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At least 685 records · Page 38Linked to original sources
PubMed2005

Modeling membrane proteins based on low-resolution electron microscopy maps: a template for the TM domains of the oxalate transporter OxlT.

The availability of both EM and high-resolution crystallographic data for several membrane proteins (MPs) permits a detailed evaluation of the ability of molecular modeling techniques to complement EM data in the development of models of MPs. A protocol for this purpose is presented, consisting of (1) identifying transmembrane (TM) domains from sequence; (2) assigning buried and lipid-exposed faces of the TM domains; and (3) assembling the TM domains into a bundle, based on geometric restraints obtained from the EM data. The protocol is validated by predicting the structures of several 7- and 12-TM MPs to within 3-5 A r.m.s.d. from their crystal structures. The protocol is applied to generate a model of the oxalate transporter OxlT, for which a high-resolution structure is not yet available.

Algorithms↗
PubMedDate not supplied

[Rotation isomerization of side chains of globular proteins and its effect on the x-ray scattering curves of proteins in a solution].

A new method has been developed for averaging the intensity of X-ray diffuse scattering of proteins by different conformations of side groups. The method is based on the algorithm allowing to calculate statistical weights of rotation isomers of side chains. It is shown that for protein structures obtained from high resolution crystallographic data, conformations of the majority of surface groups correspond to rotation isomers with the greatest statistical weight. It has been found that for medium size proteins (with molecular weight varying from 15,000 to 30,000 dalton) whose structure has been determined at high resolution, the influence of rotation isomerization of side chains on the scattering indicatrices does not exceed 5%. The influence of side chains mobility on the scattering curves of large proteins is also small. For these two classes of proteins the rotation isomerization of side groups can be ignored when interpreting significant (exceeding 10%) divergences between experimental and theoretical scattering curves.

Alkaloids↗
PubMed1996

[Impact of rapid advancement of international standardization on technical requirements for new drug registration].

Internationalization of new drug research and development is rapidly progressing. When mutual international acceptance of clinical trial data is realized, scientifically superior data will eradicate and replace all not so scientific data. This means that healthy competition would benefit the data of clinical trials. The same is true of anti-tumor drugs. Some Japan originated antitumor drugs were developed in foreign countries prior to domestic clinical development. In future, geographic centralization of clinical trials in areas which can conduct scientifically more consistent trials is expected. There are only a limited number of institutes which can conduct high-quality clinical trials of antitumor drugs, so they want Japan, a potential country, to come to other areas to produce high-quality clinical trial data. The resolution of a number of daily stumbling blocks such as informing the patient that he or she is suffering from cancer is a prerequisite for conducting high-quality clinical trials. But every effort must be made so that it will not be said: "Data produced overseas are better. There is no need for Japan to use its knowledge and effort in the field of clinical development."

Antineoplastic Agents↗
PubMed2000

Corticosteroids for the resolution of malignant bowel obstruction in advanced gynaecological and gastrointestinal cancer.

BACKGROUND: Gastrointestinal and ovarian cancers are common cancers. The incidence of associated malignant bowel obstruction in patients with advanced cancers of these types is not known, and the best management of these patients is controversial. Inappropriate management may result in uncontrolled (faeculant) vomiting, pain and distress. Management of the symptoms can include palliative surgery, nasogastric tube suction together with intravenous fluids, or pharmacological means, such as corticosteroids. There is uncertainty regarding both the efficacy and possible harmful effects of corticosteroids, and also the most effective type, dose/dosing regime, route and period of administration. OBJECTIVES: To locate, appraise and summarise evidence from scientific studies on intestinal obstruction due to advanced gynaecological and gastrointestinal cancer, in order to assess the efficacy of corticosteroids. SEARCH STRATEGY: A comprehensive list of all studies was provided by an extensive search of the electronic databases, relevant journals, reference lists, the grey literature, contact with investigators and other search strategies outlined in the methods. SELECTION CRITERIA: As the review concentrates on the 'best evidence' available of the role of corticosteroids in malignant bowel obstruction due to advanced gynaecological and gastrointestinal cancer the inclusion criteria were kept fairly broad so as to include all studies relevant to the question DATA COLLECTION AND ANALYSIS: Data extraction forms were used to collect data from the studies included in the review. The data was checked by a secondary searcher to reduce error. A qualitative analysis was performed of the dichotomous data of resolution of obstruction and death at one month, obtained from the randomised controlled trials of corticosteroids versus placebo. Both fixed and random effect models were used. Number needed to treat (NNT) was derived from the odds ratio. Kaplan-Meier survival curves from individual patient data were also analysed. Studies of lower methodological quality were assessed in a qualitative manner. MAIN RESULTS: Three unpublished, randomised, placebo, double blind controlled trials and seven published (prospective and retrospective) trials were considered eligible. Using only the randomised trials, there is a trend, which is not statistically significant, for the resolution of bowel obstruction using corticosteroids. There is no statistically significant difference in mortality at one month, nor in the Kaplan-Meier curves, which describe the survival of patients on corticosteroids or placebo. Number needed to treat is 6 (3, infinity) ie six patients need to be treated with corticosteroids to resolve one episode of bowel obstruction. The results are robust to fixed and random effects models and to 'best' and 'worst case' scenarios on the missing data from patients. The morbidity associated with corticosteroids appears to be very low, though the quality of the data limits this conclusion. No other outcomes were available from the published data or from the authors. REVIEWER'S CONCLUSIONS: There is a trend for evidence that corticosteroids of dose range 6-16 mg dexamethasone given intravenously may bring about the resolution of bowel obstruction. Equally, the incidence of side effects in all the included studies is extremely low. Corticosteroids do not seem to affect the length of survival of these patients.

