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Disordered Structure (disordered + structure)
Selected AbstractsDisordered structure of ZrW1.8V0.2O7.9 from a combined X-ray and neutron powder diffraction study at 530 KACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2009Xi Chen A novel compound, vanadium aliovalent substituted zirconium tungstate, ZrW1.8V0.2O7.9, was prepared with vanadium substituting tungsten rather than the common zirconium substitution. The structure of the high-temperature phase was refined from combined neutron and X-ray powder diffraction data gathered at 530,K. This phase is the disordered centric modification (space group Pa) and the average crystal structure is similar to that of ,-ZrW2O8. The V atom occupies only a W2 site and charge compensation is achieved through oxygen vacancy, i.e. the oxygen vacancy occurs at only the O4 site. [Atom names follow the established scheme; Evans et al. (1996). Chem. Mater.8, 2809,2823.] [source] SMAP-29 has two LPS-binding sites and a central hingeFEBS JOURNAL, Issue 4 2002Brian F. Tack The CD spectra of SMAP-29, an antimicrobial peptide from sheep, showed disordered structure in aqueous buffers, and significant helicity in membrane-like environments, including SDS micelles, lipopolysaccharide (LPS) dispersions, and trifluoroethanol buffer systems. A structure determined by NMR in 40% perdeuterated trifluoroethanol indicated that residues 8,17 were helical, residues 18,19 formed a hinge, and residues 20,28 formed an ordered, hydrophobic segment. SMAP-29 was flexible in 40% trifluoroethanol, forming two sets of conformers that differed in the relative orientation of the N-terminal domain. We used a chromogenic Limulus assay to determine the EC50 of the peptide (the concentration that bound 50% of the added LPS). Studies with full-length and truncated SMAP-29 molecules revealed that each end of the holopeptide contained an LPS-binding domain. The higher affinity LPS-binding domain was situated in the flexible N-terminal portion. LPS binding to full-length SMAP-29 showed positive cooperativity, so the EC50 of the peptide (2.6 µm) was considerably lower than that of the individual LPS-binding domains. LPS-binding studies with a mixture of truncated peptides revealed that this cooperativity was primarily intramolecular (i.e. involving the N- and C-terminal LPS-binding sites of the same peptide molecule). CAP-18[106,142], an antimicrobial cathelicidin peptide of rabbits, resembled SMAP-29 in that it contained N- and C-terminal LPS-binding domains, had an EC50 of 2.5 µm, and bound LPS with positive cooperativity. We conclude that the presence of multiple binding sites that function cooperatively allow peptides such as SMAP-29 and CAP-18 to bind LPS with high affinity. [source] A Methyl Tricyanoethylenecarboxylate-Based Room-Temperature Magnet,ADVANCED MATERIALS, Issue 20 2007I. Pokhodnya A room-temperature magnet of V[MeTCEC]2·0.6(CH2Cl2) composition (MeTCEC,=,methyl tricyanoethylenecarboxylate) is formed by the reaction of MeTCEC and V(CO)6 (see figure). Analysis of the magnetization indicates a less disordered structure of V[MeTCEC]2·0.6(CH2Cl2) with respect to similarly synthesized V[TCNE]x·0.34(CH2Cl2), presumably because of the much slower reaction of MeTCEC and V(CO)6. [source] Structure Determination in Colloidal Crystal Photonic Bandgap StructuresJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 6 2002John Ballato Structure/optical property relationships in photonic bandgap structures are evaluated by a novel combination of sample sectioning, microscopy, and image analysis. Disordered colloidal crystals of solution-derived, monosized SiO2 particles were sectioned by focused ion beam (FIB) milling and then imaged using field emission scanning electron microscopy (FE-SEM). Pair correlation and radial distribution functions of the particulate arrangement were generated directly from a binary color scale rendering of the FE-SEM images, therein defining the level of order or disorder in the structure. These experimentally obtained spatial correlation functions were used to compute the scattering spectral properties in an analogous, although inverse (i.e., solving the inverse scattering problem), method to that used in X-ray diffraction for structure determination. Using a first-order approximation to the scattering from a disordered structure, the bandwidth and midgap values for the colloidal crystal photonic bandgap materials were within 15% of those measured. This new methodology promises to provide a simple and direct approach for quantifying the structure/optical property relationships in ordered and disordered photonic crystals directly from standard microstructural imaging techniques. [source] Ba(Mg,Zr,Ta)O3:Nd3+ fine-grained ceramics: a novel laser-gain material with disordered structure for high-power laser systemsLASER PHYSICS LETTERS, Issue 4 2009A.A. Kaminskii Abstract Nd3+ -ion doped Ba(Mg,Zr,Ta)O3 ceramics is introduced as a new gain crystalline materials for lasers and laser amplifiers. By pumping laser-diode radiation at 300 K its CW stimulated emission at 1.0754 ,m wavelength was recorded. Some optical, spectroscopic and