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At least 793 records · Page 44

Structural elucidation of the cis -prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation

Cis-prenyltransferase (cis-PTase) catalyzes the rate-limiting step in the synthesis of glycosyl carrier lipids required for protein glycosylation in the lumen of endoplasmic reticulum. Here, we report the crystal structure of the human NgBR/DHDDS complex, which represents an atomic resolution structure for any heterodimeric cis-PTase. The crystal structure sheds light on how NgBR stabilizes DHDDS through dimerization, participates in the enzyme’s active site through its C-terminal -RXG- motif, and how phospholipids markedly stimulate cis-PTase activity. Comparison of NgBR/DHDDS with homodimeric cis-PTase structures leads to a model where the elongating isoprene chain extends beyond the enzyme’s active site tunnel, and an insert within the α3 helix helps to stabilize this energetically unfavorable state to enable long-chain synthesis to occur. These data provide unique insights into how heterodimeric cis-PTases have evolved from their ancestral, homodimeric forms to fulfill their function in long-chain polyprenol synthesis.

59 BASIC BIOLOGICAL SCIENCES↗

Bimetallic Coinage Metal Complexes of Tetradentate ortho Ter arylene Ligands

The synthesis, structural and photophysical properties of five bimetallic coinage metal complexes of three tetradentate charge-transfer (CT) ligands are presented. The ligand structures incorporate donor/acceptor moieties electronically decoupled by ortho connection to a bridging biphenylene group. The M M distances observed in the crystal structures of the bimetallic complexes are shorter than the sum of the Van der Waals radii of the metal ions, suggesting stabilizing interactions between the d10 metal centers. Additionally, short distances between the bridging biphenylene and metal atoms suggest arylene metal interactions. Bimetallic Cu, Ag, and Au complexes of the ligand incorporating a carbazole donor and pyridyl acceptor (N2R22-) show absorption and emission energies that trend with the ionization potential of each metal, indicating metal character in the excited state. These properties contrast with our previously reported mononuclear Zn complex of N2R22-The structural and photophysical properties of five bimetallic d10 coinage metal complexes were presented. The M M distances observed in the crystal structures of the bimetallic complexes are shorter than the sum of the metals’ Van der Waals radii, suggesting attractive interactions between the d10 metal centers. Additionally, short distances between the bridging biphenylene and metal atoms suggest arylene metal interactions. The absorption and emission spectra of the bimetallic complexes redshift based on the oxidation potential of the metal ion. This suggests involvement of metal based orbitals in the excited state transitions of the bimetallic complexes, which was corroborated by molecular modeling. High photoluminescent quantum yields were observed in solution and in rigid media (up to PL = 0.75), and the excited state lifetimes in solution were found to exceed several microseconds.

Shariaty, Darius Allen [University of Southern Cal↗

Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes

Unraveling the metabolism of Treponema pallidum is a key component to understanding the pathogenesis of the human disease that it causes, syphilis. For decades, it was assumed that glucose was the sole carbon/energy source for this parasitic spirochete. But the lack of citric-acid-cycle enzymes suggested that alternative sources could be utilized, especially in microaerophilic host environments where glycolysis should not be robust. Recent bioinformatic, biophysical, and biochemical evidence supports the existence of an acetogenic energy-conservation pathway in T . pallidum and related treponemal species. In this hypothetical pathway, exogenous D-lactate can be utilized by the bacterium as an alternative energy source. Herein, we examined the final enzyme in this pathway, acetate kinase (named TP0476), which ostensibly catalyzes the generation of ATP from ADP and acetyl-phosphate. We found that TP0476 was able to carry out this reaction, but the protein was not suitable for biophysical and structural characterization. We thus performed additional studies on the homologous enzyme (75% amino-acid sequence identity) from the oral pathogen Treponema vincentii , TV0924. This protein also exhibited acetate kinase activity, and it was amenable to structural and biophysical studies. We established that the enzyme exists as a dimer in solution, and then determined its crystal structure at a resolution of 1.36 Å, showing that the protein has a similar fold to other known acetate kinases. Mutation of residues in the putative active site drastically altered its enzymatic activity. A second crystal structure of TV0924 in the presence of AMP (at 1.3 Å resolution) provided insight into the binding of one of the enzyme’s substrates. On balance, this evidence strongly supported the roles of TP0476 and TV0924 as acetate kinases, reinforcing the hypothesis of an acetogenic pathway in pathogenic treponemes.

