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At least 667 records · Page 37Linked to original sources
PubMed1991

Multi-conformational peptide dynamics derived from NMR data: a new search algorithm and its application to antamanide.

A search algorithm, called MEDUSA, is presented which allows the determination of multiple conformations of biomolecules in solution with exchange rate constants typically between 10(3) and 10(7) s-1 on the basis of experimental high-resolution NMR data. Multiples of structures are generated which are consistent as ensembles with NMR cross-relaxation rates (NOESY, ROESY), scalar J-coupling constants, and T1 rho measurements. The algorithm is applied to the cyclic decapeptide antamanide dissolved in chloroform. The characteristic radio-frequency field dependence of the T1 rho relaxation rates found for the NH protons of Val1 and Phe6 can be explained by a dynamical exchange between two structures.

Algorithms↗
PubMed1997

Time-resolved protein crystallography with large-angle oscillations: an application of a protein data-collection system using the Weissenberg technique and a large-format imaging plate.

A diffraction-intensity data-collection system with synchrotron radiation X-rays utilizing the screenless Weissenberg technique and incorporating a large-format imaging plate is one of the most suitable apparatus for time-resolved protein crystallography with larger angle oscillations than hitherto described. The time resolution and data quality of the system have been tested using a tetragonal lysozyme crystal as a test sample in a flow-cell experiment at the bending-magnet beamline 18B at the Photon Factory, and a time resolution of 15 min is confirmed.

Journal Article↗
PubMed1996

Conservation of aconitase residues revealed by multiple sequence analysis. Implications for structure/function relationships.

Aconitases have recently regained much attention, because one member of this family, iron regulatory protein-1 (IRP-1), has been found to play a dual role as a cytoplasmic aconitase and a regulatory RNA-binding protein. This finding has highlighted a novel role for Fe-S clusters as post-translational regulatory switches. We have aligned 28 members of the Fe-S isomerase family, identified highly conserved amino acid residues, and integrated this information with data on the crystallographic structure of mammalian mitochondrial aconitase. We propose structural and/or functional roles for the previously unrecognized conserved residues. Our findings illustrate the value of detailed protein sequence analysis when high-resolution crystallographic data are already available.

Aconitate Hydratase↗
PubMed2003

Structure determination of enalapril maleate form II from high-resolution X-ray powder diffraction data.

The crystal structure of polymorphic Form II of enalapril maleate, a potent angiotensin-converting enzyme inhibitor, was determined from high-resolution X-ray diffraction data using the direct space method. Enalapril maleate Form II crystallizes in space group P2(1)2(1)2(1), Z = 4, with unit cell parameters a = 33.9898(3) A, b = 11.2109(1) A, c = 6.64195(7) A, and V = 2530.96(5) A(3). By treating the molecules as rigid bodies and using the bond lengths and angles obtained from the X-ray single crystal structures of Form I, which were solved almost 20 years ago, the total degrees of freedom of enalapril maleate were reduced from 25 to 12. This reduction in total degrees of freedom allowed the simulated annealing to complete within a reasonable computation time. In the crystal structure of Form II, the crystal packing, hydrogen-bonding pattern, and conformation of enalapril maleate resemble those in the structure of Form I. The crystal packing and conformation of enalapril maleate in the two polymorphic forms may explain the similarity of the thermal properties, (13)C nuclear magnetic resonance, Fourier transform infrared, and Raman spectra of Forms I and II. In both structures, the conformations of the main peptide chains, which are considered responsible for binding the active angiotensin-converting enzyme sites, remain largely unchanged. Lattice energy calculation showed that Form II is slightly more stable than Form I by 3.5 kcal/mole.

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2004

Evolution of multiple paralogous adenosine kinase genes in the moss genus Hygroamblystegium: phylogenetic implications.