mechanical properties were measured as well. (© 2009 by Astro Ltd., Published exclusively by WILEY-VCH Verlag GmbH & Co. KGaA) [source] Thermally-Induced Phase Transitions in the Uniaxially-Oriented , Form of Syndiotactic PolystyreneMACROMOLECULAR SYMPOSIA, Issue 1 2006E. Bhoje Gowd Abstract The empty , (,e) form of uniaxially-oriented syndiotactic polystyrene (sPS) samples were obtained by extracting the solvent molecules from the , form of sPS and solvent complex in acetone and methanol. Temperature dependence of the X-ray fiber diagrams starting from the uniaxially-oriented ,e and , form has been measured successfully at various temperatures for the first time. The transition behavior was traced clearly by separating the equatorial and layer line reflections. The ,e form transformed to the , form via an intermediate form. The intermediate form is speculated to take disordered structure due to the empty cavities present in the ,e form. Calorimetric studies showed an endotherm followed by an exotherm during this phase transition, which is consistant with such a speculation. On the other hand the , form transformed to the , form directly without passing through the intermediate form or ,e form. During the , to , phase transition the solvent molecules evaporate through the columnar structure in a broad range of temperature, allowing the transition to occur smoothly. [source] Quantitative assessment of the structural bias in protein,protein interaction assaysPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 22 2008Åsa K. Björklund Abstract With recent publications of several large-scale protein,protein interaction (PPI) studies, the realization of the full yeast interaction network is getting closer. Here, we have analysed several yeast protein interaction datasets to understand their strengths and weaknesses. In particular, we investigate the effect of experimental biases on some of the protein properties suggested to be enriched in highly connected proteins. Finally, we use support vector machines (SVM) to assess the contribution of these properties to protein interactivity. We find that protein abundance is the most important factor for detecting interactions in tandem affinity purifications (TAP), while it is of less importance for Yeast Two Hybrid (Y2H) screens. Consequently, sequence conservation and/or essentiality of hubs may be related to their high abundance. Further, proteins with disordered structure are over-represented in Y2H screens and in one, but not the other, large-scale TAP assay. Hence, disordered regions may be important both in transient interactions and interactions in complexes. Finally, a few domain families seem to be responsible for a large part of all interactions. Most importantly, we show that there are method-specific biases in PPI experiments. Thus, care should be taken before drawing strong conclusions based on a single dataset. [source] Orientational disorder and phase transitions in crystals of dioxofluoromolybdate, (NH4)2MoO2F4ACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2010Anatoly A. Udovenko Dioxotetrafluoromolybdate, (NH4)2MoO2F4, was synthesized in a single-crystal form and its structures [(I) at 297,K and (II) at 223,K] were determined by X-ray diffraction. Two independent states of a cis -MoO2F4 octahedron are characteristic of static and dynamic disorder in structure (I). The dynamically disordered Mo atom is displaced from the symmetry axis producing four possible orientations of an anion that allow O and F atoms to be identified in separate orientations owing to the inherent differences between the Mo,O and Mo,F bonding. After the phase transition at lower temperature, (I) transforms into the statically disordered structure (II) with three possible orientations of the cis -MoO2F4 octahedron. In this case, it also seemed possible to distinguish between O and F atoms on a local scale. H atoms of two independent NH4 groups in (II) which form bifurcated N,H...F(O) hydrogen bonds were localized. [source] Mechanism of the first-order phase transition of an acylurea derivative: observation of intermediate stages of transformation with a detailed temperature-resolved single-crystal diffraction methodACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2003Daisuke Hashizume The process of the first-order solid-to-solid phase transition of 1-ethyl-3-(4-methylpentanoyl)urea (1) was observed by means of a detailed temperature-resolved single-crystal diffraction method, which resembles watching a series of stop-motion photographs. The transition consists of two elementary processes, one supramolecular and the other molecular. Crystal structures from before and after the phase transition are isostructural. The straight-ribbon-like one-dimensional hydrogen-bonding structure is formed and stacked to form a molecular layer. The geometry of the layer is retained during the phase transition. The relative position of the layer with its neighbours, on the other hand, changes gradually with increasing temperature. The change is accelerated at the temperature representing the start of the endotherm seen in the DSC curves of (1). The structural variation yields void space