Crystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting Signal
Abstract not provided
Kattke, Michele D.↗
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Control of Domain Structures in Multiferroic Thin Films through Defect Engineering
Domain walls (DWs) have become an essential component in nanodevices based on ferroic thin films. The domain configuration and DW stability, however, are strongly dependent on the boundary conditions of thin films, which make it difficult to create complex ordered patterns of DWs. Here, it is shown that novel domain structures, that are otherwise unfavorable under the natural boundary conditions, can be realized by utilizing engineered nanosized structural defects as building blocks for reconfiguring DW patterns. It is directly observed that an array of charged defects, which are located within a monolayer thickness, can be intentionally introduced by slightly changing substrate temperature during the growth of multiferroic BiFeO 3 thin films. These defects are strongly coupled to the domain structures in the pretemperature-change portion of the BiFeO 3 film and can effectively change the configuration of newly grown domains due to the interaction between the polarization and the defects. Thus, two types of domain patterns are integrated into a single film without breaking the DW periodicity. The potential use of these defects for building complex patterns of conductive DWs is also demonstrated.
36 MATERIALS SCIENCE↗
Quantification of Native Lignin Structural Features with Gel–Phase 2D–HSQC 0 Reveals Lignin Structural Changes During Extraction
Our ability to study and valorize the lignin fraction of biomass is hampered by the fundamental and still unmet challenge of precisely quantifying native lignin's structural features. Here, we developed a rapid elevated-temperature 1 H– 13 C Heteronuclear Single-Quantum Coherence Zero (HSQC 0 ) NMR method that enables this precise quantification of native lignin structural characteristics even with whole plant cell wall (WPCW) NMR spectroscopy, overcoming fast spin relaxation in the gel phase. We also formulated a Gaussian fitting algorithm to perform automatic and reliable spectral integration. By combining HSQC 0 measurements with yield measurements following depolymerisation, we can confirm the combinatorial nature of radical coupling reactions during biosynthesis leading to a random sequential organization of linkages within a largely linear lignin chain. Such analyses illustrate how this analytical method can greatly facilitate the study of native lignin structure, which can then be used for fundamental studies or to understand lignin depolymerization methods like reductive catalytic fractionation or aldehyde-assisted fractionation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Quantification of Native Lignin Structural Features with Gel–Phase 2D–HSQC 0 Reveals Lignin Structural Changes During Extraction
Our ability to study and valorize the lignin fraction of biomass is hampered by the fundamental and still unmet challenge of precisely quantifying native lignin's structural features. Here, we developed a rapid elevated-temperature 1 H– 13 C Heteronuclear Single-Quantum Coherence Zero (HSQC 0 ) NMR method that enables this precise quantification of native lignin structural characteristics even with whole plant cell wall (WPCW) NMR spectroscopy, overcoming fast spin relaxation in the gel phase. We also formulated a Gaussian fitting algorithm to perform automatic and reliable spectral integration. By combining HSQC 0 measurements with yield measurements following depolymerisation, we can confirm the combinatorial nature of radical coupling reactions during biosynthesis leading to a random sequential organization of linkages within a largely linear lignin chain. Such analyses illustrate how this analytical method can greatly facilitate the study of native lignin structure, which can then be used for fundamental studies or to understand lignin depolymerization methods like reductive catalytic fractionation or aldehyde-assisted fractionation.
09 BIOMASS FUELS↗
A Hybrid Structural Method for Investigating Low Molecular Weight Oligomeric Structures of Amyloid Beta
Spurred in part by the failure of recent therapeutics targeting amyloid β plaques in Alzheimer's Disease (AD), attention is increasingly turning to the oligomeric forms of this peptide that form early in the aggregation process. However, while numerous amyloid β fibril structures have been characterized, primarily by NMR spectroscopy and cryo-EM, obtaining structural information on the low molecular weight forms of amyloid β that presumably precede and/or seed fibril formation has proved challenging. Furthermore, these transient forms are heterogeneous, and depend heavily on experimental conditions such as buffer, temperature, concentration, and degree of quiescence during measurement. Here, we present the concept for a new approach to delineating structural features of early-stage low molecular weight amyloid β oligomers, using a solvent accessibility assay in conjunction with simultaneous fluorescence measurements.
