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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Combined Normal and Disruption, Electromagnetic Transient, Thermal, and Structural Analysis of COMPASS Upgrade

We report that COMPASS Upgrade is a replacement for the COMPASS device at the Institute of Plasma Physics (IPP) of the Czech Academy of Sciences. It is a cryogenic copper machine with a major radius of 0.89 m, with 5 T at the plasma centerline and 2-MA plasma current. It is intended to develop ITER relevant plasma densities and high power fluxes in the divertor region. The entire vacuum vessel is planned to reach 500 °C. The COMPASS-U TF coil is a bitter plate-like design with radial conductor plates that extend the width of the TF inner leg. Currents redistribute radially based on resistive and inductive effects. This necessitates an electromagnetic (EM) transient analysis of the coil current distribution. For copper coils like COMPASS Upgrade, the solution must be coupled with a thermal solution to properly include the temperature-dependent resistive effects. The EM transient solution includes the TF magnetic loads, and a stress pass on the results produces in-plane loads. The EM solution chosen requires inclusion of all the conducting and nonconducting regions surrounding the TF coil. With the TF current distribution solved, the addition of the poloidal coils and resulting background fields allows the determination of the out-of-plane loads. Integration of the Joule heating produced from the EM solution produces temperature distributions throughout the shot, which can be read in to a structural pass to include thermal stresses in the evaluation. This is true of both TF and PF temperature prediction with appropriate packing fractions. Currents in the PF coils, with computed background fields, produce Lorentz loads. Time transients of the PF currents produce startup eddy currents in the structures included in the model; inclusion of the vessel and other passive structures allows these to be included in a stress pass. The EM transient solution includes all the elements needed for a disruption analysis with prescribed motions and quench of the plasma. From a model originally intended to simulate current diffusion in the TF coil, the analysis can be refined to be used to predict the performance of most of the components of the tokamak or provide boundary conditions for more detailed submodels. In this article, the use of the current diffusion model for bounding assessments of the COMPASS Upgrade TF, PF, vessel, external structure, and disruption analyses will be presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Structural Analysis of Peripheral Organs of the Immune System in the Assessment of Grippol Vaccine Safety

The safety of Grippol vaccine was assessed by macro- and microscopic methods in the experiment. The morphological features of group lymphoid nodules of the small intestine were studied on days 4, 7, 14 and 30 after vaccination. The structural morphological dynamics of lymphoid tissue under these conditions is shown. Because of the use of the vaccine, the lymphocytopoietic processes in the body are activated, which indicates the formation of an immune response.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A structural analysis of ordered Cs3Sb films grown on single crystal graphene and silicon carbide substrates

Alkali antimonides are well established as high efficiency, low intrinsic emittance photocathodes for accelerators and photon detectors. However, conventionally grown alkali antimonide films are polycrystalline with surface disorder and roughness that can limit achievable beam brightness. Ordering the crystalline structure of alkali antimonides has the potential to deliver higher brightness electron beams by reducing surface disorder and enabling the engineering of material properties at the level of atomic layers. In this report, we demonstrate the growth of ordered Cs3Sb films on single crystal substrates 3C-SiC and graphene-coated 4H-SiC using pulsed laser deposition and conventional thermal evaporation growth techniques. The crystalline structures of the Cs3Sb films were examined using reflection high energy electron diffraction and x-ray diffraction diagnostics, while film thickness and roughness estimates were made using x-ray reflectivity. With these tools, we observed ordered domains in less than 10 nm thick films with quantum efficiencies greater than 1% at 530 nm. Moreover, we identify structural features such as Laue oscillations indicative of highly ordered films. We found that Cs3Sb films grew with flat, fiber-textured surfaces on 3C-SiC and with multiple ordered domains and sub-nanometer surface roughness on graphene-coated 4H-SiC under our growth conditions. We identify the crystallographic orientations of Cs3Sb grown on graphene-coated 4H-SiC substrates and discuss the significance of examining the crystal structure of these films for growing epitaxial heterostructures in future experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural analysis and functional evaluation of the disordered ß–hexosyltransferase region from Hamamotoa (Sporobolomyces) singularis