between the neighbouring layers. When the void space grows enough that the crystal is unstable, the 3-methylbutyl group on the last of the molecules turns into a disordered structure with drastic conformational changes to fill up the void space. The phase transition process is well supported with simple force-field calculations. A crystal of 1-(4-methylpentanoyl)-3-propylurea (2), which shows no solid-to-solid phase transitions, was also analysed by the same method for comparison. [source] Hexacopper(I) phosphorus(V) bromide penta(selenide/sulfide), Cu6P(Se0.7S0.3)5BrACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2008A. Gagor This work illustrates possible diffusion paths for CuI ions in a highly disordered structure of a superionic conductor of the argyrodite family. The Cu6P(Se0.7S0.3)5Br cubic structure is built from a [P(Se0.7S0.3)5Br] framework in which CuI ions are distributed in various tetrahedral, triangular and linear sites. There are two types of disorder in the structure. The first type results from the fact that there are fewer CuI ions than the number of positions available for them in the unit cell. The second type is due to the static distribution of Se and S atoms in the [P(Se0.7S0.3)5Br] framework. The title compound is a solid solution of two efficient ionic conductors, namely Cu6PSe5Br and Cu6PS5Br, in which high ionic conductivity results from order,disorder phenomena in the copper substructure. To shed light on the distribution of CuI ions in disordered Cu6P(Se0.7S0.3)5Br, we refined their positions using a combination of a nonharmonic approach and a split-atom model. At room temperature, CuI ions show strong anharmonic vibrations along the edge of the (Br)4 tetrahedra. The probability density functions of the CuI ions overlap and reveal possible diffusion paths. [source] The conversion of an organometallic compound into an intercalated thin-layer amorphous structureAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 10 2009M. R. Othman Abstract A thin alumina-hydrotalcite (Al-HT) film was fabricated from the synthesized boehmite and HT sol samples. The sols were a Newtonian fluid within 12 h of the sol synthesis and pseudo-plastic flow thereon. Co-precipitated HT demonstrated poorly crystallized periclase and spinel structures and apparent doublet peak of hydrotalcite at 2, = 39,44°, indicative of a disordered structure. The heated Al-HT sample demonstrated highly amorphous structure with single hydrotalcite peak but barely observed ,-alumina and ,-boehmite phases. The exfoliation of the spinel, gibbsite and periclase in the Al-HT was caused by the intercalation of boehmite into the HT layers that impeded the formation of the oxides phases. Copyright © 2009 John Wiley & Sons, Ltd. [source] The effect of heavy atoms on the conformation of the active-site polypeptide loop in human ABO(H) blood-group glycosyltransferase BACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2007James A. Letts The human ABO(H) blood-group antigens are oligosaccharide structures that are expressed on erythrocyte and other cell surfaces. The terminal carbohydrate residue differs between the blood types and determines the immune reactivity of this antigen. Individuals with blood type A have a terminal N -acetylgalactosamine residue and those with blood type B have a terminal galactose residue. The attachment of these terminal carbohydrates are catalyzed by two different glycosyltransferases: an ,(1,3)N -acetylgalactosaminyltransferase (GTA) and an ,(1,3)galactosyltransferase (GTB) for blood types A and B, respectively. GTA and GTB are homologous enzymes that differ in only four of 354 amino-acid residues (Arg/Gly176, Gly/Ser235, Leu/Met266 and Gly/Ala268 in GTA and GTB, respectively). Diffraction-quality crystals of GTA and GTB have previously been grown from as little as 10,mg,ml,1 stock solutions in the presence of Hg, while diffraction-quality crystals of the native enzymes require much higher concentrations of protein. The structure of a single mutant C209A has been determined in the presence and absence of heavy atoms and reveals that when mercury is complexed with Cys209 it forces a significant level of disorder in a polypeptide loop (amino acids 179,195) that is known to cover the active site of the enzyme. The observation that the more highly disordered structure is more amenable to crystallization is surprising and the derivative provides insight into the mobility of this polypeptide loop compared with homologous enzymes. [source] Crystal structure of human Rad GTPase of the RGK-familyGENES TO CELLS, Issue 8 2006Arry Yanuar Rad (Ras associated with diabetes) is an RGK-family small GTPase that is over-expressed in the skeletal muscle of humans with type II diabetes. Unlike other small GTPases, RGK family members including Rad lack several conserved residues in the GTPase domain. Here, we report the crystal structure of the GTPase domain of human Rad in the GDP-bound form at 1.8 Å resolution. The structure revealed unexpected disordered structures of both switches I and II. We showed that the conformational flexibility of both switches is caused by non-conservative substitutions in the G2 and