, subject to a minimum-wavelength constraint, until they produce a disoriented pattern that fits the observed diffraction data. The results from this deconvolution provide a measure of the properly scaled cylindrically averaged squared structure factors, which can be used with other structural information to construct a physically plausible trial model suitable for further refinement. Sample deconvolutions of simulated X-ray patterns from partially oriented gap junction membranes are presented and the results from point-model deconvolutions are compared to those from constrained deconvolutions that began with the transform of a physically plausible trial model.

Intercellular Junctions↗
PubMed2002

Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus.

RNA polymerase holoenzyme from Thermus thermophilus, consisting of six protein subunits (alpha(2), beta, beta', omega and sigma(70)) and having a total molecular mass of about 450 kDa, was purified and crystallized by the hanging-drop vapour-diffusion technique under mild near-physiological conditions. The crystals diffract beyond 3 A resolution. Careful analysis of diffraction data revealed that the crystals belong to space group P3(2), with unit-cell parameters a = b = 236.35, c = 249.04 A, and have perfect twinning along the threefold axis. A complete data set at 3 A resolution was collected and an unambiguous molecular-replacement solution was found using the structure of T. aquaticus RNA polymerase core enzyme as a search model. The refinement of structure and model building of the sigma(70) subunit is now in progress.

Crystallization↗
PubMed2004

Crystallization and preliminary X-ray analysis of the apo form of Escherichia coli tryptophanase.

Tryptophanase from Escherichia coli is a pyridoxal phosphate-dependent homotetrametic enzyme with a subunit weight of 52 kDa. It has been crystallized in the apo form by the hanging-drop vapour-diffusion method using polyethylene glycol 400 as a precipitant and magnesium chloride as an additive. The crystals belong to the orthorhombic space group F222, with unit-cell parameters a = 118.4, b = 120.1, c = 171.2 A. A 97.8% complete data set to 1.9 A resolution was collected at a rotating-anode source from a single frozen crystal. Packing-density considerations agree with a monomer in the asymmetric unit with a solvent content of 55%. Tryptophanase mutants W330F and Y74F were crystallized under the same conditions and the crystals diffracted to a resolution limit of 1.9 A. Data sets of wild-type crystals soaked with L-tryptophan or pyridoxal phosphate were collected, as well as of Y74F mutant soaked with both.

Apoenzymes↗
PubMedDate not supplied

Pseudo-shading technique in the two-dimensional domain: a post-processing algorithm for enhancing the Z-buffer of a three-dimensional binary image.

Three-dimensional (3D) medical graphics is becoming popular in clinical use on tomographic scanners. Research work in 3D reconstructive display of computerized tomography (CT) and magnetic resonance imaging (MRI) scans on conventional computers has produced many so-called pseudo-3D images. The quality of these images depends on the rendering algorithm, the coarseness of the digitized object, the number of grey levels and the image screen resolution. CT and MRI data are fundamentally voxel based and they produce images that are coarse because of the resolution of the data acquisition system. 3D images produced by the Z-buffer depth shading technique suffer loss of detail when complex objects with fine textural detail need to be displayed. Attempts have been made to improve the display of voxel objects, and existing techniques have shown the improvement possible using these post-processing algorithms. The improved rendering technique works on the Z-buffer image to generate a shaded image using a single light source in any direction. The effectiveness of the technique in generating a shaded image has been shown to be a useful means of presenting 3D information for clinical use.

Algorithms↗
PubMed1992

[Fundamental study of helical scanning CT--evaluation of spatial resolution in the longitudinal axis].

We evaluated spatial resolution in the longitudinal axis with helical scanning CT using a fourth-generation fast CT scanner. We made a phantom by stringing acrylic balls (65 mm phi x 8 and 9 mm phi x 6). The acquired images were processed by MPR and assessed visually to evaluate axis resolution. With the conventional scanning method, the partial volume effect varied with the starting position, but helical scanning was able to reconstruct high-resolution images using continuous raw data. During helical scanning, axis resolution varied depending on the slice width and sliding speed of the couch top. Even if the sliding speed was kept constant at 4 mm/sec, axis resolution was superior with a slice width of 2 mm than with one of 5 mm.