Hamamotoa (Sporobolomyces) singularis codes for an industrially important membrane bound ß-hexosyltransferase (BHT), (BglA, UniprotKB: Q564N5) that has applications in the production of natural fibers such as galacto-oligosaccharides (GOS) and natural sugars found in human milk. When heterologously expressed by Komagataella phaffii GS115, BHT is found both membrane bound and soluble secreted into the culture medium. In silico structural predictions and crystal structures support a glycosylated homodimeric enzyme and the presence of an intrinsically disordered region (IDR) with membrane binding potential within its novel N-terminal region (1–110 amino acids). Additional in silico analysis showed that the IDR may not be essential for stable homodimerization. Thus, we performed progressive deletion analyses targeting segments within the suspected disordered region, to determine the N-terminal disorder region’s impact on the ratio of membrane-bound to secreted soluble enzyme and its contribution to enzyme activity. The ratio of the soluble secreted to membrane-bound enzyme shifted from 40% to 53% after the disordered N-terminal region was completely removed, while the specific activity was unaffected. Furthermore, functional analysis of each glycosylation site found within the C-terminal domain revealed reduced total secreted protein activity by 58%–97% in both the presence and absence of the IDR, indicating that glycosylation at all four locations is required by the host for the secretion of active enzyme and independent of the removed disordered N-terminal region. Overall, the data provides evidence that the disordered region only partially influences the secretion and membrane localization of BHT.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mass spectrometry structural analysis of intrinsically disordered phosphoproteins

Phosphorylation is a ubiquitous protein modification that is known to play important roles in many biological phenomena including cell signaling, the opening and closing of membrane protein channels, and even triggering of amyloid protein aggregation. Despite the effects phosphorylation has on protein function, the impact phosphorylation has on the structure of proteins is not well understood. Here, to determine how phosphorylation affects the structure of proteins, top-down mass spectrometry (TD-MS) and ion mobility-mass spectrometry (IM-MS) were performed on various phosphorylated proteins and their dephosphorylated proteoforms. TD-MS with collision- and electron-based fragmentation techniques was utilized to locate phosphorylation sites on the intrinsically disordered amyloid proteins β-casein and α-synuclein. TD-MS also provided evidence that alkaline phosphatase dephosphorylates β-casein from the N-terminus to the C-terminus. Furthermore, IM-MS of common phosphorylated proteins such as β-casein, α-casein, ovalbumin, and phosvitin indicates that phosphorylation promotes compaction of protein structure in denaturing as well as native conditions. Increases in abundance of more compact conformers are also observed when the disease related amyloid protein α-synuclein is phosphorylated at serine 129. We interpret the increased abundance of more compact conformers when proteins are phosphorylated as evidence that salt bridges form between negatively charged phosphates and positively charged residues, which alters protein structure. Salt bridge formation due to phosphorylation could be a mechanism for regulating protein function and be responsible for many of the phenomena observed in nature.

Amyloid proteins↗
DOE OSTI2011

Optical and structural analysis of lead bismuth silicate glasses

Glasses having compositions 20PbO(79.5-x)Bi{sub 2}O{sub 3}xSiO{sub 2} (x = 10,30,50) doped with 0.5 mole% of Nd{sup 3+} ions were prepared by melt quench technique. The spectroscopic properties of the glasses were investigated using optical absorption and fluorescence spectra. The structural investigations of these glasses were carried out by recording the IR spectra. The variation of {Omega}{sub 2} with Bi{sub 2}O{sub 3} content has been attributed to changes in the asymmetry of the ligand field at the rare earth ion site and to the changes in the rare earth oxygen covalency. Heavy metal oxide glasses have been used as potential candidate in solid state laser, solar concentrators, optical detector, optical fiber and fluorescent display devices.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor Zfp206

Zfp206 (also named as Zscan10) belongs to the subfamily of C2H2 zinc finger transcription factors, which is characterized by the N-terminal SCAN domain. The SCAN domain mediates selfassociation and association between the members of SCAN family transcription factors, but the structural basis and selectivity determinants for complex formation is unknown. Zfp206 is important for maintaining the pluripotency of embryonic stem cells presumably by combinatorial assembly of itself or other SCAN family members on enhancer regions. To gain insights into the folding topology and selectivity determinants for SCAN dimerization, we solved the 1.85 A° crystal structure of the SCAN domain of Zfp206. In vitro binding studies using a panel of 20 SCAN proteins indicate that the SCAN domain Zfp206 can selectively associate with other members of SCAN family transcription factors. Deletion mutations showed that the N-terminal helix 1 is critical for heterodimerization. Double mutations and multiple mutations based on the Zfp206SCAN–Zfp110SCAN model suggested that domain swapped topology is a possible preference for Zfp206SCAN–Zfp110SCAN heterodimer. Together, we demonstrate that the Zfp206SCAN constitutes a protein module that enables C2H2 transcription factor dimerization in a highly selective manner using a domain-swapped interface architecture and identify novel partners for Zfp206 during embryonal development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography

Candida boidinii NAD + -dependent formate dehydrogenase (CbFDH) has gained significant attention for its potential application in the production of biofuels and various industrial chemicals from inorganic carbon dioxide. The present study reports the atomic X-ray crystal structures of wild-type CbFDH at cryogenic and ambient temperatures, as well as that of the Val120Thr mutant at cryogenic temperature, determined at the Turkish Light Source ‘Turkish DeLight’. The structures reveal new hydrogen bonds between Thr120 and water molecules in the active site of the mutant CbFDH, suggesting increased stability of the active site and more efficient electron transfer during the reaction. Further experimental data is needed to test these hypotheses. Collectively, these findings provide invaluable insights into future protein-engineering efforts that could potentially enhance the efficiency and effectiveness of CbFDH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Characterization and structural analysis of a thermophilic GH11 xylanase from compost metatranscriptome

Xylanase is efficient for xylan degradation and widely applied in industries. We found a GH11 family xylanase (Xyn11A) with high thermostability and catalytic activity from compost metatranscriptome. This xylanase has the optimal reaction temperature at 80 °C with the activity of 2907.3 U/mg. The X-ray crystallographic structure shows a typical “right hand” architecture, which is the characteristics of the GH11 family enzymes. Comparing it with the mesophilic XYN II, a well-studied GH11 xylanase from Trichoderma reesei, Xyn11A is more compact with more H-bonds. Our mutagenic results show that the electrostatic interactions in the thumb and palm region of Xyn11A could result in its high thermostability and activity. Introducing a disulfide bond at the N-terminus further increased its optimal reaction temperature to 90 °C with augmented activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural analysis of extracellular ATP-independent chaperones of streptococcal species and protein substrate interactions

ABSTRACT During infection, bacterial pathogens rely on secreted virulence factors to manipulate the host cell. However, in gram-positive bacteria, the molecular mechanisms underlying the folding and activity of these virulence factors after membrane translocation are not clear. Here, we solved the protein structures of two secreted parvulin and two secreted cyclophilin-like peptidyl-prolyl isomerase (PPIase) ATP-independent chaperones found in gram-positive streptococcal species. The extracellular parvulin-type PPIase, PrsA inStreptococcus pneumoniaeandStreptococcus mutansmaintain dimeric crystal structures reminiscent of folding catalysts that consist of two domains, a PPIase and foldase domain. Structural comparison of the two cyclophilin-like extracellular chaperones fromS. pneumoniaeandStreptococcus pyogeneswith other cyclophilins demonstrates that this group of cyclophilin-like chaperones has novel structural appendages formed by 9- and 24-residue insertions. Furthermore, we demonstrate that deletion ofprsAandslrAgenes impairs the secretion of the cholesterol-dependent pore-forming toxin, pneumolysin inS. pneumoniae. Using protein pull-down and biophysical assays, we demonstrate a direct interaction between PrsA and SlrA with Ply. Then, we developed chaperone-assisted folding assays that show that theS. pneumoniaePrsA and SlrA extracellular chaperones accelerate pneumolysin folding. In addition, we demonstrate that SlrA and, for the first time,S. pyogenes PpiA exhibit PPIase activity and can bind the immunosuppressive drug, cyclosporine A. Altogether, these findings suggest a mechanistic role for streptococcal PPIase chaperones in the activity and folding of secreted virulence factors such as pneumolysin. IMPORTANCE Streptococcal species are a leading cause of lower respiratory infections that annually affect millions of people worldwide. During infection, streptococcal species secrete a medley of virulence factors that allow the bacteria to colonize and translocate to deeper tissues. In many gram-positive bacteria, virulence factors are secreted from the cytosol across the bacterial membrane in an unfolded state. The bacterial membrane-cell wall interface is exposed to the potentially harsh extracellular environment, making it difficult for native virulence factors to fold before being released into the host. ATP-independent PPIase-type chaperones, PrsA and SlrA, are thought to facilitate folding and stabilization of several unfolded proteins to promote the colonization and spread of streptococci. Here, we present crystal structures of the molecular chaperones of PrsA and SlrA homologs from streptococcal species. We provide evidence that theStreptococcus pyogenesSlrA homolog, PpiA, has PPIase activity and binds to cyclosporine A. In addition, we show thatStreptococcus pneumoniaePrsA and SlrA directly interact and fold the cholesterol-dependent pore-forming toxin and critical virulence determinant, pneumolysin.