Deka, Ranjit K.↗

Orientational Disorder of NH3 in Hexammine Magnesium Borohydride

Hexammine magnesium borohydride, Mg(NH3)6(BH4)2, consists of adducted NH3 molecules locked in a matrix of Mg cations and borohydride anions. It is a candidate material for hydrogen storage, with 16.8 wt % hydrogen stored in both the NH3 and borohydride anions. It may also be of interest as an Mg2+-conducting electrolyte in solid-state batteries. Its crystal structure has, until now, eluded a proper structural solution due to ambiguity regarding the NH3 position and behavior. In this work, we show using synchrotron X-ray diffraction that the room-temperature structure can be solved only with a model assuming the orientational disorder of ammonia molecules within the crystal structure. Cooling the sample to 120 K yields additional Bragg peaks, which can be solved only with a unit cell expansion consistent with the freezing of the orientational freedom of ammonia molecules. Using this insight from the structure solution, we performed a full assignment of the vibrational modes in the room-temperature infrared spectrum.

08 HYDROGEN↗

Statistically averaged molecular dynamics simulations of hydrogen diffusion in magnesium and magnesium hydrides

Magnesium has a different crystal structure from its dihydride with hydrogenation leading to a phase transition from the hexagonal closely packed Mg into a tetragonal α-MgH 2 rutile type structure. Such materials exhibit complex hydrogen uptake and release kinetics because hydrogen diffusivities significantly change when the crystal structure changes. To provide a foundational understanding of (de)hydrogenation kinetics that is applicable to all stages of the reaction, we performed statistically averaged molecular dynamics simulations to derive hydrogen diffusivities as a function of temperature and hydrogen content for both magnesium and magnesium hydride. Furthermore, our studies confirm that hydrogen diffusivities in magnesium hydride are much lower than in magnesium, in agreement with experimental data. Additionally, we observe that in either magnesium or magnesium hydride, higher hydrogen compositions result in reduced diffusivities. The latter was not revealed by prior experiments, which were conducted at fixed hydrogen composition. Finally, we discover a non-Arrhenius behavior in magnesium hydride. The physical origin of this behavior is also discussed.

36 MATERIALS SCIENCE↗

Intermediate phases in some rare earth-ruthenium systems

The phase equilibria and crystal structures of intermediate phases were investigated in eight representative RE-Ru systems using powder X-ray diffraction and metallographic techniques. The Fe3C, Mn5C2 and Er5Ru3 structures occur in all but the Ce-Ru systems. Phases analogous to Er5Ru3 possess an unknown crystal structure similar to Er5Rh3(I). MgCu2 and MgZn2 type Laves phases are encountered in the light rare earth and heavy rare earth systems, respectively, and RERu2 phases, where RE = Nd and Sm, possess both the Laves phase structures. An intermediate phase, NdRu, with an unknown structure, occurs only in the Nd-Ru system. A bcc structure with 40 atoms per unit cell is encountered in the phases Er3Ru2 and Y3Ru2. The behavior of cerium in Ce-Ru alloys is unique in that four unidentified structures, not encountered in other RE-Ru systems, have been encountered. Also a phase designated as Ce3Ru is found with the Th7Fe3 type structure.

Sharifrazi, P.↗

Pinning, flow and plastic deformation of flux vortices in high T(sub c) superconductors

In high temperature superconductor (HTSC) materials the vortices are highly mobile and flexible. This is reflected in different models of melt of a vortex lattice. Another aspect of the problem is stressed: an easy nucleation and high mobility of dislocations in the vortex lattice. Some models of plastic deformation of vortex lattice are considered as a result of its interaction with a real crystal structure. Depinning is interpreted as yield of plastic flow is vortex medium. Effect of macroscopic defects in crystal structures (pores, inclusions, grain and domain boundaries) is being considered in detail. Available experimental facts on magnetization and a critical current in HTSC and conventional superconductors are discussed from the points of view of depinning to vortices vs. plastic flow of vortices vs. plastic flow of vortices medium.

