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At least 613 records · Page 34

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↗

Thermal and Structural Analysis of Helicopter Transmission Housings Using NASTRAN

The application of NASTRAN to improve the design of helicopter transmission housings is described. A finite element model of the complete forward rotor transmission housing for the Boeing Vertol CH-47C helicopter was used to study thermal distortion and stress, stress and deflection due to static and dynamic loads, load paths, and design optimization by the control of structural energy distribution. The analytical results are correlated with test data and used to reduce weight and to improve strength, service life, failsafety, and reliability. The techniques presented, although applied herein to helicopter transmissions, are sufficiently general to be applicable to any power transmission system.

Howells, R. W.↗

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↗

Structural analysis of stratocumulus convection

The 1 and 20 Hz data are examined from the Electra flights made on July 5, 1987. The flight legs consisted of seven horizontal turbulent legs at the inversion, midcloud, and below clouds, plus 4 soundings made within the same period. The Rosemont temperature sensor and the top and bottom dewpoint sensors were used to measure temperature and humidity at 1 Hz. Inversion structure and entrainment; local dynamics and large scale forcing; convective elements; and decoupling of cloud and subcloud are discussed in relationship to the results of the Electra flight.

Siems, S. T.↗

Structural Analysis of Inhibitor Binding to CAMKK1 Identifies Features Necessary for Design of Specific Inhibitors

The calcium/calmodulin-dependent protein kinases (CAMKKs) are upstream activators of CAMK1 and CAMK4 signalling and have important functions in neural development, maintenance and signalling, as well as in other aspects of biology such as Ca 2+ signalling in the cardiovascular system. To support the development of specific inhibitors of CAMKKs we have determined the crystal structure of CAMKK1 with two ATP-competitive inhibitors. The structures reveal small but exploitable differences between CAMKK1 and CAMKK2, despite the high sequence identity, which could be used in the generation of specific inhibitors. Screening of a kinase inhibitor library revealed molecules that bind potently to CAMKK1. Isothermal titration calorimetry revealed that the most potent inhibitors had binding energies largely dependent on favourable enthalpy. Together, the data provide a foundation for future inhibitor development activities.

59 BASIC BIOLOGICAL SCIENCES↗

Structural analysis of some sodium and alumina rich high-level nuclear waste glasses

Sodium and aluminum rich high level nuclear waste glasses are prone to nepheline (NaAlSiO4) crystallization. Since nepheline removes three moles of glass forming oxides (Al2O3 and SiO2) per each mole of Na2O, its formation can result in sever deterioration of the chemical durability. The present study aims at investigating the relationships between the molecular-level structure of sodium alumino-borosilicate based simulated high-level nuclear waste glasses and their crystallization behavior by infrared spectroscopy (FTIR) and x-ray diffraction, respectively. The molecular structure of most of the investigated glasses comprises of a mixture of Q2 and Q3 (Si) units while aluminum and boron are predominantly present in tetrahedral and trigonal coordination, respectively. The increasing boron content has been shown to suppress the nepheline formation in the glasses. The structural influence of various glass components on nepheline crystallization has been discussed.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Massive compression for high data rate macromolecular crystallography (HDRMX): impact on diffraction data and subsequent structural analysis

New higher-count-rate, integrating, large-area X-ray detectors with framing rates as high as 17400 images per second are beginning to be available. These will soon be used for specialized macromolecular crystallography experiments but will require optimal lossy compression algorithms to enable systems to keep up with data throughput. Some information may be lost. Can we minimize this loss with acceptable impact on structural information? To explore this question, we have considered several approaches: summing short sequences of images, binning to create the effect of larger pixels, use of JPEG-2000 lossy wavelet-based compression, and use of Hcompress, which is a Haar-wavelet-based lossy compression borrowed from astronomy. We also explore the effect of the combination of summing, binning, and Hcompress or JPEG-2000. In each of these last two methods one can specify approximately how much one wants the result to be compressed from the starting file size. These provide particularly effective lossy compressions that retain essential information for structure solution from Bragg reflections.

47 OTHER INSTRUMENTATION↗

Resonance Assignments and Secondary Structure Analysis of Dynein Light Chain 8 by Magic-angle Spinning NMR Spectroscopy

Dynein light chain LC8 is the smallest subunit of the dynein motor complex and has been shown to play important roles in both dynein-dependent and dynein-independent physiological functions via its interaction with a number of its binding partners. It has also been linked to pathogenesis including roles in viral infections and tumorigenesis. Structural information for LC8-target proteins is critical to understanding the underlying function of LC8 in these complexes. However, some LC8-target interactions are not amenable to structural characterization by conventional structural biology techniques owing to their large size, low solubility, and crystallization difficulties. Here, we report magic-angle spinning (MAS) NMR studies of the homodimeric apo-LC8 protein as a first effort in addressing more complex, multi-partner, LC8-based protein assemblies. We have established site-specific backbone and side-chain resonance assignments for the majority of the residues of LC8, and show TALOS+-predicted torsion angles ø and ψ in close agreement with most residues in the published LC8 crystal structure. Data obtained through these studies will provide the first step toward using MAS NMR to examine the LC8 structure, which will eventually be used to investigate protein–protein interactions in larger systems that cannot be determined by conventional structural studies.