Microbiology↗
DOE OSTI2011

Structural Analysis of the Receptor Binding Domain of Botulinum Neurotoxin Serotype D

Botulinum neurotoxins (BoNTs) are the most toxic proteins known. The mechanism for entry into neuronal cells for serotypes A, B, E, F, and G involves a well understood dual receptor (protein and ganglioside) process, however, the mechanism of entry for serotypes C and D remains unclear. To provide structural insights into how BoNT/D enters neuronal cells, the crystal structure of the receptor binding domain (S863-E1276) for this serotype (BoNT/D-HCR) was determined at 1.65{angstrom} resolution. While BoNT/D-HCR adopts an overall fold similar to that observed in other known BoNT HCRs, several major structural differences are present. These structural differences are located at, or near, putative receptor binding sites and may be responsible for BoNT/D host preferences. Two loops, S1195-I1204 and K1236-N1244, located on both sides of the putative protein receptor binding pocket, are displaced >10{angstrom} relative to the corresponding residues in the crystal structures of BoNT/B and G. Obvious clashes were observed in the putative protein receptor binding site when the BoNT/B protein receptor synaptotagmin II was modeled into the BoNT/D-HCR structure. Although a ganglioside binding site has never been unambiguously identified in BoNT/D-HCR, a shallow cavity in an analogous location to the other BoNT serotypes HCR domains is observed in BoNT/D-HCR that has features compatible with membrane binding. A portion of a loop near the putative receptor binding site, K1236-N1244, is hydrophobic and solvent-exposed and may directly bind membrane lipids. Liposome-binding experiments with BoNT/D-HCR demonstrate that this membrane lipid may be phosphatidylethanolamine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structural Analysis and Electrochemical Properties of Bimetallic Palladium-Platinum Aerogels Prepared by a Two-Step Gelation Process

Multimetallic aerogels have emerged as promising unsupported and high-surface-area metal materials for different applications in heterogeneous catalysis and electrochemistry, which are fabricated using a gelation process characterized by the controlled aggregation of metallic nanoparticles to form a macroscopic network structure in aqueous solution. However, the achievement of the structural homogeneity of the multimetallic aerogels in terms of the diameter of the nanochains and the chemical composition at the nano- and the macro-scale is still a great challenge. In this paper, we investigated two Pd-Pt aerogels prepared by the two-step gelation method. The structural homogeneity and chemical distribution of both metals inside the aerogels were analyzed by using high-resolution (scanning) transmission microscopy, energy-dispersive X-ray spectroscopy, extended X-ray absorption fine structure spectroscopy and cyclic voltammetry. The Pd-Pt aerogels show the presence of Pd/Pt-rich domains inside the long-range framework. It is evident that the initial monometallic features dominate over alloying during the gelation process. Although the same synthetic approach for Pd-Pt aerogels with different atomic ratios was used, we observed that the sizes of these monometallic domains varied strongly between the Pd-rich and Pt-rich aerogels. The presence of such metal clusters influenced the electrochemical robustness of the Pd-Pt aerogels dramatically. Further, electrochemical durability investigations revealed that the aerogels with a high content of Pd are less stable because of the gradual dissolution of the less noble metal particularly inside the Pd-rich domains. A chemical and structural homogeneity might improve the lifetime of the Pd-Pt aerogels under electrochemical conditions. In this work, we provide a better understanding of the structure and chemical distribution of the bimetallic aerogel framework prepared by the two-step gelation process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Enhancing Plastic Recycling Through Nano-Scale Structure Analysis in Custom Block Copolymer Filaments (Rev.1)

As plastic production continues to increase, new methods to combat plastic waste are needed. This paper explores upcycling, a way to increase the utility or value of waste plastic. This can be done using block copolymers as compatibilizers. Block copolymers are made of two immiscible polymer blocks that phase separate on the nanoscale, forming small structures. The orientation of these nano-scale structures influences mechanical properties, and we show that orientation can be controlled by directional 3D (three dimensional) printing. Using small-angle X-ray scattering (SAXS), we analyze block copolymer filaments extruded at varying speeds. The SAXS data provide a baseline understanding of nano-scale structure in these unique filaments for future use in 3D printing experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Structure analysis of a Mn-doped willemite-type compound, H{sub 0.12}(Zn{sub 1.89(3)}Mn{sub 0.05(1)}□{sub 0.06})Si{sub 1.00(1)}O{sub 4}