Microcomputers↗
PubMed1994

Analysis of anisotropy decays in terms of correlation time distributions, measured by frequency-domain fluorometry.

We describe the theory and practical aspects of analyzing fluorescence anisotropy decays in terms of correlation times distributions. In our model the rotational motions of the fluorophores were described using Gaussian or Lorentzian distributions of the correlation times. The theory is presented both for time and frequency-domain measurements, although the simulations and measurements are focused on the frequency-domain measurements of the anisotropy decays. Analysis of simulated data is presented to illustrate the nature of the data and the resolution which can be expected with presently available frequency-domain measurements. Additionally, we describe experimental data for samples where one can reasonably expect a single exponential and/or discrete multi-exponential correlation time distributions, and for samples where the anisotropy decay might be expected to display a distribution of correlation times. These samples include small single tryptophan peptides in propylene glycol, the single tryptophan residue in S. Nuclease, and the single tryptophan residue in the native and partially unfolded states of ribonuclease T1.

Amino Acid Sequence↗
PubMed1994

Carotid-subclavian bypass: a twenty-two-year experience.

PURPOSE: A retrospective review of 124 patients who underwent carotid-subclavian bypass from 1968 to 1990 was done to assess primary patency and symptom resolution. METHODS: Preoperative data included age, atherosclerosis risk factors, and indications for surgery. Perioperative data included mortality and morbidity rates and graft conduit. Postoperative follow-up assessed graft patency, resolution of symptoms, and late survival. RESULTS: Age ranged from 42 to 78 years (mean 57.9). Indications for surgery were vertebrobasilar insufficiency in 24 (19%), extremity ischemia (EI) in 33 (27%), transient ischemic attacks (TIAs) in 13 (11%), both vertebrobasilar insufficiency and EI in 31 (25%), and both TIAs and EI in 23 (18%) patients. Graft conduits were polytetrafluoroethylene in 44 (35%) and Dacron in 80 (65%) cases. Concomitant ipsilateral carotid endarterectomy was done in 32 (26%) patients. During operation, death occurred in one patient (0.8%), and complications occurred in 10 (8%) patients. Thirty-day primary patency and symptom-free survival rates were 100%. Long-term follow-up ranging from 5 to 164 months was available for the 60 cases done between 1975 and 1990. Three grafts occluded at 30, 36, and 51 months after surgery for a primary patency rate of 95% at 5 and 10 years. Twenty-two patients died, yielding survival rates of 83% at 5 years and 59% at 10 years. Symptom recurrence occurred in six (10%) patients from 9 to 66 months after surgery. The symptom-free survival rate was 98% at 1 year, 90% at 5 years, and 87% at 10 years. Symptoms recurred in three patients with occluded grafts and three with patent grafts. The preoperative symptoms of drop attacks and TIAs did not recur. EI recurred in 5% and was noted only in the presence of graft occlusion. Dizziness recurred in 17% of patients admitted with this symptom and was observed despite graft patency. CONCLUSION: Carotid-subclavian bypass was a safe and durable procedure for relief of symptomatic occlusive disease of the subclavian artery. Long-term symptomatic relief appeared particularly likely in patients with drop attacks or upper extremity ischemia.

Adult↗
PubMed2005

Scaling and assessment of data quality.

The various physical factors affecting measured diffraction intensities are discussed, as are the scaling models which may be used to put the data on a consistent scale. After scaling, the intensities can be analysed to set the real resolution of the data set, to detect bad regions (e.g. bad images), to analyse radiation damage and to assess the overall quality of the data set. The significance of any anomalous signal may be assessed by probability and correlation analysis. The algorithms used by the CCP4 scaling program SCALA are described. A requirement for the scaling and merging of intensities is knowledge of the Laue group and point-group symmetries: the possible symmetry of the diffraction pattern may be determined from scores such as correlation coefficients between observations which might be symmetry-related. These scoring functions are implemented in a new program POINTLESS.

Algorithms↗