Maximum likelihood analyses of DNA sequences from two chloroplast regions, trnL-trnF and atpB-rbcL, and the internal transcribed spacers of 18S-5.8S-26S rRNA gene array, were performed to resolve species relationships within the moss genus Hygroamblystegium. Constraining morphospecies to monophyly resulted in significantly less likely trees for H. tenax, but not for the other species. The lack of support for most clades and the partial incongruence among topologies necessitated the use of another independent, more variable region, namely the adenosine kinase gene (adk). Sequences for adk were polymorphic but were present as multiple copies within individuals, making parology a problem for phylogenetic analyses. Adk evolution was reconstructed using a reconciled gene tree approach in which duplications and losses were minimized in the context of an estimate of the species tree derived from the analysis of the cp and nrDNA sequence data. Additional resolution of the species tree was then obtained by searching for reconstructions that further reduced adk duplications and losses. All the traditionally recognized morphospecies appeared to be polyphyletic in the resulting tree. Together with previous data from different molecular markers, the results support the interpretation that Hygroamblystegium represents a recent radiation in which molecular and morphological evolution have been uncoupled.

Adenosine Kinase↗
PubMed1996

Structure and functional mechanism of porins.

Cellular organisms such as gram-negative bacteria are enclosed by a dual lipid bilayer system. The outer membranes of the dual bilayer envelopes predominantly contain large numbers of water-filled transmembrane protein channels known as porins. The recent availability of the molecular structures of several bacterial porins has provided the opportunity for comparing the results of a wide range of functional studies with the atomic level structural details of these membrane channels. Taken together, the structure and function data present the most comprehensive set of boundary conditions available for the evaluation of theory and models predicting the characteristics of solute transport through membrane protein channels. In this paper, we review the high-resolution structure data from the bacterial porins, as well as recent theoretical studies, in the context of biophysical and biochemical observations and discuss the molecular mechanisms responsible for the transport of solutes through porin channels. Particular emphasis has been placed on the features and roles of common structural elements, channel sterics and electrostatics, and voltage-dependent gating. A model for water-coordinated transport, providing a qualitative view of the porin transport mechanism, is also described.

Biological Transport↗
PubMed1995

Crystallographic extraction and averaging of data from small image areas.

The accuracy of structure factor phases determined from electron microscope images is determined mainly by the level of statistical significance, which is limited by the low level of allowed electron exposure and by the number of identical unit cells that can be averaged. It is shown here that Fourier transforms of small image fields of purple membrane (a two-dimensional crystal consisting of bacteriorhodopsin and endogenous lipids) can be combined to provide the same quality of phases as are obtained from Fourier transforms of large image fields of the same total area. Although Fourier transforms of such small image fields are statistically significant only at lower resolution, the data from many such image fields can be averaged at the calculated positions of high-resolution reciprocal lattice points to give accurate phases. More specifically, when images of a size that can be recorded with CCD cameras are processed individually, key parameters including lattice vectors, defocus, crystal and beam tilts, and common phase origin can be accurately determined.

Crystallography, X-Ray↗
PubMed1993

Ten years in the library: new data confirm paleontological patterns.

A comparison is made between compilations of times of origination and extinction of fossil marine animal families published in 1982 and 1992. As a result of ten years of library research, half of the information in the compendia has changed: families have been added and deleted, low-resolution stratigraphic data been improved, and intervals of origination and extinction have been altered. Despite these changes, apparent macroevolutionary patterns for the entire marine fauna have remained constant. Diversity curves compiled from the two data bases are very similar, with a goodness-of-fit of 99%; the principal difference is that the 1992 curve averages 13% higher than the older curve. Both numbers and percentages of origination and extinction also match well, with fits ranging from 83% to 95%. All major events of radiation and extinction are identical. Therefore, errors in large paleontological data bases and arbitrariness of included taxa are not necessarily impediments to the analysis of pattern in the fossil record, so long as the data are sufficiently numerous.

Animals↗
PubMed1994

Structure and orientation of the transmembrane domain of glycophorin A in lipid bilayers.

