Local and average structures of BaTiO[subscript 3]-Bi(Zn[subscript 1/2]Ti[subscript 1/2])O[subscript 3]
Abstract not provided
Usher, Tedi-Marie↗
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Results for “structural”
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The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions
The second crystal structure of a parasite protein preferentially enriched in the brain cyst of T. gondii has been solved at 2.75 Å resolution. Bradyzoite enolase 1 is reported to have differential functions as a glycolytic enzyme and a transcriptional regulator in bradyzoites. In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein in Toxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated in vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Structure of the lutein-binding domain of human StARD3 at 1.74 Å resolution and model of a complex with lutein
A crystal structure of the lutein-binding domain of human StARD3 (StAR-related lipid-transfer protein 3; also known as MLN64) has been refined to 1.74 Å resolution. A previous structure of the same protein determined to 2.2 Å resolution highlighted homology with StARD1 and shared cholesterol-binding character. StARD3 has since been recognized as a carotenoid-binding protein in the primate retina, where its biochemical function of binding lutein with specificity appears to be well suited to recruit this photoprotective molecule. The current and previous structures correspond closely to each other (r.m.s.d. of 0.25 Å), especially in terms of the helix-grip fold constructed around a solvent-filled cavity. Regions of interest were defined with alternate conformations in the current higher-resolution structure, including Arg351 found within the cavity and Ω1, a loop of four residues found just outside the cavity entrance. Models of the complex with lutein generated by rigid-body docking indicate that one of the ionone rings must protrude outside the cavity, and this insight has implications for molecular interactions with transport proteins and enzymes that act on lutein. Interestingly, models with the ϵ-ionone ring characteristic of lutein pointing towards the bottom of the cavity were associated with fewer steric clashes, suggesting that steric complementarity and ligand asymmetry may play a role in discriminating lutein from the other ocular carotenoids zeaxanthin and meso -zeaxanthin, which only have β-ionone rings.
Biochemistry & Molecular Biology↗
Hydrodynamics of the rivulet flow over corrugated sheet used in structured packings
Not Available
Singh, Rajesh K.↗
Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation
Abstract not provided
Kim, Jeong Joo↗
Structure, Function, and Dynamics of the Gα Binding Domain of Ric-8A
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99 GENERAL AND MISCELLANEOUS↗
Probing the electronic structures of low oxidation-state uranium fluoride molecules UF{sub x}{sup −} (x = 2−4)
We report the experimental observation of gaseous UF{sub x}{sup −} (x = 2−4) anions, which are investigated using photoelectron spectroscopy and relativistic quantum chemistry. Vibrationally resolved photoelectron spectra are obtained for all three species and the electron affinities of UF{sub x} (x = 2−4) are measured to be 1.16(3), 1.09(3), and 1.58(3) eV, respectively. Significant multi-electron transitions are observed in the photoelectron spectra of U(5f{sup 3}7s{sup 2})F{sub 2}{sup −}, as a result of strong electron correlation effects of the two 7s electrons. The U−F symmetric stretching vibrational modes are resolved for the ground states of all UF{sub x} (x = 2−4) neutrals. Theoretical calculations are performed to qualitatively understand the photoelectron spectra. The entire UF{sub x}{sup −} and UF{sub x} (x = 1−6) series are considered theoretically to examine the trends of U−F bonding and the electron affinities as a function of fluorine coordination. The increased U−F bond lengths and decreased bond orders from UF{sub 2}{sup −} to UF{sub 4}{sup −} indicate that the U−F bonding becomes weaker as the oxidation state of U increases from I to III.