Large single crystals of a well-known green phosphor, Mn-doped willemite (α-Zn{sub 2}SiO{sub 4})-type compound were grown from molten MnF{sub 2}/Li{sub 2}MoO{sub 4}. In this structure Mn{sup 2+} and defects partially replace Zn{sup 2+} at two independent sites, and there are no cation species in the middle of six-membered ring channels. As a consequence of 3% defective sites (□), this structure may have protons for ensuring its electrostatic neutrality. Although the position of H{sup +} could not be clearly found the present study indicates the presence of protons in the vicinity of oxygens to make relative short H⋯O bonds below 1.6 Å. Two unusual, broad IR bands about 1780 and 2360 cm{sup −1} can be explained by disordering of strongly bonded O···H groups. This compound represents a structural unit, H{sub 0.12}(Zn{sub 1.89(3)}Mn{sub 0.05(1)}□{sub 0.06})Si{sub 1.00(1)}O{sub 4}, based on X-ray single crystal diffraction, electron microprobe, and FT-IR spectroscopy. - Graphical abstract: A willemite-type compound, H{sub 0.12}(Zn{sub 1.89(3)}Mn{sub 0.05(1)}□{sub 0.06})Si{sub 1.00(1)}O{sub 4} exhibits protons near to oxygens in the skirt of four- and six-membered ring channels, as a result of defects at two crystallographically different Zn sites. Display Omitted - Highlights: • Structure properties of a 0.05 Mn-doped α-Zn{sub 2}SiO{sub 4} compound using X-ray single crystal diffraction. • Static disorder of Zn, Mn, and defects in the framework of α-Zn{sub 2}SiO{sub 4}. • Sign of strong H⋯O bonds, observed in FT-IR spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Contemporary Use of Anomalous Diffraction in Biomolecular Structure Analysis

The normal elastic X-ray scattering that depends only on electron density can be modulated by an ?anomalous? component due to resonance between X-rays and electronic orbitals. Anomalous scattering thereby precisely identifies atomic species, since orbitals distinguish atomic elements, which enables the multi- and single-wavelength anomalous diffraction (MAD and SAD) methods. SAD now predominates in de novo structure determination of biological macromolecules, and we focus here on the prevailing SAD method. We describe the anomalous phasing theory and the periodic table of phasing elements that are available for SAD experiments, differentiating between those readily accessible for at-resonance experiments and those that can be effective away from an edge. We describe procedures for present-day SAD phasing experiments and we discuss optimization of anomalous signals for challenging applications. We also describe methods for using anomalous signals as molecular markers for tracing and element identification. Emerging developments and perspectives are discussed in brief.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Molecular Basis for Genetic Resistance of Anopheles gambiae to Plasmodium : Structural Analysis of TEP1 Susceptible and Resistant Alleles

Thioester-containing protein 1 (TEP1) is a central component in the innate immune response of Anopheles gambiae to Plasmodium infection. Two classes of TEP1 alleles, TEP1*S and TEP1*R, are found in both laboratory strains and wild isolates, related by a greater or lesser susceptibility, respectively to both P. berghei and P. falciparum infection. We report the crystal structure of the full-length TEP1*S1 allele which, while similar to the previously determined structure of full-length TEP1*R1, displays flexibility in the N-terminal fragment comprising domains MG1-MG6. Amino acid differences between TEP1*R1 and TEP1*S1 are localized to the TED-MG8 domain interface that protects the thioester bond from hydrolysis and structural changes are apparent at this interface. As a consequence cleaved TEP1*S1 (TEP1*S1 cut ) is significantly more susceptible to hydrolysis of its intramolecular thioester bond than TEP1*R1 cut . TEP1*S1 cut is stabilized in solution by the heterodimeric LRIM1/APL1C complex, which preserves the thioester bond within TEP1*S1 cut . These results suggest a mechanism by which selective pressure on the TEP1 gene results in functional variation that may influence the vector competence of A. gambiae towards Plasmodium infection.

59 BASIC BIOLOGICAL SCIENCES↗