Environmental Molecular Sciences Laboratory↗

Thermal structural analysis of the RCC chin panel

This paper presents the design constraints, flight environments, conceptual design iterations and analytical methods used in the design and flight certification of the Reinforced Carbon-Carbon (RCC) chin panel for the Space Shuttle Orbiter. A discussion of the thermal/structural response of the chin panel to the imposed environments is presented. As with all critical airframe components, it was desirable to conduct a structural test to verify design adequacy. However, with the chin panel, a meaningful test to simulate the critical thermal stresses was not considered feasible.

Bohlmann, Frank J.↗

Structural analysis of mycobacterial homoserine transacetylases central to methionine biosynthesis reveals druggable active site

Mycobacterium tuberculosis is the cause of the world’s most deadly infectious disease. Efforts are underway to target the methionine biosynthesis pathway, as it is not part of the host metabolism. The homoserine transacetylase MetX converts L-homoserine to O-acetyl-L-homoserine at the committed step of this pathway. In order to facilitate structure-based drug design, we determined the high-resolution crystal structures of three MetX proteins, including M. tuberculosis (MtMetX), Mycolicibacterium abscessus (MaMetX), and Mycolicibacterium hassiacum (MhMetX). A comparison of homoserine transacetylases from other bacterial and fungal species reveals a high degree of structural conservation amongst the enzymes. Utilizing homologous structures with bound cofactors, we analyzed the potential ligandability of MetX. The deep active-site tunnel surrounding the catalytic serine yielded many consensus clusters during mapping, suggesting that MtMetX is highly druggable.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ECAR-6585 MARVEL Core Support Structure Analysis: Project #33526

Idaho National Laboratory (INL) is developing a small microreactor to produce electrical power utilizing a small nuclear core and stirling engines for power output under the Microreactor Application Research Validation and Evaluation (MARVEL) program. The MARVEL Reactor (Figure 1) will be installed in the Transient Reactor Test (TREAT) Facility. Walsh Engineering Services, PC (WES) has contracted with the INL to detail the final design. There are six main systems in the MARVEL, one of which is the Fuel and Core System (FCS). The FCS contains a subsystem–the Core Support Structures Subsystem (CSS)–that supports and orients each of the 36 nuclear fuel pins in the MARVEL Reactor System. The FCS (apart from the fixed Beryllium Oxide radial reflectors) is shown in light green and is depicted in more detail in Figure 1 and Figure 2. The main subject of this analysis is the lower grid plate, which is the principal item in the CSS which supports the fuel, see Figure 3. Additionally, the upper grid plate thermal expansion of the upper grid plate is presented in Appendix A.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Multi-technique structural analysis of zinc carboxylates (soaps)

A series of medium- and long-chain zinc carboxylates (zinc octanoate, zinc nonanoate, zinc decanoate, zinc undecanoate, zinc dodecanoate, zinc pivalate, zinc stearate, zinc palmitate, zinc oleate, and zinc azelate) was analyzed by ultra-high-field 67 Zn NMR spectroscopy up to 35.2 T, as well as 13 C NMR and FTIR spectroscopy. We also report the single-crystal X-ray diffraction structures of zinc nonanoate, zinc decanoate, and zinc oleate—the first long-chain carboxylate single-crystals to be reported for zinc. The NMR and X-ray diffraction data suggest that the carboxylates exist in three distinct geometric groups, based on structural and spectroscopic parameters. The ssNMR results presented here present a future for dynamic nuclear polarization (DNP)-NMR-based minimally invasive methods for testing artwork for the presence of zinc carboxylates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

3D structure analysis of PAKs: A clue to the rational design for affinity reagents and blockers

The p21-activated kinase (PAK) family plays a versatile role in cell signaling by forming a hub of interactions. PAKs bind the GTPases like RAC and CDC42. Their proline-rich motifs bind SH3 adaptor proteins such as PIX and NCK. PAKs display nuclear localization signal sites and a potential Integrin binding site. No fully complete structure of the PAKs has been published; partial 3D structures of the PAK family kinases include portions of the auto-inhibited PAK1, GTPase bound to small peptides from PAKs, and the kinase domains from PAK1 and PAK4–6 (with small ligands in a few cases). This review focuses on exploring the intermolecular interaction regions in these 3D structures and we offer insights on the missing regions in crystal structure of the auto-inhibited PAK1. Understanding and modulation of PAK intermolecular interactions can pave the way for PAK blockers and biosensors.

