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Structural Details (structural + detail)
Selected AbstractsThe Death of Countess Agusta in Portofino (Northern Italy) and the Soil from Two Mismatched SlippersJOURNAL OF FORENSIC SCIENCES, Issue 2 2009Gianni Lombardi Ph.D. Abstract:, Accident, suicide, or homicide might have caused the death of Countess Agusta who fell from the 80-m tall cliff of her villa. Two mismatched slippers were recovered along the cliff. Use was made of microscope, X-ray diffractometry, scanning electron microscopy, and microprobe techniques to compare 40 mg of soil collected from the slipper soles with samples from the villa garden. Structural details of the slipper soles were consistent with the lady wearing them during the fall. Analysis of the soil residues confirmed that they originated from the garden only. The features of a few, minute glass chips adhering to the slipper soles reasonably matched those of other fragments that were found on a small ledge on the cliff beyond the garden parapet. Based on this and other evidence, the case was closed with a verdict of accidental fall. [source] Chromium-based clinopyroxene-type germanates NaCrGe2O6 and LiCrGe2O6 at 298,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2008Günther J. Redhammer The structure analyses of sodium chromium digermanate, NaCrGe2O6, (I), and lithium chromium digermanate, LiCrGe2O6, (II), provide important structural information for the clinopyroxene family, and form part of our ongoing studies on the phase transitions and magnetic properties of clinopyroxenes. (I) shows C2/c symmetry at 298,K, contains one Na, one Cr (both site symmetry 2 on special position 4e), one Ge and three O-atom positions (on general positions 8f) and displays the well known clinopyroxene topology. The basic units of the structure of (I) are infinite zigzag chains of edge-sharing Cr3+O6 octahedra (M1 site), infinite chains of corner-sharing GeO4 tetrahedra, connected to the M1 chains by common corners, and Na sites occupying interstitial space. (II) was found to have P21/c symmetry at 298,K. The structure contains one Na, one Cr, two distinct Ge and six O-atom positions, all on general positions 4e. The general topology of the structure of (II) is similar to that of (I); however, the loss of the twofold symmetry makes it possible for two distinct tetrahedral chains, having different conformation states, to exist. While sodium is (6+2)-fold coordinated, lithium displays a pure sixfold coordination. Structural details are given and chemical comparison is made between silicate and germanate chromium-based clinopyroxenes. [source] USING INCIDENT LIGHT TO MAXIMIZE RESOLUTION OF STRUCTURE ON DIATOM VALVES WITH A LIGHT MICROSCOPEJOURNAL OF PHYCOLOGY, Issue 2001Article first published online: 24 SEP 200 Siver, P. A. Botany Department, Connecticut College, New London, CT 06320 Because of their abundance in a diverse array of aquatic habitats and chemical conditions, and the fact that their species-specific siliceous outer coverings remain for millennia in sediments, diatoms have become one of the most powerful organismal groups used in the reconstruction of historical environmental conditions. Although SEM is now needed to identify some species, the bulk of the identifications and data collection is still accomplished with a light microscope. In this paper I will demonstrate the use of interference reflection contrast (incident light) for the examination of diatoms that significantly improves the resolution of structural detail. Using incident light one can routinely distinguish between structures close to the theoretical limit of resolution for visible light, and about 70 nm closer together than resolvable with standard transmitted light optics. Examples of how the incident light technique can improve data collection with light microscopy will be given. Most research light microscopes could be easily and inexpensively outfitted to use this technique. [source] Atmospheric pressure chemical ionisation reversed-phase liquid chromatography/ion trap mass spectrometry of intact bacteriohopanepolyolsRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 7 2003Helen M. Talbot Atmospheric pressure chemical ionisation liquid chromatography/multi-stage ion trap mass spectrometry (APCI-LC/MSn) has been applied to the study of intact bacteriohopanepolyols. Spectral characterisation of bacteriohopanepolyols of known structure present in bacterial extracts (Zymomonas mobilis and a fermenter containing methanotrophs including Methylococcus capsulatus) has revealed greater structural detail than previous liquid chromatography/mass spectrometry (LC/MS) methods and identified characteristic fragmentations indicative of numerous biohopanoid structures. Analysis of a Recent sedimentary extract from Lake Druzhby (Antarctica) has demonstrated the power of this technique to detect biohopanoids in complex samples