60 APPLIED LIFE SCIENCES↗
Comparing the Performance of Three Land Models in Global C Cycle Simulations: A Detailed Structural Analysis: Structural Analysis of Land Models
Land models are valuable tools to understand the dynamics of global carbon (C) cycle. Various models have been developed and used for predictions of future C dynamics but uncertainties still exist. Diagnosing the models’ behaviors in terms of structures can help to narrow down the uncertainties in prediction of C dynamics. In this study three widely used land surface models, namely CSIRO’s Atmosphere Biosphere Land Exchange (CABLE) with 9 C pools, Community Land Model (version 3.5) combined with Carnegie-Ames-Stanford Approach (CLM-CASA) with 12 C pools and Community Land Model (version 4) (CLM4) with 26 C pools were driven by the observed meteorological forcing. The simulated C storage and residence time were used for analysis. The C storage and residence time were computed globally for all individual soil and plant pools, as well as net primary productivity (NPP) and its allocation to different plant components’ based on these models. Remotely sensed NPP and statistically derived HWSD, and GLC2000 datasets were used as a reference to evaluate the performance of these models. Results showed that CABLE exhibited better agreement with referenced C storage and residence time for plant and soil pools, as compared with CLM-CASA and CLM4. CABLE had longer bulk residence time for soil C pools and stored more C in roots, whereas, CLM-CASA and CLM4 stored more C in woody pools due to differential NPP allocation. Overall, these results indicate that the differences in C storage and residence times in three models are largely due to the differences in their fundamental structures (number of C pools), NPP allocation and C transfer rates. Our results have implications in model development and provide a general framework to explain the bias/uncertainties in simulation of C storage and residence times from the perspectives of model structures.
54 ENVIRONMENTAL SCIENCES↗
Novel Theoretical Prediction of Structural Properties, Ferromagnetic Ordering, and Electronic Structure of Fe{sub 2}PbC MAX Phase
In this study, we have investigated the magnetic stability; ferromagnetic ordering; and structural, elastic, and electronic properties of Fe{sub 2}PbC compound. The calculations are performed by the use of full-potential linearized augmented plane wave method implemented in WIEN2k code. We have found that the ferromagnetic state of Fe{sub 2}PbC is more stable than non-magnetic state configuration at their equilibrium lattice parameters. The structural and elastic properties suggest that Fe{sub 2}PbC is an anisotropic material, which is stable in the hexagonal MAX phase. The electronic structures show that Fe{sub 2}PbC has metallic-covalent-ionic character. The ferromagnetic performance of Fe{sub 2}PbC is confirmed by the total magnetic moment of 4.15 μ{sub B}, where its main contribution is originated from Fe atoms.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Analysis of Extended X-ray Absorption Fine Structure (EXAFS) Data Using Artificial Intelligence Tech
Explore the source record for details and available documents.
Terry, Jeff↗
Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum
Graphical abstract: - Highlights: • HypBA1 β-L-arabinofuranosidase belongs to glycoside hydrolase family 127. • Crystal structure of HypBA1 was determined. • HypBA1 consists of a catalytic barrel and two additional β-sandwich domains. • The active site contains a Zn{sup 2+} coordinated by glutamate and three cysteines. • A possible reaction mechanism involving cysteine as the nucleophile is proposed. - Abstract: Enzymes acting on β-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of β-L-arabinofuranosyl oligosaccharides in plant cells. Recently, a β-L-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system of hydroxyproline-linked β-L-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and β-L-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional β-sandwich domains, with one β-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn{sup 2+} coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the β-L-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed.
60 APPLIED LIFE SCIENCES↗
Measurements of structures and concentrations of carbon particle species in premixed flames by the use of in-situ wide angle X-ray scattering
In-situ wide-angle X-ray scattering (WAXS) measurements have been conducted on atmospheric-pressure fuel-rich premixed freely propagating ethylene/oxygen flames with argon and nitrogen dilution. In this work, a novel analysis methodology able to provide quantitative information on soot/carbon particle species and concentrations was tested under heavy sooting conditions. The particle composition and concentrations were retrieved by fitting theoretical calculations of structural components from major molecular and nanometric species to the experimental WAXS data. The results show that argon dilution yields predominantly graphenelike components that are less stacked and amorphous carbon that is less structured than under nitrogen dilution. This finding was later confirmed by electron microscopy analysis on samples extracted from similar flames. In addition, the WAXS showed that most of the carbon present in the flames was bound as particles. These results constitute some of the first in-situ observations on structures and concentrations of carbon species in laboratory burner flames operating without stabilization plates.