59 BASIC BIOLOGICAL SCIENCES↗

Structure analysis of BaCe{sub 0.8}Y{sub 0.2}O{sub 3−δ} in dry and wet atmospheres by high-temperature X-ray diffraction measurement

High temperature X-ray diffraction measurements were performed under dry and wet atmospheres to investigate phase behavior of BaCe{sub 0.8}Y{sub 0.2}O{sub 3−δ} (BCY20). In the temperature range of 30–400 °C, BCY20 was identified to be rhombohedral and monoclinic structures in dry and wet atmospheres, respectively. Larger lattice volumes were obtained in a wet atmosphere due to a chemical expansion induced by water incorporation. A gradual change in diffraction peak shape due to a phase transformation from rhombohedral to monoclinic was observed at 300 °C when moisture was introduced into the atmosphere. These results indicated clearly the dependence of phase behavior of BCY20 on partial pressure of water vapor in atmosphere. - Graphical abstract: A BaCe{sub 0.8}Y{sub 0.2}O{sub 3−δ} rhombohedral phase transited to a monoclinic phase at 300 °C when moisture was introduced into the atmosphere. Display Omitted - Highlights: • Different structures for hydrated and dehydrated BaCe{sub 0.8}Y{sub 0.2}O{sub 3−δ} (BCY20). • Slow phase transition from rhombohedral to monoclinic at 300 °C in wet atmosphere. • Chemical expansion of BCY20 in wet atmosphere. • Importance of considering moisture when discussing phase behavior of BCY20.

36 MATERIALS SCIENCE↗

Structural analysis of the Sil1-Bip complex reveals the mechanism for Sil1 to function as a nucleotide-exchange factor

Sil1 functions as a NEF (nucleotide-exchange factor) for the ER (endoplasmic reticulum) Hsp70 (heat-shock protein of 70 kDa) Bip in eukaryotic cells. Sil1 may catalyse the ADP release from Bip by interacting directly with the ATPase domain of Bip. In the present study we show the complex crystal structure of the yeast Bip and the NEF Sil1 at the resolution of 2.3 {angstrom} (1 {angstrom} = 0.1 nm). In the Sil1-Bip complex structure, the Sil1 molecule acts as a 'clamp' which binds lobe IIb of the Bip ATPase domain. The binding of Sil1 causes the rotation of lobe IIb {approx} 13.5{sup o} away from the ADP-binding pocket. The complex formation also induces lobe Ib to swing in the opposite direction by {approx} 3.7{sup o}. These conformational changes open up the nucleotide-binding pocket in the Bip ATPase domain and disrupt the hydrogen bonds between Bip and bound ADP, which may catalyse ADP release. Mutation of the Sil1 residues involved in binding the Bip ATPase domain compromise the binding affinity of Sil1 to Bip, and these Sil1 mutants also abolish the ability to stimulate the ATPase activity of Bip.

59 BASIC BIOLOGICAL SCIENCES↗

Finite-Element Modeling For Structural Analysis

Report presents study of finite-element mathematical modeling as used in analyzing stresses and strains at joints between thin, shell-like components (e.g., ducts) and thicker components (e.g., flanges or engine blocks). First approach uses global/local model to evaluate system. Provides correct total response and correct representation of stresses away from any discontinuities. Second approach involves development of special transition finite elements to model transitions between shells and thicker structural components.

Min, J. B.↗

Structure Analysis of a Precipitate Phase in an Ni-Rich High Temperature NiTiHf Shape Memory Alloy

Thermal aging of the high temperature shape memory alloy 50.3Ni-29.7Ti-20Hf (at.%) introduces a novel precipitate phase, which plays an important role in improving shape memory properties. The precipitate phase was investigated by conventional electron diffraction, high resolution scanning transmission electron microscopy (STEM) and three dimensional atom probe tomography. An unrelaxed orthorhombic atomic structural model is proposed based on these observations. This model was subsequently relaxed by ab initio calculations. As a result of the relaxation, atom shuffle displacements occur, which in turn yields improved agreement with the STEM images. The relaxed structure, which is termed the “H-phase”, has also been verified to be thermodymanically stable at 0 K.

Atom probe tomography, Ni-Ti-Hf alloy, shape memor↗

Local structure analysis of diluted magnetic semiconductor Co and Al co-doped ZnO nanoparticles

In this study, Co and Al ions co-doped ZnO nanoparticles (Zn(Al, Co)O NPs) were prepared by our original chemical preparation method. The obtained samples prepared by this method, were encapsulated in amorphous SiO{sub 2}. X-ray diffraction (XRD) results showed Zn(Al, Co)O NPs had a single-phase nature with hexagonal wurtzite structure. These particle sizes could be controlled to be approximately 30 nm. We investigate the effect that the increase in the carrier has on the magnetization by doping Al to Co-doped ZnO NPs. The local structures were qualitatively analyzed using X-ray absorption fine structure (XAFS) measurements.

36 MATERIALS SCIENCE↗