including at least partial characterisation of previously unknown composite structures. Copyright © 2003 John Wiley & Sons, Ltd. [source] Soil-borne wheat mosaic virus inclusion bodies: structural, compositional and staining propertiesANNALS OF APPLIED BIOLOGY, Issue 2 2003L J LITTLEFIELD Summary Anatomy and cytochemistry of inclusion bodies induced by Soil-borne wheat mosaic virus infection were studied in roots and leaves to learn more about the nature of inclusions and their roles in pathogenesis. Acid Fuchsin, Giemsa stain, Toluidine Blue and Trypan Blue stains facilitated visualization of inclusion bodies. Combined, simultaneous staining with Acid Fuchsin and Toluidine Blue clearly differentiated inclusion bodies from host nuclei. The overall anatomy, composition and structure of virus inclusions in leaves and roots were generally similar, as shown by phase contrast, differential interference contrast, epifluorescence, laser scanning confocal and transmission electron microscopy. Both were often closely associated with host nuclei; both were comprised of intertwined masses of tubular material, presumably endoplasmic reticulum, and in which varied numbers and sizes of vacuolar cavities occurred. Leaf inclusions, however, were typically larger and more vacuolate than those in roots. Lipids were found to be significant constituents of both the tubular and vacuolar components of inclusions, indicated by positive staining with Nile Red and Sudan Black. Inclusion bodies in both leaves and roots lost their structural and compositional integrity, eventually becoming disorganized and devoid of clearly identifiable components as host tissue aged and symptom expression advanced. Significant results of this study include the first published examination of virus inclusion bodies in root tissue, the degree of structural detail of inclusion body anatomy revealed by laser scanning confocal microscopy and the presence of an extensive lipid component in virus inclusion bodies. [source] Structure of native laccase from Trametes hirsuta at 1.8,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Konstantin M. Polyakov This paper describes the structural analysis of the native form of laccase from Trametes hirsuta at 1.8,Å resolution. This structure provides a basis for the elucidation of the mechanism of catalytic action of these ubiquitous proteins. The 1.8,Å resolution native structure provided a good level of structural detail compared with many previously reported laccase structures. A brief comparison with the active sites of other laccases is given. [source] Games in Dynamic-Epistemic LogicBULLETIN OF ECONOMIC RESEARCH, Issue 4 2001Johan Van Benthem The author discusses games of both perfect and imperfect information at two levels of structural detail: players' local actions, and their global powers for determining outcomes of the game. Matching logical languages are proposed for both. In particular, at the ,action level', imperfect information games naturally model a combined ,dynamic-epistemic language', and correspondences are found between special axioms in this language and particular modes of playing games with their information dynamics. At the ,outcome level', the paper presents suitable notions of game equivalence, and some simple representation results. [source] Computational prediction of fatigue crack paths in ship structural detailsFATIGUE & FRACTURE OF ENGINEERING MATERIALS AND STRUCTURES, Issue 1-2 2005Y. SUMI ABSTRACT The characteristics of fatigue crack propagation and the remaining life assessment of ship structures are investigated focusing attention on a curved crack path due to the effects of welds, complicated stress distributions at three-dimensional structural joints and structural redundancy. An advanced numerical simulation method is demonstrated for the remaining life assessment for curved crack propagation. The simulation method is based on a step-by-step finite-element analysis. The crack path is predicted by the perturbation method with the local symmetry criterion, which gives a higher order approximation of the crack path, while the finite-element re-zoning is carried out by an improved paving method. Fatigue crack paths in the welded structural details of the transverse girder of a ship structure are investigated by experiments and simulation. The present method may offer an efficient simulation-based tool for the design of critical details, which prevents the failure of the plates forming a compartment boundary. [source] Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicleFEBS JOURNAL, Issue 4 2008Silvia Vilasi The potent immunomodulatory, anti-inflammatory and procoagulant properties of protein no. 4 secreted from the rat seminal vesicle epithelium (SV-IV) have previously been found to be modulated by a supramolecular monomer,trimer equilibrium. More structural details that integrate experimental data into a predictive framework have recently