Female↗
PubMed1990

Mode of interaction of the zinc finger protein TFIIIA with a 5S RNA gene of Xenopus.

The zinc finger protein TFIIIA, a positive transcription factor of the 5S RNA gene, binds to an internal control region of 50 nucleotides. Two modes of binding have been considered for the TFIIIA-DNA complex, one of which has been proposed on the basis of nuclease and chemical protection experiments and the other on model building. Since then, evidence has accumulated on the structures of individual components of the complex--for example, zinc finger polypeptides studied by NMR and a segment of the binding site analyzed by x-ray crystallography, but no high-resolution structural data on the TFIIIA-DNA complex itself are available. Probes used previously to study the TFIIIA-DNA complex do not react with every nucleotide of DNA, unlike hydroxyl radical, which cleaves DNA at every backbone position. We describe here the quantitative analysis of high-resolution hydroxyl radical footprints and suggest how the array of zinc fingers might interact with the double helix.

Animals↗
PubMed1998

Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands.

Antiherpes therapies are principally targeted at viral thymidine kinases and utilize nucleoside analogs, the triphosphates of which are inhibitors of viral DNA polymerase or result in toxic effects when incorporated into DNA. The most frequently used drug, aciclovir (Zovirax), is a relatively poor substrate for thymidine kinase and high-resolution structural information on drugs and other molecules binding to the target is therefore important for the design of novel and more potent chemotherapy, both in antiherpes treatment and in gene therapy systems where thymidine kinase is expressed. Here, we report for the first time the binary complexes of HSV-1 thymidine kinase (TK) with the drug molecules aciclovir and penciclovir, determined by X-ray crystallography at 2.37 A resolution. Moreover, from new data at 2.14 A resolution, the refined structure of the complex of TK with its substrate deoxythymidine (R = 0.209 for 96% of all data) now reveals much detail concerning substrate and solvent interactions with the enzyme. Structures of the complexes of TK with four halogen-containing substrate analogs have also been solved, to resolutions better than 2.4 A. The various TK inhibitors broadly fall into three groups which together probe the space of the enzyme active site in a manner that no one molecule does alone, so giving a composite picture of active site interactions that can be exploited in the design of novel compounds.

Acyclovir↗
PubMed2004

Accelerating cardiac cine 3D imaging using k-t BLAST.

By exploiting spatiotemporal correlations in cardiac acquisitions using k-t BLAST, gated cine 3D acquisitions of the heart were accelerated by a net factor of 4.3, making single breathhold acquisitions possible. Sparse sampling of k-t space along a sheared grid pattern was implemented into a cine 3D SSFP sequence. The acquisition of low-resolution training data, which was required to resolve aliasing in the k-t BLAST method, was either interleaved into the sampling process or obtained in a separate prescan to allow for shorter breathhold durations in patients with heart disease. Volumetric datasets covering the heart with 20 slices at a spatial resolution of 2 x 2 x 5 mm3 were recorded with 20 cardiac phases in a total breathhold duration of 25-27 sec, or 18 sec if partial Fourier sampling was additionally employed. The feasibility of the method was demonstrated on healthy volunteers and on patients. The comparison of endocardial area derived from single slices of the 3D dataset with values extracted from separate single-slice acquisitions showed no significant differences. By shortening the acquisition substantially, k-t BLAST may greatly facilitate volumetric imaging of the heart for evaluation of regional wall motion and the assessment of ventricular volume and ejection fraction.