Concentrations↗
Structural Basis for Promoter ;#8722;10 Element Recognition by the Bacterial RNA Polymerase [sigma] Subunit
The key step in bacterial promoter opening is recognition of the -10 promoter element (T-{sub 12}A-{sub 11}T-{sub 10}A-{sub 9}A-{sub 8}T{sub -7} consensus sequence) by the RNA polymerase {alpha} subunit. We determined crystal structures of {alpha} domain 2 bound to single-stranded DNA bearing -10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every -10 element nucleotide. Base-specific interactions occur primarily with A{sub -11} and T{sub -7}, which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the -10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by {alpha}. These results provide a detailed structural basis for the critical roles of A{sub -11} and T{sub -7} in promoter melting and reveal important insights into the initiation of transcription bubble formation.
59 BASIC BIOLOGICAL SCIENCES↗
Impact load-induced micro-structural damage and micro-structure associated mechanical response of concrete made with different surface roughness and porosity aggregates
The relationship between the nature of micro damage under impact loading and changes in mechanical behavior associated with different microstructures is studied for concretes made with two different coarse aggregates having significant differences mainly in roughness and porosity - sintered fly ash and uncrushed gravel. A range of techniques including X-ray diffraction, digital image analysis, mercury porosimetry, X-ray computed tomography, laser surface profilometry and scanning electron microscopy were used to characterize the aggregates and micro-structures. The concrete prepared with lightweight aggregates was stronger in compression than the gravel aggregate concrete due to enhanced hydration as a result of internal curing. In the lightweight concrete, it was deduced that an inhomogeneous micro-structure led to strain incompatibilities and consequent localized stress concentrations in the mix, leading to accelerated failure. The pore structure, compressibility, and surface texture of the aggregates are of paramount importance for the micro-cracking growth.
36 MATERIALS SCIENCE↗
A structural insight into the P1 S1 binding mode of diaminoethylphosphonic and phosphinic acids, selective inhibitors of alanine aminopeptidases
Not Available
Węglarz-Tomczak, Ewelina↗
A numerical approach for simulating fluid structure interaction of flexible thin shells undergoing arbitrarily large deformations in complex domains
We present a new numerical methodology for simulating fluid–structure interaction (FSI) problems involving thin flexible bodies in an incompressible fluid. The FSI algorithm uses the Dirichlet–Neumann partitioning technique. The curvilinear immersed boundary method (CURVIB) is coupled with a rotation-free finite element (FE) model for thin shells enabling the efficient simulation of FSI problems with arbitrarily large deformation. Turbulent flow problems are handled using large-eddy simulation with the dynamic Smagorinsky model in conjunction with a wall model to reconstruct boundary conditions near immersed boundaries. The CURVIB and FE solvers are coupled together on the flexible solid–fluid interfaces where the structural nodal positions, displacements, velocities and loads are calculated and exchanged between the two solvers. Loose and strong coupling FSI schemes are employed enhanced by the Aitken acceleration technique to ensure robust coupling and fast convergence especially for low mass ratio problems. The coupled CURVIB-FE-FSI method is validated by applying it to simulate two FSI problems involving thin flexible structures: 1) vortex-induced vibrations of a cantilever mounted in the wake of a square cylinder at different mass ratios and at low Reynolds number; and 2) the more challenging high Reynolds number problem involving the oscillation of an inverted elastic flag. For both cases the computed results are in excellent agreement with previous numerical simulations and/or experiential measurements. Grid convergence tests/studies are carried out for both the cantilever and inverted flag problems, which show that the CURVIB-FE-FSI method provides their convergence. Finally, the capability of the new methodology in simulations of complex cardiovascular flows is demonstrated by applying it to simulate the FSI of a tri-leaflet, prosthetic heart valve in an anatomic aorta and under physiologic pulsatile conditions.