been reported. Unfortunately, homology modelling and fold-recognition strategies were not successful in creating a theoretical model of the structural organization of SV-IV. It was inferred that the global structure of SV-IV is not similar to that of any protein of known three-dimensional structure. Reversing the classical approach to the sequence,structure,function paradigm, in this paper we report novel information obtained by comparing the physicochemical parameters of SV-IV with two datasets composed of intrinsically unfolded and ideally globular proteins. In addition, we analyse the SV-IV sequence by several publicly available disorder-oriented predictors. Overall, disorder predictions and a re-examination of existing experimental data strongly suggest that SV-IV needs large plasticity to efficiently interact with the different targets that characterize its multifaceted biological function, and should therefore be better classified as an intrinsically disordered protein. [source] Self-Assembled Nanostructures: Role of Water in Directing Diphenylalanine Assembly into Nanotubes and Nanowires (Adv. Mater.ADVANCED MATERIALS, Issue 5 20105/2010) The controllable assembly behavior of diphenylalanine molecules to form nanowires (NWs) and nanotubes (NTs) and their structural details are presented. Hyotcherl Ihee, Sang Ouk Kim and co-workers show on p. 583 that the nanoscale morphologies are closely related to molecular arrangements of diphenylalanine as revealed by Rietveld refinement of powder X-ray diffraction patterns and electron-density distributions in NTs and NWs via the maximum entropy method analysis. [source] Role of Water in Directing Diphenylalanine Assembly into Nanotubes and NanowiresADVANCED MATERIALS, Issue 5 2010Jangbae Kim The controllable assembly behavior of diphenylalanine molecules to form nanowires (NWs) and nanotubes (NTs) and their structural details are presented (see figure). The nanoscale morphologies are closely related to molecular arrangements of diphenylalanine as revealed by Rietveld refinement of powder X-ray diffraction patterns and electron-density distributions in NTs and NWs via the maximum entropy method analysis. [source] Multi-scale domain decomposition method for large-scale structural analysis with a zooming technique: Application to plate assemblyINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 4 2009A. Mobasher Amini Abstract This article is concerned with a multi-scale domain decomposition method (DDM), based on the FETI-DP solver, for large-scale structural elastic analysis and suited to problems that exhibit structural heterogeneities, such as plate assemblies in the presence of structural details. In this approach once a partition of the global fine mesh into subdomains has been performed (all subdomains possess a fine mesh) and to optimize the computational time, the fine mesh is preserved only in the zones of interest (with local phenomena due to discontinuity, hole, etc.) while the remaining subdomains are replaced by numerical homogenized coarse elements. Indeed, the multi-scale aspect is introduced by the description of subdomains with either a fine or a coarse scale mesh. As a result, an extension of the FETI-DP DDM is proposed in this article (called herein FETI-DP micro,macro) that allows the simultaneous usage of different discretizations: fine (microscopic) mesh for subdomains in zones of interest and coarse (macroscopic or homogenized) mesh for the complementary part of the structure. Using this strategy raises the problem of the determination of the stiffness of coarse subdomains, and of the incompatible finite element connection between fine and coarse subdomains. Two approaches (collocation and Mortar) are presented and compared. The article ends with patch tests and some numerical examples in 2D and 3D. The obtained numerical results exemplify the efficiency and capability of the FETI-DP micro,macro approach and reveal that the Mortar approach is more accurate, at constant cost, than the collocation approach. Copyright © 2009 John Wiley & Sons, Ltd. [source] The salmon vertebral body develops through mineralization of two preformed tissues that are encompassed by two layers of boneJOURNAL OF ANATOMY, Issue 2 2005Kari Nordvik Abstract The teleost backbone consists of amphicoelous vertebrae and intervertebral ligaments, both of which include notochord-derived structures. On the basis of a sequential developmental study of the vertebral column of Atlantic salmon (Salmo salar L.) from the egg stage up to early fry stage (300,2500 day-degrees) we show that the vertebral body consists of four layers or compartments, two of which are formed through mineralization of preformed collagenous tissue (the notochordal sheath and the intervertebral ligament) and two of which are formed through ossification. The three inner layers have ordered lamellar collagen matrixes, which alternate perpendicularly from