Computer Simulation↗
PubMedDate not supplied

Ultra-fast automated brain volumetry based on bispectral MR imaging data.

In this paper we present a fast automated three-dimensional brain segmentation and brain volumetry method providing minimal requirements of the number of spectral MR image channels and the performance of the computer equipment employed. The presented method is based on standard non-iterative two-dimensional grey level segmentation techniques in combination with pixel vector-oriented classificators and morphological operators and requires a bispectral high resolution MR data base. In its current design, the method provides for the largely partial volume-corrected determination of the cerebrospinal fluid (CSF) and the white and grey brain matter volumes of the human brain. For the verification of our approach, the results of applications to clinical data were compared to those of studies found in the literature.

Algorithms↗
PubMed2026

Reconstructing the early spatial spread of pandemic respiratory viruses in the United States.

Understanding the geographic spread of emerging respiratory viruses is critical for pandemic preparedness, yet the early spatiotemporal dynamics of the 2009 H1N1 pandemic influenza and severe acute respiratory syndrome coronavirus 2 in the United States remain unclear. While mobility and genomic data have revealed important aspects of pandemic spatial spread, several key questions remain: Did the two pandemics follow similar spatial transmission routes? How rapidly did they spread across the United States? What role did stochastic processes play in early spatial transmission? To address these questions, we integrated high-resolution disease data with a robust, data-efficient inference framework combining air travel, commuting flows, and pathogen superspreading potentials to reconstruct their spatial spread across US metropolitan areas. The two pandemics exhibited distinct transmission pathways across locations; however, both pandemics established local circulation in most metropolitan areas within weeks, driven by several shared transmission hubs. Early spatial spread was more strongly associated with air travel than with commuting, though stochastic dynamics introduced substantial uncertainty in transmission routes, creating challenges for timely detection and control. Simulations indicate that broad wastewater surveillance coverage beyond top transmission hubs coupled with effective infection control may slow initial spatial expansion. Our findings highlight the rapid, stochastic spread of pandemic respiratory pathogens and the difficulties of early outbreak containment.

Humans↗
PubMed2000

Refinement of framework disorder in dehydrated CaA zeolite from single-crystal synchrotron data.

An accurate knowledge of zeolite structure is required for understanding their selective sorption capacities and their catalytic properties. In particular, the positions of the exchangeable cations and their interactions with the framework are essential. The present study deals with the accurate crystal structure determination of a fully exchanged and fully dehydrated CaA zeolite (Ca(48)Al(96)Si(96)O(384), Fm3c, a = 24.47 A) using single-crystal high-resolution synchrotron X-ray diffraction [(sin straight theta/lambda)(max) = 1.4 A(-1)]. It is shown that cation exchange severely distorts the skeleton, especially around the O2 atom. The high-resolution synchrotron data reveal that this latter O atom is disordered and lies out of the mirror plane it occupies in other A-type zeolites. This feature is related to that observed for Ca(2+) cations.

Journal Article↗
PubMed1993

Structure determination of feline panleukopenia virus empty particles.

Various crystal forms of the single-stranded DNA, feline panleukopenia virus (FPV), a parvovirus, have been grown of both full virions and empty particles. The structure of empty particles crystallized in an orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions a = 380.1 A, b = 379.3 A, and c = 350.9 A, has been determined to 3.3 A resolution. The data were collected using oscillation photography with synchrotron radiation. The orientations of the empty capsids in the unit cell were determined using a self-rotation function and their positions were obtained with an R-factor search using canine parvovirus (CPV) as a model. Phases were then calculated, based on the CPV model, to 6.0 A resolution and gradually extended to 3.3 A resolution by molecular replacement electron density averaging. The resultant electron density was readily interpreted in terms of the known amino acid sequence. The structure is contrasted to that of CPV in terms of host range, neutralization by antibodies, hemagglutination properties, and binding of genomic DNA.

Amino Acid Sequence↗
PubMed1994

Refined structure of concanavalin A complexed with methyl alpha-D-mannopyranoside at 2.0 A resolution and comparison with the saccharide-free structure.