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Crystal structure analysis of tungsten bronzes {beta}-SrTa{sub 2}O{sub 6} and {beta} Prime -SrTa{sub 2}O{sub 6} by synchrotron X-ray and neutron powder diffraction
Strontium ditantalum oxide SrTa{sub 2}O{sub 6} exists in {alpha}-, {beta}-, and {beta} Prime -polymorphs. Herein the crystal structures of the latter two were studied using synchrotron X-ray and constant-wavelength neutron powder diffraction. While {beta} Prime -SrTa{sub 2}O{sub 6} [space group P4/mbm, a=12.47099(1) A, c=3.898210(5) A, V=606.271(2) Angstrom-Sign {sup 3}, Z=5] belongs to the regular tetragonal tungsten bronze (TTB) family, it contains locally disordered strontium atoms within the pentagonal channel. {beta}-SrTa{sub 2}O{sub 6} [space group Pnam, a=12.36603(2) Angstrom-Sign , b=12.43467(2) A, c=7.72403(1) A, V=1187.705(4) Angstrom-Sign {sup 3}, Z=10] can be described as an orthorhombic modification of the TTB, where the octahedral tilting distortion effectively alleviates the bonding strains around TaO{sub 6} and SrO{sub 13} polyhedra. For comparison, rynersonite type {alpha}-SrTa{sub 2}O{sub 6} [space group Pnma, a=11.00610(6) Angstrom-Sign , b=7.63397(3) Angstrom-Sign , c=5.62634(3) Angstrom-Sign , V=472.727(5) Angstrom-Sign {sup 3}, and Z=4] is built from edge-shared dimer units of TaO{sub 6} octahedra. As measured by diffuse-reflection absorption spectroscopy, {alpha}-, {beta}-, and {beta} Prime -SrTa{sub 2}O{sub 6} have indirect band gap energies of 4.4, 4.0, and 3.8 eV, respectively. - Graphical Abstract: Difference Fourier map for {beta} Prime -SrTa{sub 2}O{sub 6} at z=0. Highlights: Black-Right-Pointing-Pointer Structure refinements of {beta}-SrTa{sub 2}O{sub 6} and {beta} Prime -SrTa{sub 2}O{sub 6}. Black-Right-Pointing-Pointer Strontium disorder in tetragonal tungsten bronze {beta} Prime -SrTa{sub 2}O{sub 6}. Black-Right-Pointing-Pointer Orthorhombic distortion and cell doubling in {beta}-SrTa{sub 2}O{sub 6}.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structure and physical properties of single crystal PrCr{sub 2}Al{sub 20} and CeM{sub 2}Al{sub 20} (M=V, Cr): A comparison of compounds adopting the CeCr{sub 2}Al{sub 20} structure type
Crystal growth and full structure determination of compounds adopting the CeCr{sub 2}Al{sub 20} structure type, LnTi{sub 2}Al{sub 20} (Ln=La-Pr, Sm, and Yb), LnV{sub 2}Al{sub 20} (Ln=La-Pr, and Sm), and LnCr{sub 2}Al{sub 20} (Ln=La-Pr, Sm, and Yb), are reported. Resistivity, magnetic susceptibility, and heat capacity of flux grown single crystals of the nonmagnetic CeM{sub 2}Al{sub 20} (Ln=Ce, Yb; M=Ti, V) compounds are compared to PrCr{sub 2}Al{sub 20}. Of particular interest is PrCr{sub 2}Al{sub 20} which does not show any phase transition down to the lowest temperature of the measurement (400 mK in resistivity measurement and 1.8 K for magnetic susceptibility measurements) and exhibits Kondo behavior at low temperatures. - Graphical abstract: Crystal structure of SmV{sub 2}Al{sub 20} showing the interpenetrating diamond-like samarium network and pyrochlore-like vanadium network. Highlights: Black-Right-Pointing-Pointer Single crystals of LnM{sub 2}Al{sub 20} were grown from a molten aluminum flux. Black-Right-Pointing-Pointer Magnetic, electrical, and specific heat of single crystal LnM{sub 2}Al{sub 20} are presented. Black-Right-Pointing-Pointer PrCr{sub 2}Al{sub 20} exhibits evidence of Kondo effect.
36 MATERIALS SCIENCE↗