layer to layer, whereas the outer layer consists of cancellous bone with a woven matrix. The bone layers also differ in osteocyte content. In this study we describe the structural details of the layers, and their modes of formation. The results are compared with previous descriptions, and possible phylogenetic implications are discussed. [source] Modeling the semi-empirical electrotopological index in QSPR studies for aldehydes and ketonesJOURNAL OF CHEMOMETRICS, Issue 5 2009Érica Silva Souza Abstract The semi-empirical electrotopological index, ISET, used for quantitative structure,retention relationship (QSRR) models firstly developed for alkanes and alkenes, was remodeled for organic functions such as ketones and aldehydes. The ISET values for hydrocarbons are calculated through the atomic charge values obtained from a Mulliken population analysis using the semi-empirical AM1 method and their correlation with the SETi values attributed to the different types of carbon atoms according to experimental data. For ketones and aldehydes the interactions between the molecules and the stationary phase are slowly increased relative to the hydrocarbons, due to the charge redistribution that occurs in the presence of heteroatoms. For these polar molecules the increase in the interactions was included in the calculation of the ISET values through the dipole moment of the whole molecule and also through an equivalent local dipole moment related to the net charges of the atoms of the CO and HCO functional groups. Our findings show that the best definition of an equivalent local dipole moment is clearly dependent on the specific features of the charge distribution in the polar region of the molecules (e.g. ketones and aldehydes), which allows them to be distinguished. Thus, the QSRR models for 15 aldehydes and 42 ketones obtained using the remodeled ISET were of good quality as shown by the statistical parameters. The ability of this remodeled index to include charge distribution and structural details opens a new way to study the correlations between the molecular structure and retention indices in gas chromatography. Copyright © 2009 John Wiley & Sons, Ltd. [source] The observation of intact hepatic endothelial cells by cryo-electron microscopyJOURNAL OF MICROSCOPY, Issue 2 2003F. Braet Summary Liver sinusoidal endothelial cells (LSECs) can optimally be imaged by whole mount transmission electron microscopy (TEM). However, TEM allows only investigation of vacuum-resistant specimens and this usually implies the study of chemically fixed and dried specimens. Cryo-electron microscopy (cryo-EM) can be used as a good alternative for imaging samples as whole mounts. Cryo-EM offers the opportunity to study intact, living cells while avoiding fixation, dehydration and drying, at the same time preserving all solubles and water as vitrified ice. Therefore, we compared the different results obtained when LSECs were vitrified using different vitrification conditions. We collected evidence that manual blotting at ambient conditions and vitrification by the guided drop method results in the production of artefacts in LSECs, such as the loss of fenestrae, formation of gaps and lack of structural details in the cytoplasm. We attribute these artefacts to temperature and osmotic effects during sample preparation just prior to vitrification. By contrast, by using an environmentally controlled glove box and a vitrification robot (37 °C and 100% relative humidity), these specific structural artefacts were nearly absent, illustrating the importance of controlled sample preparation. Moreover, data on glutaraldehyde-fixed cells and obtained by using different vitrification methods suggested that chemical prefixation is not essential when vitrification is performed under controlled conditions. Conditioned vitrification therefore equals chemical fixation in preserving and imaging cellular fine structure. Unfixed, vitrified LSECs show fenestrae and fenestrae-associated cytoskeleton rings, indicating that these structures are not artefacts resulting from chemical fixation. [source] Survey of the year 2005: literature on applications of isothermal titration calorimetryJOURNAL OF MOLECULAR RECOGNITION, Issue 1 2007Adessamad Ababou Abstract Isothermal titration calorimetry (ITC) can provide a full thermodynamic characterization of an interaction. Its usage does not suffer from constraints of molecular size, shape or chemical constitution. Neither is there any need for chemical modification or attachment to solid support. This ease of use has made it an invaluable instrumental resource and led to its appearance in many laboratories. Despite this, the value of the thermodynamic parameterization has, only quite recently, become widely appreciated. Although our understanding of the correlation between thermodynamic data and structural details continues to be somewhat naïve, a large number of publications have