G3 motifs forming the switch cores together with other substitutions in the structural elements interacting with the switches. Glycine-rich sequences of the switches would also contribute to the flexibility. Switch I lacks the conserved phenylalanine that makes non-polar interactions with the guanine base in H-Ras. Instead, water-mediated hydrogen bonding interactions were observed in Rad. The GDP molecule is located at the same position as in H-Ras and adopts a similar conformation as that bound in H-Ras. This similarity seems to be endowed by the conserved hydrogen bonding interactions with the guanine base-recognition loops and the magnesium ion that has a typical octahedral coordination shell identical to that in H-Ras. [source] Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculationsACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2010Jacco Van De Streek This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095,Å (0.084,Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25,Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect. [source] Mullite-type Ga4B2O9: structure and order,disorder phenomenonACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2010Rihong Cong Ga4B2O9, an aluminium-free mullite-type compound, was prepared by a boric-acid flux method and its structure was determined using powder X-ray diffraction techniques, in combination with transmission electron microscopy, solid-state 11B MAS-NMR and IR spectroscopies. GaO6 octahedra share edges in a trans -manner forming one-dimensional chains along the b direction, and the chains are further cross-linked by GaO5, BO3 and BO4 groups into a three-dimensional mullite-type structure. The disorder of the inter-chain groups results in a small unit cell for Ga4B2O9 compared with that for Al4B2O9, an ordered compound with a superstructure. By deconstructing the structure of Ga4B2O9, we were able to identify the fundamental building units and their linking rules which can be used to reconstruct the ordered and disordered structures. For Ga4B2O9, we found that the structure is intrinsically disordered within the ac plane, but ordered along the b axis. The three-dimensional structure can then be constructed by stacking the disordered ac sheets along the b axis (½b) with a ½a shift. The fundamental building units and exclusivity rules identified in this gallium borate mullite may also be useful for understanding other related mullite phases. The structure analysis applying the proposed method is used to recognize the structural features of Al4B2O9 and Al18B4O33. [source] Changes in protein conformation and dynamics upon complex formation of brain-derived neurotrophic factor and its receptor: Investigation by isotope-edited Fourier transform IR spectroscopyBIOPOLYMERS, Issue 1 2002Tiansheng Li Abstract The interactions of brain-derived neurotrophic factor (BDNF) with the extracellular domain of its receptor (trkB) are investigated by employing isotope-edited Fourier transform IR (FTIR) spectroscopy. The protein secondary structures of individual BDNF and trkB in solutions are compared with those in their complex. The temperature dependence of the secondary structures of BDNF, trkB, and their complex is also investigated. Consistent with the crystal structure, we observe by FTIR spectroscopy that BDNF in solution contains predominantly , strands (,53%) and relatively low contents of other secondary structures including , turns (,16%), disordered structures (,12%), and loops (,18%) and is deficient in , helix. We also observe that trkB in solution contains mostly , strands (52%) and little , helix. Conformational changes in both BDNF and trkB are observed upon complex formation. Specifically, upon binding of BDNF, the conformational changes in trkB appear to involve mostly , turns and disordered structures while the majority of the ,-strand conformation remains unchanged. The IR data indicate that some of the disordered structures in the loop regions are likely converted to , strands upon complex formation. The FTIR spectral data of BDNF, trkB, and their complex indicate that more amide NH groups of trkB undergo H,D exchange within the complex than those of the ligand-free receptor and that the thermal stability of trkB is decreased slightly upon binding of BDNF. The FT-Raman spectra of BDNF, trkB, and their complex show that the six intramolecular disulfide bonds of trkB undergo significant conformational changes upon binding of BDNF as a result of changes in the tertiary structure of trkB. Taken together, the FTIR and Raman data are consistent with the loosening of the tertiary structure of trkB upon binding of BDNF, which leads to more solvent exposure of the amide NH group and decreased thermal stability of trkB. This finding reveals an intriguing structural property of the neurotrophin ligand,receptor complex that is in contrast to other ligand,receptor complexes such as a cytokine,receptor complex that usually shows protection of the amide NH group and increased thermal stability upon complex formation. © 2002 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 67: 10,19, 2002; DOI 10.1002/bip.10038 [source] | |||||||||||||||||||||||||