Rotational resonance (RR) NMR, circular dichroism (CD), and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy are used to establish the secondary structure and orientation of peptides corresponding to the transmembrane domain of human glycophorin A in dimyristoylphosphatidylcholine bilayers. An amide I vibrational frequency of 1650 cm-1 and negative CD absorption bands at 208 and 222 nm indicate that the peptide is largely alpha-helical, while an order parameter of 0.35-0.50 in the ATR-FTIR measurements indicates that the peptide orientation is generally perpendicular to the bilayer plane. High-resolution structural data on the glycophorin A transmembrane (GPA-TM) peptides were obtained by measuring the rate of magnetization exchange between pairs of specific 13C labels using RR NMR. The exchange rates are translated into internuclear distances with a resolution on the order of 0.3 A. These experiments are similar in design to previous experiments on crystalline peptides where the 13C labels were incorporated into amino acids separated by 2-3 residues in the peptide sequence but close together in space due to a helical peptide geometry [Peersen, O.B., Yoshimura, S., Hojo, H., Aimoto, S., & Smith, S.O. (1992) J. Am. Chem. Soc. 114, 4332-4335]. In the GPA-TM peptides, magnetization exchange rates measured between [1-13C]V80 and [2-13C] G83 between [1-13C]M81 and [2-13C]G83 in the middle of the transmembrane sequence correspond to internuclear distances of approximately 4.5 A and are consistent with a helical peptide structure.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1994

Biomagnetic localization of electrical current sources in the human heart with realistic volume conductors using the single-current-dipole model.

The boundary element method was applied in order to investigate the localization accuracy for focal sources measured from MCG data. Various homogeneous volume conductor models were composed: the individually shaped torso, a scaled standard torso, an unscaled standard torso, a scaled cuboid and a scaled ellipsoid. We implemented these models in single-dipole inverse solution techniques. High resolution multichannel data were analysed from two patients showing ventricular extrasystoles and two patients suffering from Wolff-Parkinson-White syndrome. Moreover, we report the localization of shallow- and deep-lying catheters (depth 9 cm and depth 17.5 cm below the measurement grid). Using an individually shaped homogeneous torso yields a localization error of less than 3 cm even for the deepest sources (mean error 2.4 cm). Probability-based dipole localization shows that the remaining error could only partly be explained by data noise statistics. Therefore it seems to be due to either inner inhomogeneities or the inadequacy of the single current dipole or a combination of the two. Thus clinically useful localization accuracy in the millimetre range requires more sophisticated volume conductor and source models. The evaluation of measurement data and simulation study shows that a scaled cuboid model can provide nearly the same localization accuracy as the individually shaped torso model. Single dipole reconstruction with this model is computationally faster than that with the individually shaped model of the human body and is fast enough for use in clinical applications.

Arrhythmias, Cardiac↗
PubMed2006

Multiple myeloma of the cervical spine: treatment strategies for pain and spinal instability.

OBJECT: Metastases of multiple myeloma often occur in the cervical spine. These metastases may cause pain and associated spinal instability. The authors report the results of radiotherapy and surgical treatment for myeloma involving the cervical spine. The results of radiation therapy for multiple myeloma metastases to the cervical spine that cause clinical or radiographically documented instability have not been reported previously. METHODS: A retrospective chart review of patients with multiple myeloma metastases to the cervical spine was undertaken. Between 1993 and 2005, 35 patients were treated with external-beam radiation and/or surgical stabilization at the University of Texas M. D. Anderson Cancer Center in Houston, Texas. Nineteen of 20 patients with sufficient follow-up data experienced resolution of their pain when treated with radiation without surgical intervention. Twenty-three patients had evidence of spinal instability on radiographic images; 15 of these were treated with radiation alone. Of these, 10 had sufficient follow-up data, and none showed any clinical progression of instability. Radiographic follow-up images demonstrated an arrest of further progression of instability and, in some cases, healing of pathological fractures by means of radiation alone. CONCLUSIONS: The results of this series suggest that, in selected cases, external-beam radiation for multiple myeloma metastases to the cervical spine is an effective palliative treatment, even in cases involving clinical or radiographically documented instability.