The three-dimensional structure of the complex between methyl alpha-D-mannopyranoside and concanavalin A has been refined at 2.0 A resolution. Diffraction data were recorded from a single crystal (space group P2(1)2(1)2(1), a = 123.7, b = 128.6, c = 67.2 A) using synchrotron radiation at a wavelength of 1.488 A. The final model has good geometry and an R factor of 19.9% for 58 871 reflections (82% complete), within the resolution limits of 8 to 2 A, with F > 1.0sigma(F). The asymmetric unit contains four protein subunits arranged as a dimer of dimers with approximate 222 point symmetry. Each monomer binds one saccharide molecule. Each sugar is bound to the protein by hydrogen bonds and van der Waals contacts. Although the four subunits are not crystallographically equivalent, the protein-saccharide interactions are nearly identical in each of the four binding sites. The differences that do occur between the four sites are in the structure of the water network which surrounds each saccharide; these networks are involved in crystal packing. The structure of the complex is compared with a refined saccharide-free concanavalin A structure. The saccharide-free structure is composed of crystallographically identical subunits, again assembled as a dimer of dimers, but with exact 222 symmetry. In the saccharide complex the tetramer association is different in that the monomers tend to separate resulting in fewer intersubunit interactions. The average temperature factor of the mannoside complex is considerably higher than that of the saccharide-free protein. The binding site in the saccharide-free structure is occupied by three ordered water molecules and the side chain of Asp71 from a neighbouring molecule in the crystal. These occupy positions similar to those of the four saccharide hydroxyls which are hydrogen bonded to the site. Superposition of the saccharide-binding site from each structure shows that the major changes on binding involve expulsion of these ordered solvents and the reorientation of the side chain of Tyrl00. Overall the surface accessibility of the saccharide decreases from 370 to 100 A(2) when it binds to the protein. This work builds upon the earlier studies of Derewenda et al. [Derewenda, Yariv, Helliwell, Kalb (Gilboa), Dodson, Papiz, Wan & Campbell (1989). EMBO J. 8, 2198-2193] at 2.9 A resolution, which was the first detailed study of lectin-saccharide interactions.

Journal Article↗
PubMed1998

1.85 A resolution structure of the zinc (II) beta-lactamase from Bacillus cereus.

Class B beta-lactamases are wide spectrum enzymes which require bivalent metal ions for activity. The structure of the class B zinc-ion-dependent beta-lactamase from Bacillus cereus (BCII) has been refined at 1.85 A resolution using data collected on cryocooled crystals (100 K). The enzyme from B. cereus has a molecular mass of 24 946 Da and is folded into a beta-sandwich structure with helices on the external faces. The active site is located in a groove running between the two beta-sheets [Carfi et al. (1995). EMBO J. 14, 4914-4921]. The 100 K high-resolution BCII structure shows one fully and one partially occupied zinc sites. The zinc ion in the fully occupied site (the catalytic zinc) is coordinated by three histidines and one water molecule. The second zinc ion is at 3.7 A from the first one and is coordinated by one histidine, one cysteine, one aspartate and one unknown molecule (most likely a carbonate ion). In the B. cereus zinc beta-lactamase the affinity for the second metal-ion is low at the pH of crystallization (Kd = 25 mM, 293 K; [Baldwin et al. (1978). Biochem. J. 175, 441-447] and the dissociation constant of the second zinc ion was thus apparently decreased at the cryogenic temperature. In addition, the structure of the apo enzyme was determined at 2.5 A resolution. The removal of the zinc ion by chelating agents causes small changes in the active-site environment.

Amino Acid Sequence↗
PubMed2006

Live imaging of fluorescent proteins in chordate embryos: from ascidians to mice.

Although we have advanced in our understanding of the molecular mechanisms intrinsic to the morphogenesis of chordate embryos, the question of how individual developmental events are integrated to generate the final morphological form is still unresolved. Microscopic observation is a pivotal tool in developmental biology, both for determining the normal course of events and for contrasting this with the results of experimental and pathological perturbations. Since embryonic development takes place in three dimensions over time, to fully understand the events required to build an embryo we must investigate embryo morphogenesis in multiple dimensions in situ. Recent advances in the isolation of naturally fluorescent proteins, and the refinement of techniques for in vivo microscopy offer unprecedented opportunities to study the cellular and molecular events within living, intact embryos using optical imaging. These technologies allow direct visual access to complex events as they happen in their native environment, and thus provide greater insights into cell behaviors operating during embryonic development. Since most fluorescent protein probes and modes of data acquisition are common across species, we have chosen the mouse and the ascidian, two model organisms at opposite ends of the chordate clade, to review the use of some of the current genetically-encoded fluorescent proteins and their visualization in vivo in living embryos for the generation of high-resolution imaging data.