begun to improve the situation. In this overview of the literature for 2005, we have attempted to highlight works of interest and novelty. Furthermore, we draw attention to those works which we feel have provided a route to better analysis and increased our ability to understand the meaning of thermodynamic change on binding. Copyright © 2006 John Wiley & Sons, Ltd. [source] Solid-state kinetics from time-resolved in situ XAFS investigations: reduction and oxidation of molybdenum oxidesJOURNAL OF SYNCHROTRON RADIATION, Issue 2 2001T. Ressler The reduction of MoO3 with hydrogen was studied by in situ X-ray absorption spectroscopy. The experiments performed focused on elucidating phase composition and evolution with time under isothermal reduction conditions. From temperature programmed experiments short-range structural details about the early stage of the reduction were obtained. [source] Intact corneal stroma visualization of GFP mouse revealed by multiphoton imagingMICROSCOPY RESEARCH AND TECHNIQUE, Issue 12 2006Wen Lo Abstract The aim of this work is to demonstrate that multiphoton microscopy is a preferred technique to investigate intact cornea structure without slicing and staining. At the micron resolution, multiphoton imaging can provide both large morphological features and detailed structure of epithelium, corneal collagen fibril bundles and keratocytes. A large area multiphoton cross-section across an intact eye excised from a GFP mouse was obtained by a homebuilt multiphoton microscope. The broadband multiphoton fluorescence (435,700 nm) and second harmonic generation (SHG, 360,400 nm) signals were generated by the 760 nm output of a femtosecond titanium-sapphire laser. A water immersion objective (Fluor Ô, 40X, NA 0.8; Nikon) was used to facilitate imaging the curve ocular surface. The multiphoton image over entire cornea provides morphological information of epithelial cells, keratocytes, and global collagen orientation. Specifically, our planar, large area multiphoton image reveals a concentric pattern of the stroma collagen, indicative of the laminar collagen organization throughout the stroma. In addition, the green fluorescence protein (GFP) labeling contributed to fluorescence contrast of cellular area and facilitated visualizing of inactive keratocytes. Our results show that multiphoton imaging of GFP labeled mouse cornea manifests both morphological significance and structural details. The second harmonic generation imaging reveals the collagen orientation, while the multiphoton fluorescence imaging indicates morphology and distribution of cells in cornea. Our results support that multiphoton microscopy is an appropriate technology for further in vivo investigation and diagnosis of cornea. Microsc. Res. Tech., 2006. © 2006 Wiley-Liss, Inc. [source] Triad of polar residues implicated in pH specificity of acidic mammalian chitinasePROTEIN SCIENCE, Issue 3 2009Andrea M. Olland Abstract Acidic mammalian chitinase (AMCase) is a mammalian chitinase that has been implicated in allergic asthma. One of only two active mammalian chinases, AMCase, is distinguished from other chitinases by several unique features. Here, we present the novel structure of the AMCase catalytic domain, both in the apo form and in complex with the inhibitor methylallosamidin, determined to high resolution by X-ray crystallography. These results provide a structural basis for understanding some of the unique characteristics of this enzyme, including the low pH optimum and the preference for the ,-anomer of the substrate. A triad of polar residues in the second-shell is found to modulate the highly conserved chitinase active site. As a novel target for asthma therapy, structural details of AMCase activity will help guide the future design of specific and potent AMCase inhibitors. [source] On a fast calculation of structure factors at a subatomic resolutionACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2004P. V. Afonine In the last decade, the progress of protein crystallography allowed several protein structures to be solved at a resolution higher than 0.9,Å. Such studies provide researchers with important new information reflecting very fine structural details. The signal from these details is very weak with respect to that corresponding to the whole structure. Its analysis requires high-quality data, which previously were available only for crystals of small molecules, and a high accuracy of calculations. The calculation of structure factors using direct formulae, traditional for `small-molecule' crystallography, allows a relatively simple accuracy control. For macromolecular crystals, diffraction data sets at a subatomic resolution contain hundreds of thousands of reflections, and the number of parameters used to describe the corresponding models may reach the same order. Therefore, the direct way of calculating structure factors becomes very time expensive when applied