Adult↗
PubMed2003

The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure.

Bulged-G motifs are ubiquitous internal RNA loops that provide specific recognition sites for proteins and RNAs. To establish the common and distinctive features of the motif we determined the structures of three variants and compared them with related structures. The variants are 27-nt mimics of the sarcin/ricin loop (SRL) from Escherichia coli 23S ribosomal RNA that is an essential part of the binding site for elongation factors (EFs). The wild-type SRL has now been determined at 1.04 A resolution, supplementing data obtained before at 1.11 A and allowing the first calculation of coordinate error for an RNA motif. The other two structures, having a viable (C2658U*G2663A) or a lethal mutation (C2658G*G2663C), were determined at 1.75 and 2.25 A resolution, respectively. Comparisons reveal that bulged-G motifs have a common hydration and geometry, with flexible junctions at flanking structural elements. Six conserved nucleotides preserve the fold of the motif; the remaining seven to nine vary in sequence and alter contacts in both grooves. Differences between accessible functional groups of the lethal mutation and those of the viable mutation and wild-type SRL may account for the impaired elongation factor binding to ribosomes with the C2658G*G2663C mutation and may underlie the lethal phenotype.

Animals↗
PubMed1985

Adrenal scintigraphy in the morphological and functional evaluation of Cushing's syndrome.

In recent years, cholesterol adrenal scintigraphy has been employed in the morphofunctional study of adrenal hypercorticism. Particularly in Cushing's syndrome, this noninvasive procedure can give a determinant contribution to distinguish ACTH-dependent from ACTH-independent forms. In our Institute, adrenal scintigraphy was performed in 77 patients with Cushing's syndrome diagnosed on clinical grounds confirmed by laboratory investigations and functional tests (17 with cortisol-secreting adenoma, 54 with pituitary ACTH-dependent bilateral adrenal hyperplasia, 2 with ectopic ACTH-dependent bilateral hyperplasia and 4 with bilateral nodular hyperplasia). Three distinct scintigraphic patterns have been identified. The 56 patients with ACTH-dependent Cushing's syndrome showed bilateral symmetric or slightly asymmetric visualization of the adrenal glands; in the 17 patients with ACTH-independent Cushing's syndrome the adrenal scintigraphy only visualized the gland harboring the adenoma; finally, a marked asymmetric visualization of the glands was observed in the 4 patients with adrenal nodular hyperplasia. These data confirm that adrenal scintigraphy is able to distinguish between ACTH-dependent and ACTH-independent Cushing's syndrome and reliably lateralizes adenomas when they are present. Moreover, the morphofunctional information obtained by this procedure, together with the high resolution morphological data by computerized tomography, allows to recognize the presence of bilateral nodular hyperplasia, an uncommon cause of Cushing's syndrome.

ACTH Syndrome, Ectopic↗
PubMed1983

Topography of brain electrical activity: a bioengineering approach.

The aim of this work is to describe a system for the mono- and bi-dimensional analysis of brain electrical activity. The analysis was carried on either by visual inspection of mono- and bi-dimensional data, or by automatic feature extraction from the bidimensional data. Because of the importance of visual inspection for the analysis of experimental data, particular care was devoted to optimize the displayed data perceptually. For automatic screening of large amounts of data (and to allow long term studies of clinical records), statistical facilities were also provided. One purpose of the system was to develop image processing algorithms oriented toward biomedical images, that could be easily implemented on special purpose, low cost hardware, like VLSI or microcomputer arrays. This was possible because of the modularity of the larger part of bidimensional processing, such as interpolation and statistical analysis. Results of an experiment on Visual Evoked Response are presented, showing that through abidimensional analysis of the recorded data the resolution achievable in the localization of brain electrical activity can be increased to less than 1 cm.

Brain↗
PubMed2003

Reduction of spectral ghost artifacts in high-resolution echo-planar spectroscopic imaging of water and fat resonances.