74 ATOMIC AND MOLECULAR PHYSICS↗
Synthesis, structure, and spectroscopic characterization of three uranyl phosphates with unique structural units
Single crystals of Zn{sub 4}(OH){sub 2}[(UO{sub 2})(PO{sub 4}){sub 2}(OH){sub 2}(H{sub 2}O)] (UZnP), Cs[(UO{sub 2})(HPO{sub 4})NO{sub 3}] (UCsP), and In{sub 3}[(UO{sub 2}){sub 2}(PO{sub 4}){sub 4}OH(H{sub 2}O){sub 6}].2H{sub 2}O (UInP) were obtained from hydrothermal reactions and have been structurally and chemically characterized. UZnP crystallizes in space group Pbcn, a=8.8817(7), b=6.6109(5), c=19.569(1) A; UCsP crystallizes in P-1, a=7.015(2), b=7.441(1), c=9.393(2) A, {alpha}=72.974(2), {beta}=74.261(2), {gamma}=79.498(2); and UInP crystallizes in P-1, a=7.9856(5), b=9.159(1), c=9.2398(6) A {alpha}=101.289(1), {beta}=114.642(1), {gamma}=99.203(2). The U{sup 6+} cations are present as (UO{sub 2}){sup 2+} uranyl ions coordinated by five O atoms to give pentagonal bipyramids. The structural unit in UZnP is a finite cluster containing a uranyl pentagonal bipyramid that shares corners with two phosphate tetrahedra. The structural unit in UCsP is composed of uranyl pentagonal bipyramids with one chelating nitrate group that are linked into chains by three bridging hydrogen phosphate tetrahedra. In UInP, the structural unit contains pairs of edge-sharing uranyl pentagonal bipyramids with two chelating phosphate tetrahedra that are linked into chains through two bridging phosphate tetrahedra. Indium octahedra link these uranyl phosphate chains into a 3-dimensional framework. All three compounds exhibit unique structural units that deviate from the typical layered structures observed in uranyl phosphate solid-state chemistry. - Graphical abstract: Three new uranyl phosphates with unique structural units are reported. Black-Small-Square Highlights: Black-Right-Pointing-Pointer Three new uranyl phosphates have been synthesized hydrothermally. Black-Right-Pointing-Pointer Single crystal analyses reveal unique structural units. Black-Right-Pointing-Pointer The dimensionality of these compounds deviate from typical U{sup 6+} layered structures.
36 MATERIALS SCIENCE↗
Odd–Even Structural Sensitivity on Dynamics in Network-Forming Ionic Liquids
As a compelling case of sensitive structure–property relationship, an odd–even effect refers to the alternating trend of physical or chemical properties on odd/even number of repeating structural units. In crystalline or semicrystalline materials, such odd–even effects emerge as manifestations of differences in the periodic packing patterns of molecules. Therefore, due to the lack of long-range order, such an odd–even phenomenon is not expected for dynamic properties in amorphous state. Herein, we report the discovery of a remarkable odd–even effect of dynamical properties in the liquid phase. In a class of glass-forming diammonium citrate ionic liquids, using incoherent quasi-elastic neutron scattering measurements, we measured the dynamical properties including diffusion coefficient and rotational relaxation time. These directly measured molecular dynamics showed pronounced alternating trends with increased number of methylene (-CH2-) groups in the backbone. Meanwhile, the structure factor S(Q) showed no long-range periodic packing of molecules, while the pair distribution function G(r) revealed subtle differences in the local molecular morphology. The observed dynamical odd–even phenomenon in liquids showed that profound dynamical changes originate from subtle local structural differences.
36 MATERIALS SCIENCE↗
A comparative study on the oxidation of two-dimensional Ti 3 C 2 MXene structures in different environments
The oxidation of two-dimensional Ti 3 C 2 MXene structures has been recognized as a promising method for the formation of hybrid structures of carbon supported nanotitania. Here, we studied the oxidation of Ti 3 C 2 MXene structures using reactive force field (ReaxFF) based molecular dynamics simulations. To investigate the effect of oxidizing agent, we used three different environments including dry air (oxygen molecules), wet air (oxygen and water molecules) and hydrogen peroxide (H 2 O 2 molecules). Oxidation simulations were performed at different temperatures of 1000, 1500, 2000, 2500 and 3000 K. We found that by controlling the temperature, carbon supported titania can be formed by diffusion of Ti atoms to the surface of MXene structures during the oxidation. These results were confirmed by the increase in the average bond orders of C–C and Ti–O and decrease in the average bond orders of Ti–C. Moreover, it was revealed that by increasing the temperature, the oxidation rate increases, and the rate depends on the oxidant according to the following order: H 2 O 2 > wet air > dry air. This was validated by heating the MXene in wet air and dry air followed by examining the products using X-ray diffraction and Raman spectroscopy. To investigate the effect of the presence of the oxidant, the MXene structure was also heated under vacuum, and it was found that in this case the MXene structure was converted to cubic TiC. Furthermore, it was indicated that during the heating process of the MXene structure in a vacuum, the average bond orders for C–C, Ti–C and Ti–O do not change significantly due to the lack of oxidants in the environment, leaving room for only topotactic transformation of atoms during the heating. In conclusion, the formation of the TiC structure by heating the MXene in an inert environment was confirmed experimentally as well.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