to large molecules. These problems of high accuracy and computational efficiency require a re-examination of computer tools and algorithms. The calculation of model structure factors through an intermediate generation of an electron density [Sayre (1951). Acta Cryst.4, 362,367; Ten Eyck (1977). Acta Cryst. A33, 486,492] may be much more computationally efficient, but contains some parameters (grid step, `effective' atom radii etc.) whose influence on the accuracy of the calculation is not straightforward. At the same time, the choice of parameters within safety margins that largely ensure a sufficient accuracy may result in a significant loss of the CPU time, making it close to the time for the direct-formulae calculations. The impact of the different parameters on the computer efficiency of structure-factor calculation is studied. It is shown that an appropriate choice of these parameters allows the structure factors to be obtained with a high accuracy and in a significantly shorter time than that required when using the direct formulae. Practical algorithms for the optimal choice of the parameters are suggested. [source] Atomic resolution studies of carbonic anhydrase IIACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Craig A. Behnke Carbonic anhydrase has been well studied structurally and functionally owing to its importance in respiration. A large number of X-ray crystallographic structures of carbonic anhydrase and its inhibitor complexes have been determined, some at atomic resolution. Structure determination of a sulfonamide-containing inhibitor complex has been carried out and the structure was refined at 0.9,Å resolution with anisotropic atomic displacement parameters to an R value of 0.141. The structure is similar to those of other carbonic anhydrase complexes, with the inhibitor providing a fourth nonprotein ligand to the active-site zinc. Comparison of this structure with 13 other atomic resolution (higher than 1.25,Å) isomorphous carbonic anhydrase structures provides a view of the structural similarity and variability in a series of crystal structures. At the center of the protein the structures superpose very well. The metal complexes superpose (with only two exceptions) with standard deviations of 0.01,Å in some zinc,protein and zinc,ligand bond lengths. In contrast, regions of structural variability are found on the protein surface, possibly owing to flexibility and disorder in the individual structures, differences in the chemical and crystalline environments or the different approaches used by different investigators to model weak or complicated electron-density maps. These findings suggest that care must be taken in interpreting structural details on protein surfaces on the basis of individual X-ray structures, even if atomic resolution data are available. [source] Temperature-dependent macromolecular X-ray crystallographyACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Martin Weik X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100,K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15,K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography. [source] Crystallization and preliminary X-ray crystallographic analysis of the N domain of p97/VCP in complex with the UBX domain of FAF1ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2010Hwa Young Shin p97/VCP is a multifunctional AAA+ -family ATPase that is involved in diverse cellular processes. p97/VCP directly interacts with various adaptors for activity in different biochemical contexts. Among these adaptors are p47 and Fas-associated factor 1 (FAF1), which contain a common UBX domain through which they bind to the N domain of p97/VCP. In the ubiquitin,proteasome pathway, p97/VCP acts as a chaperone that presents client proteins to the proteasome for degradation, while FAF1 modulates the process by interacting with ubiquitinated client proteins and also with p97/VCP. In an effort to elucidate the structural details of the interaction between p97/VCP and FAF1, the p97/VCP N domain was crystallized in complex with the FAF1 UBX domain. X-ray data were collected to 2.60,Å resolution and the crystals belonged to space group C2221, with unit-cell parameters a = 58.24, b = 72.81, c = 132.93,Å. The Matthews coefficient and solvent content were estimated to be 2.39,Å3,Da,1 and 48.4%, respectively, assuming that the asymmetric unit contained p97/VCP N domain and FAF1 molecules in a 1:1 ratio, which was subsequently confirmed by molecular-replacement calculations. [source] Conformations within soluble oligomers and insoluble aggregates revealed by resonance energy transferBIOPOLYMERS, Issue 4 2010Jyothi L. Digambaranath Abstract A fluorescently labeled 20-residue polyglutamic acid (polyE) peptide 20 amino acid length polyglutamic acid (E20) was used to study structural changes which occur in E20 as it co-aggregates with other unlabeled polyE peptides. Resonance energy transfer (RET) was performed using an o -aminobenzamide donor at the N-terminus and 3-nitrotyrosine acceptor at the C-terminus of E20. PolyE aggregates were not defined as amyloid, as they were nonfibrillar and did not bind congo red. Circular dichroism measurements indicate that polyE aggregation involves a transition from ,-helical monomers to aggregated ,-sheets. Soluble oligomers are also produced along with aggregates in the reaction, as determined through size exclusion chromatography. Time-resolved and steady-state RET measurements reveal four dominant E20 conformations: (1) a partially collapsed conformation (24 Å donor,acceptor distance) in monomers, (2) an extended conformation in soluble oligomers (>29 Å donor,acceptor distance), (3) a minor partially collapsed conformation (22 Å donor-acceptor distance) in aggregates, and (4) a major highly collapsed conformation (13 Å donor,acceptor distance) in aggregates. These findings demonstrate the use of RET as a means of determining angstrom-level structural details of soluble oligomer and aggregated states of proteins. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 299,317, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of bacterioferritin A from Mycobacterium tuberculosisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2008Vibha Gupta Bacterioferritins (Bfrs) comprise a subfamily of the ferritin superfamily of proteins that play an important role in bacterial iron storage and homeostasis. Bacterioferritins differ from ferritins in that they have additional noncovalently bound haem groups. To assess the physiological role of this subfamily of ferritins, a greater understanding of the structural details of bacterioferritins from various sources is required. The gene encoding bacterioferritin A (BfrA) from Mycobacterium tuberculosis was cloned and expressed in Escherichia coli. The recombinant protein product was purified by affinity chromatography on a Strep-Tactin column and crystallized with sodium chloride as a precipitant at pH 8.0 using the vapour-diffusion technique. The crystals diffracted to 2.1,Å resolution and belonged to space group P42, with unit-cell parameters a = 123.0, b = 123.0, c = 174.6,Å. [source] Formation of Superoxo Species by Interaction of O2 with Na Atoms Deposited on MgO Powders: A Combined Continuous-Wave EPR (CW-EPR), Hyperfine Sublevel Correlation (HYSCORE) and DFT StudyCHEMISTRY - A EUROPEAN JOURNAL, Issue 23 2010Francesco Napoli Dr. Abstract The formation of O2, radical anions by contact of O2 molecules with a Na pre-covered MgO surface is studied by a combined EPR and quantum chemical approach. Na atoms deposited on polycrystalline MgO samples are brought into contact with O2. The typical EPR signal of isolated Na atoms disappears when the reaction with O2 takes place and new paramagnetic species are observed, which are attributed to different surface-stabilised O2, radicals. Hyperfine sublevel correlation (HYSCORE) spectroscopy allows the superhyperfine interaction tensor of O2,Na+ species to be determined, demonstrating the direct coordination of the O2, adsorbate to surface Na+ cations. DFT calculations enable the structural details of the formed species to be determined. Matrix-isolated alkali superoxides are used as a standard to enable comparison of the formed species, revealing important and unexpected contributions of the MgO matrix in determining the electronic structure of the surface-stabilised Na+O2, complexes. [source] The Structure of a Novel Neutral Lipid,A from the Lipopolysaccharide of Bradyrhizobium elkanii Containing Three Mannose Units in the BackboneCHEMISTRY - A EUROPEAN JOURNAL, Issue 9 2010Iwona Komaniecka Dr. Abstract The chemical structure of the lipid,A of the lipopolysaccharide (LPS) from Bradyrhizobium elkanii USDA 76 (a member of the group of slow-growing rhizobia) has been established. It differed considerably from lipids,A of other Gram-negative bacteria, in that it completely lacks negatively charged groups (phosphate or uronic acid residues); the glucosamine (GlcpN) disaccharide backbone is replaced by one consisting of 2,3-dideoxy-2,3-diamino- D -glucopyranose (GlcpN3N) and it contains two long-chain fatty acids, which is unusual among rhizobia. The GlcpN3N disaccharide was further substituted by three D -mannopyranose (D -Manp) residues, together forming a pentasaccharide. To establish the structural details of this molecule, 1D and 2D,NMR spectroscopy, chemical composition analyses and high-resolution mass spectrometry methods (electrospray ionisation Fourier-transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) and tandem mass spectrometry (MS/MS)) were applied. By using 1D and 2D,NMR spectroscopy experiments, it was confirmed that one D -Manp was linked to C-1 of the reducing GlcpN3N and an ,-(1,6)-linked D -Manp disaccharide was located at C-4, of the non-reducing GlcpN3N (,-linkage). Fatty acid analysis identified 12:0(3-OH) and 