Echo-planar spectroscopic imaging (EPSI) can be used for fast spectroscopic imaging of water and fat resonances at high resolution to improve structural and functional imaging. Because of the use of oscillating gradients during the free induction decay (FID), spectra obtained with EPSI are often degraded by Nyquist ghost artifacts arising from the inconsistency between the odd and even echoes. The presence of the spectral ghost lines causes errors in the evaluation of the true spectral lines, and this degrades images derived from high-resolution EPSI data. A technique is described for reducing the spectral ghost artifacts in EPSI of water and fat resonances, using echo shift and zero-order phase corrections. These corrections are applied during the data postprocessing. This technique is demonstrated with EPSI data acquired from human brains and breasts at 1.5 Tesla and from a water phantom at 4.7 Tesla. Experimental results indicate that the present approach significantly reduces the intensities of spectral ghosts. This technique is most useful in conjunction with high-resolution EPSI of water and fat resonances, but is less applicable to EPSI of metabolites due to the complexity of the spectra.

Adipose Tissue↗
PubMed2003

[A comparison of high resolution computerized tomography and magnetic resonance imaging in the evaluation of allergic bronchopulmonary aspergillosis].

Apart from serologic markers structural changes of bronchi and adjacent lung tissue are key factors determining the diagnosis and course of allergic bronchopulmonary aspergillosis (ABPA). Due to problems relating to procedural hazards and radiation exposure using bronchography and computerized tomography we evaluated the efficacy of magnetic resonance imaging of the lung in ABPA. Direct comparison of high resolution computerized tomography (HR-CT) and magnetic resonance imaging (MR) in 5 patients with ABPA revealed that image resolution and data acquisition of present MR technique are insufficient to accurately delineate the extent and activity of structural damage of bronchi and adjacent lung tissue. Although major bronchiectasis may be identified, MR was unable to demonstrate even extensive patchy infiltrates seen in high resolution computerized tomography. At present, magnetic resonance imaging cannot be recommended for determining diagnosis or course of ABPA.

Adolescent↗
PubMed1992

Inside polyomavirus at 25-A resolution.

Empty capsids and complete virions of polyomavirus crystallize isomorphously. Here we use difference Fourier analysis of X-ray diffraction data at 25-A resolution from these crystals to obtain an electron-density map of the inside of the virion. The polyomavirus capsid is built from 72 pentamers of VP1 that form three different types of connections in the T = 7d icosahedral surface lattice. Self-assembly of purified recombinant VP1 into capsid-like aggregates has shown that switching of the bonding specificity to form the unanticipated non-equivalent connections is an inherent property of the VP1 pentamers. Our map of the inside of the virion displays 72 prongs of electron density extending from the core into the axial cavities of the VP1 pentamers. We identify these prongs with the VP2 and VP3 molecules, which may function to guide the assembly of the highly ordered capsid on the nucleohistone core. The atomic structure of the closely related simian virus-40 capsid has been determined from the high-resolution diffraction data. Our polyomavirus map, calculated using all the low-resolution diffraction data, shows no indication of regular order inside the spherical core.

Capsid↗
PubMed2004

Coupling of agonist binding to channel gating in an ACh-binding protein linked to an ion channel.

Neurotransmitter receptors from the Cys-loop superfamily couple the binding of agonist to the opening of an intrinsic ion pore in the final step in rapid synaptic transmission. Although atomic resolution structural data have recently emerged for individual binding and pore domains, how they are linked into a functional unit remains unknown. Here we identify structural requirements for functionally coupling the two domains by combining acetylcholine (ACh)-binding protein, whose structure was determined at atomic resolution, with the pore domain from the serotonin type-3A (5-HT3A) receptor. Only when amino-acid sequences of three loops in ACh-binding protein are changed to their 5-HT3A counterparts does ACh bind with low affinity characteristic of activatable receptors, and trigger opening of the ion pore. Thus functional coupling requires structural compatibility at the interface of the binding and pore domains. Structural modelling reveals a network of interacting loops between binding and pore domains that mediates this allosteric coupling process.

Acetylcholine↗