Animals↗
PubMed1993

Multiple hydration layers in cubic insulin crystals.

Cubic insulin crystals contain approximately 30-A-diameter channels filled with aqueous solvent, providing a useful system in which to analyze hydration structure at a variety of distances from protein surfaces. Beginning with an atomic model for the protein and ordered water molecules, the density distribution in the solvent volume of the phasing model was iteratively refined to improve the fit of calculated structure factors with x-ray diffraction data. The free R value, which compares calculated structure factors with a subset of observed structure factors deliberately omitted from the refinement, was used to provide an objective confirmation of the effectiveness of the refinement procedure. Electron density maps of the solvent, computed using the solvent-refined phases and complete low-resolution diffraction data, reveal multiple hydration layers around the protein.

Animals↗
PubMed2001

Interactive 3-dimensional segmentation of MRI data in personal computer environment.

We describe a method of interactive three-dimensional segmentation and visualization for anatomical magnetic resonance imaging (MRI) data in a personal computer environment. The visual feedback necessary during 3-D segmentation was provided by a ray casting algorithm, which was designed to allow users to interactively decide the visualization quality depending on the task-requirement. Structures such as gray matter, white matter, and facial skin from T1-weighted high-resolution MRI data were segmented and later visualized with surface rendering. Personal computers with central processing unit (CPU) speeds of 266, 400, and 700 MHz, were used for the implementation. The 3-D visualization upon each execution of the segmentation operation was achieved in the order of 2 s with a 700 MHz CPU. Our results suggest that 3-D volume segmentation with semi real-time visual feedback could be effectively implemented in a PC environment without the need for dedicated graphics processing hardware.

Adult↗
PubMed2002

Novel NMR tools to study structure and dynamics of biomembranes.

Nuclear magnetic resonance (NMR) studies on biomembranes have benefited greatly from introduction of magic angle spinning (MAS) NMR techniques. Improvements in MAS probe technology, combined with the higher magnetic field strength of modern instruments, enables almost liquid-like resolution of lipid resonances. The cross-relaxation rates measured by nuclear Overhauser enhancement spectroscopy (NOESY) provide new insights into conformation and dynamics of lipids with atomic-scale resolution. The data reflect the tremendous motional disorder in the lipid matrix. Transfer of magnetization by spin diffusion along the proton network of lipids is of secondary relevance, even at a long NOESY mixing time of 300 ms. MAS experiments with re-coupling of anisotropic interactions, like the 13C-(1)H dipolar couplings, benefit from the excellent resolution of 13C shifts that enables assignment of the couplings to specific carbon atoms. The traditional 2H NMR experiments on deuterated lipids have higher sensitivity when conducted on oriented samples at higher magnetic field strength. A very large number of NMR parameters from lipid bilayers is now accessible, providing information about conformation and dynamics for every lipid segment. The NMR methods have the sensitivity and resolution to study lipid-protein interaction, lateral lipid organization, and the location of solvents and drugs in the lipid matrix.

Animals↗
PubMed2003

Measurements of near-surface bubble plumes in the open ocean with implications for high-frequency sonar performance.

This study examines near-surface bubble data obtained with a self-contained 200-kHz inverted echo-sounder deployed at Ocean Station Papa (NE Pacific, 1400 km west of Vancouver Is.) over an 81-day period in the spring of 1996. The instrument operated continuously, recording calibrated volume scattering profiles from near-surface bubbles with 3-s and 30-cm resolution. The data show the frequent occurrence of bubbles organized into vertical, plume-like structures, presumably drawn downwards by turbulence and other near-surface circulations. Average bubble plume penetrations of up to 15 m were observed, with maximum penetrations up to 25 m. Within the plumes, the backscatter cross section exhibited an exponential decay with depth, with e-folding scale in the range 0.5 to 3 m, increasing proportionally to the square of average plume depth. Using standard models for bubble scattering, and incorporating recent acoustic resonator measurements of bubble-size distributions along with actual bubble plume data, high-frequency near-surface sonar performance models were developed. These models show that on a ping-to-ping basis the bubble plume structures can induce significant spatial variations in the reverberation level and path-integrated extinction losses to near-surface targets.

Models, Theoretical↗