R -Nb 2 O 5 has an ‘idealized’ V 2 O 5 structure and Wadsley–Roth-like structural stability during Li-ion battery cycling
The adoption of batteries across diverse applications requires electrode materials with a wider range of performance metrics, such as cost, safety, and material availability. Along the path to discovering new commercially viable materials, a fundamental understanding of chemical and atomic structure features that provide structural stability and effective ion transport is essential. In support of new understanding, we report the cycling behavior of metastable R-Nb 2 O 5 . R-Nb 2 O 5 adopts an ‘idealized’ V 2 O 5 structure, in which [NbO 6 ] octahedra alternate in edge- and corner-sharing resulting in ReO 3 -like slabs, whereas Wadsley–Roth materials have ReO 3 -like blocks, linked through edge-sharing octahedra at intersecting crystallographic shear planes. We find that this slab structure is stable during cycling, with minor atomic structure changes and cycling curves that are symmetric on discharge and charge, resembling the behavior of Wadsley–Roth materials more than other related materials, such as ReO 3 , V 2 O 5 , or Nb 3 O 7 F. Based on our findings, R-Nb 2 O 5 can serve as a ‘structural bridge’ between Wadsley–Roth block structures and V 2 O 5 , through which we can relate inter- and intra-polyhedral structures to cycling behavior and structural stability during cycling.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural morphology of zinc oxide structures with antibacterial application of calamine lotion
In this study, we report the structural morphology of a zinc oxide (ZnO) sample and antibacterial application of the ZnO structures in calamine lotion. Antibacterial activities of the calamine lotion towards Staphylococcus aureus and Pseudomonas aeruginosa were investigated. The structural morphology of ZnO sample was studied using a transmission electron microscope (TEM) and a field-emission scanning electron microscope (FESEM). The morphologies of the ZnO structure consisted of many rod and spherical structures. The particle sizes of the sample ranged from 40 nm to 150 nm. A calamine lotion was prepared through mixing the ZnO structures with other constituents in suitable proportion. The energy-dispersive x-ray spectroscopy (EDS) revealed the presence of large amount of ZnO structures whiles the X-ray diffraction (XRD) results showed a good crystalline property of ZnO in the calamine lotion mixture. The morphological structures of ZnO were found to remain unchanged in the calamine lotion mixture through FESEM imaging. In the antibacterial test, prepared calamine lotion exhibited a remarkable bacterial inhibition on Staphylococcus aureus and Pseudomonas aeruginosa after 24 h of treatment. The bactericidal capability of calamine lotion was largely due to the presence of ZnO structures which induce high toxicity and killing effect on the bacteria.
36 MATERIALS SCIENCE↗
Injection moulding of optical functional micro structures using laser structured, PVD-coated mould inserts
Micro structured optical plastics components are intensively used i. e. in consumer electronics, for optical sensors in metrology, innovative LED-lighting or laser technology. Injection moulding has proven to be successful for the large-scale production of those parts. However, the production of those parts still causes difficulties due to challenges in the moulding and demoulding of plastics parts created with laser structured mould inserts. A complete moulding of the structures often leads to increased demoulding forces, which then cause a breaking of the structures and a clogging of the mould. An innovative approach is to combine PVD-coated (physical vapour deposition), laser structured inserts and a variothermal moulding process to create functional mic8iüro structures in a one-step process. Therefore, a PVD-coating is applied after the laser structuring process in order to improve the wear resistance and the anti-adhesive properties against the plastics melt. In a series of moulding trials with polycarbonate (PC) and polymethylmethacrylate (PMMA) using different coated moulds, the mould temperature during injection was varied in the range of the glass transition and the melt temperature of the polymers. Subsequently, the surface topography of the moulded parts is evaluated by digital 3D laser-scanning microscopy. The influence of the moulding parameters and the coating of the mould insert on the moulding accuracy and the demoulding behaviour are being analysed. It is shown that micro structures created by ultra-short pulse laser ablation can be successfully replicated in a variothermal moulding process. Due to the mould coating, significant improvements could be achieved in producing micro structured optical plastics components.