14:0(3-OH), which were amide-linked to GlcpN3N. Other lipid,A constituents were long (,-1)-hydroxylated fatty acids with 26,33 carbon atoms, as well as their oxo forms (28:0(27-oxo) and 30:0(29-oxo)). The 28:0(27-OH) was the most abundant acyl residue. As confirmed by high-resolution mass spectrometry techniques, these long-chain fatty acids created two acyloxyacyl residues with the 3-hydroxy fatty acids. Thus, lipid,A from B. elkanii comprised six acyl residues. It was also shown that one of the acyloxyacyl residues could be further acylated by 3-hydroxybutyric acid (linked to the (,-1)-hydroxy group). [source] Synthesis, X-ray Single-Crystal Structure Determination, and Magnetic Properties of [Rb(benzo[18]crown-6)]+ Salts Containing Well-Ordered Fulleride Trianions C603,,CHEMISTRY - A EUROPEAN JOURNAL, Issue 13 2009Bele Boeddinghaus Dipl.-Chem. Abstract Finally, a structure with well-resolved C603,ions and S=1/2 spin system: The two novel title compounds have clearly S=1/2 and not S=3/2 electronic states, as expected for the occupation of the triply degenerate LUMO of C60. These structures with well-ordered fullerene trianions show that the expected Jahn,Teller distortion is not observable in X-ray diffraction experiments. Crystals of the composition [Rb(benzo[18]crown-6)]3[,3 -C60](C7H8)(C3H7NO)4.5 (1) and [Rb(benzo[18]crown-6)]3[C60](C3H7NO)5.33(C4H8O)1.66 (2) were synthesized by reduction of C60 with elemental rubidium in a mixture of dimethylformamide/tetrahydrofuran in the presence of benzo[18]crown-6. X-ray single-crystal structure determinations reveal well-ordered C60 trianions in both compounds. In contrast to previously reported structures of compounds containing C603, ions the present structure refinements allow the description of the buckyballs with good resolution (R1/wR2 for I>2,(I) (all data) are 0.030/0.069 (0.051/0.071) and 0.042/0.101 (0.076/0.108) for 1 and 2, respectively). In 1 the C603, unit coordinates in an ,3 -fashion to one Rb atom, whose coordination sphere is completed by one benzo[18]crown-6 and one dimethylformamide molecule. In 2 no coordination of the alkali metal atom to the C60 trianion is observed. Magnetic measurements for 1 reveal a magnetic moment of 1.74,,B, as expected for an isolated S=1/2 spin system. The high-quality data of the present studies allowed a comparison of structural details of C603, ions with other C60n, units (n=0, 2, 3) and a discussion of the structural Jahn,Teller distortions. [source] pH-Controlled Molecular Switches and the Substrate-Directed Self-Assembly of Molecular Capsules with a Calix[4]pyrrole DerivativeCHEMISTRY - A EUROPEAN JOURNAL, Issue 36 2008Grazia Cafeo Dr. Abstract 10,,20,-Bis(4-nitrophenyl)calix[4]pyrrole (1) forms 1:1 complexes with anions of selected aromatic hydroxy acids in which the host orientation within the guest is controlled by a change in the pH,value. Some bis-anionic guests, including those obtained from 4-hydroxybenzoic acid, 1,4- and 1,3-benzenedicarboxylic acids, induce the self-assembly of molecular capsules involving two molecules of the receptor. 1H,NMR data and solid-state structures of the 1:1 complex of 1 with p -C6H4(COOH)(COO,)+NMe4 and the 2:1 capsule [(1)2m -C6H4(COO,)2(+NMe4)2] provide structural details in solution and in the solid state. [source] Exploring Chemical Modifications for siRNA Therapeutics: A Structural and Functional OutlookCHEMMEDCHEM, Issue 3 2010Siddharth Shukla Abstract RNA interference (RNAi) is a post-transcriptional gene silencing mechanism induced by small interfering RNAs (siRNAs) and micro-RNAs (miRNAs), and has proved to be one of the most important scientific discoveries made in the last century. The robustness of RNAi has opened up new avenues in the development of siRNAs as therapeutic agents against various diseases including cancer and HIV. However, there had remained a lack of a clear mechanistic understanding of messenger RNA (mRNA) cleavage mediated by Argonaute2 of the RNA-induced silencing complex (RISC), due to inadequate structural data. The X-ray crystal structures of the Argonaute (Ago),DNA,RNA complexes reported recently have proven to be a breakthrough in this field, and the structural details can provide guidelines for the design of the next generation of siRNA therapeutics. To harness siRNAs as therapeutic agents, the prudent use of various chemical modifications is warranted to enhance nuclease resistance, prevent immune activation, decrease off-target effects, and to improve pharmacokinetic and pharmacodynamic properties. The focus of this review is to interpret the tolerance of various chemical modifications employed in siRNAs toward RNAi by taking into account the crystal structures and biochemical studies of Ago,RNA complexes. Moreover, the challenges and recent progress in imparting druglike properties to siRNAs along with their delivery strategies are discussed. [source] | ||||||||||||||||||||||||||||||||||