36 MATERIALS SCIENCE↗
Electronically- and crystal-structure-driven magnetic structures and physical properties of RScSb (R = rare earth) compounds. A neutron diffraction, magnetization and heat capacity study
The synthesis of the new equiatomic RScSb ( R = La-Nd, Sm, Gd-Tm, Lu, Y) compounds has been recently reported. These rare earth compounds crystallize in two different crystal structures, adopting the CeScSi-type ( I 4/ mmm) for the lighter R (La-Nd, Sm) and the CeFeSi-type (P4 /nmm) structure for the heavier R ( R = Gd-Tm, Lu, Y). Here we report the results of neutron diffraction, magnetization and heat capacity measurements on some of these compounds ( R = Ce, Pr, Nd, Gd and Tb). Band structure calculations have also been performed on CeScSb and GdScGe (CeScSi-type), and on GdScSb and TbScSb (CeFeSi-type) to compare and understand the exchange interactions in CeScSi and CeFeSi structure types. The neutron diffraction investigation shows that all five compounds order magnetically, with the highest transition temperature of 66 K in TbScSb and the lowest of about 9 K in CeScSb. The magnetic ground state is simple ferromagnetic (τ = [0 0 0]) in CeScSb, as well in NdScSb for 32 >T > 22 K. Below 22 K a second magnetic transition, with propagation vector τ = [¼ ¼ 0], appears in NdScSb. PrScSb has a magnetic structure within, determined by mostly ferromagnetic interactions and antiferromagnetic alignment of the Pr-sites connected through the I-centering ( τ = [1 0 0]). A cycloidal spiral structure with a temperature dependent propagation vector τ = [δ δ ½] is found in TbScSb. The results of magnetization and heat capacity lend support to the main conclusions derived from neutron diffraction. As inferred from a sharp peak in magnetization, GdScSb orders antiferromagnetically at 56 K. First principles calculations show lateral shift of spin split bands towards lower energy from the Fermi level as the CeScSi-type structure changes to the CeFeSi-type structure. This rigid shift may force the system to transform from exchange split ferromagnetic state to the antiferromagnetic state in RScSb compounds (as seen for example in GdScSb and TbScSb) and is proposed to explain the change-over from a ferromagnetic structure as found in the CeScSi-type compounds CeScSb and NdScSb to the antiferromagnetic state as found in TbScSb and GdScSb.
36 MATERIALS SCIENCE↗
Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding
Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the cobalamin riboswitch with predicted structural features was identified in Bacillus subtilis over a decade ago, but its structure and mechanisms of cobalamin selectivity and translational control have remained unsolved. We present the crystal structure of the aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, including its expression platform domain. We demonstrate that this riboswitch binds to multiple cobalamin derivatives and correlate its promiscuous behavior to its structure and unique arrangement of peripheral elements. Comparative structural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promiscuous ligand binding is intrinsic structural adaptability encoded in the RNA structure. It suggests that cobalamin selectivity might ultimately be viewed as existing on a spectrum of affinity for each derivative rather than as belonging to distinct types based on ligand specificities. Our work provides an interesting and notable example of functional coupling of ligand-sensing and adaptive folding by a structured RNA molecule.
59 BASIC BIOLOGICAL SCIENCES↗
Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data
Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in structure determination. Here, native SAD procedures are described for enhancing the signal to noise in anomalous diffraction by using multiple crystals are described. Five applications demonstrate that truly routine structure determination is possible without the need for heavy atoms. Structure determinations for biological macromolecules that have no known structural antecedents typically involve the incorporation of heavier atoms than those found natively in biological molecules. Currently, selenomethionyl proteins analyzed using single- or multi-wavelength anomalous diffraction (SAD or MAD) data predominate for such de novo analyses. Naturally occurring metal ions such as zinc or iron often suffice in MAD or SAD experiments, and sulfur SAD has been an option since it was first demonstrated using crambin 30 years ago; however, SAD analyses of structures containing only light atoms (Z{sub max} ≤ 20) have not been common. Here, robust procedures for enhancing the signal to noise in measurements of anomalous diffraction by combining data collected from several crystals at a lower than usual X-ray energy are described. This multi-crystal native SAD method was applied in five structure determinations, using between five and 13 crystals to determine substructures of between four and 52 anomalous scatterers (Z ≤ 20) and then the full structures ranging from 127 to 1200 ordered residues per asymmetric unit at resolutions from 2.3 to 2.8 Å. Tests were devised to assure that all of the crystals used were statistically equivalent. Elemental identities for Ca, Cl, S, P and Mg were proven by f′′ scattering-factor refinements. The procedures are robust, indicating that truly routine structure determination of typical native macromolecules is realised. Synchrotron beamlines that are optimized for low-energy X-ray diffraction measurements will facilitate such direct structural analysis.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