Roytburd, A.↗

Airborne Measurements of Cirrus Reflectance and Heights with Comparison to Polder Observations

The NASA ER-2 high altitude aircraft cloud observation experiment includes visible, infrared and microwave radiometric imaging of cloud tops and combined lidar profiling of cloud tops. A special instrument is the Tilt Scan CCD Camera (TSCC) for measurements of cloud top multidirectional reflectance and polarization. Data have been acquired on the bi-directional reflectance of cirrus in the FIRE, TOGA/COARE, SUCCESS and WINCE cloud observation experiments. The FIRE, TOGA/COARE and SUCCESS observations include some cases of combined in situ crystal measurements and in all measurements, multispectral visible/IR cirrus microphysics retrievals are possible. The results for bi-directional reflectance for mid-latitude cirrus in the FIRE and SUCCESS missions are consistent with models for complex, multi-type crystal structure. These may be contrasted with tropical cirrus observation for which results are more typical of simple crystal structure. The cirrus multidirectional results may be compared and contrasted with those available from POLDER. In addition, during the WINCE experiment of January 1997 there were several targeted ER-2 for cloud observation underflights of POLDER on ADEOS, Comparison of direct cloud height measurement and multispectral radiometer analysis from ER-2 data with POLDER results are made.

Spinhirne, James↗

Measuring Shock Stage of ltokawa Regolith Grains by Electron Back-Scattered Diffraction and Synchrotron X-Ray Diffraction

We have been analyzing Itokawa samples in order to definitively establish the degree of shock experienced by the regolith of asteroid Itokawa, and to devise a bridge between shock determinations by standard light optical petrography, crystal structures as determined by electron and X-ray diffraction techniques. We are making measurements of olivine crystal structures and using these to elucidate critical regolith impact processes. We use electron back-scattered diffraction (EBSD) and synchrotron X-ray diffraction (SXRD). We are comparing the Itokawa samples to L and LL chondrite meteorites chosen to span the shock scale experienced by Itokawa, specifically Chainpur (LL3.4, Shock Stage 1), Semarkona (LL3.00, S2), Kilabo (LL6, S3), NWA100 (L6, S4) and Chelyabinsk (LL5, S4). In SXRD we measure the line broadening of olivine reflections as a measure of shock stage. In this presentation we concentrate on the EBSD work. We employed JSC's Supra 55 variable pressure FEG-SEM and Bruker EBSD system. We are not seeking actual strain values, but rather indirect strain-related measurements such as extent of intra-grain lattice rotation, and determining whether shock state "standards" (meteorite samples of accepted shock state, and appropriate small grain size) show strain measurements that may be statistically differentiated, using a sampling of particles (number and size range) typical of asteroid regoliths. Using our system we determined that a column pressure of 9 Pa and no C-coating on the sample was optimal. We varied camera exposure time and gain to optimize mapping performance, concluding that 320x240 pattern pixilation, frame averaging of 3, 15 kV, and low extractor voltage yielded an acceptable balance of hit rate (>90%), speed (11 fps) and map quality using an exposure time of 30 ms (gain 650). We found that there was no strong effect of step size on Grain Orientation Spread (GOS) and Grain Reference Orientation Deviation angle (GROD-a) distribution; there was some effect on grain average Kernel Average Misorientation (KAM) (reduced with smaller step size for the same grain), as expected. We monitored GOS, Maximum Orientation Spread (MOS) and GROD-a differences between whole olivine grains and sub-sampled areas, and found that there were significant differences between the whole grain dataset and subsets, as well as between subsets, likely due to sampling-related "noise". Also, in general (and logically) whole grains exhibit greater degrees of cumulative lattice rotation. Sampling size affects the apparent strain character of the grain, at least as measured by GOS, MOS and GROD-a. There were differences in the distribution frequencies of GOS and MOS between shock stages, and in plots of MOS and GOS vs. grain diameter. These results are generally consistent with those reported this year. However, it is unknown whether the differences between samples of different shock states exceeds the clustering of these values to the extent that shock stage determinations can still be made with confidence. We are investigating this by examination of meteorites with higher shock stage 4 to 5. Our research will improve our understanding of how small, primitive solar system bodies formed and evolved, and improve understanding of the processes that determine the history and future of habitability of environments on other solar system bodies. The results will directly enrich the ongoing asteroid and comet exploration missions by NASA and JAXA, and broaden our understanding of the origin and evolution of small bodies in the early solar system, and elucidate the nature of asteroid and comet regolith.

Zolensky, Michael↗

Observation of high-pressure polymorphs in bulk silicon formed at relativistic laser intensities

Silicon polymorphs with exotic electronic and optical properties have recently attracted significant attention due to their wide range of useful band gap characteristics. They are typically formed by static high-pressure techniques, which limits the crystal structures that can be made. This constitutes a major obstacle to study these polymorphs and their incorporation into existing technology. Approaches have attempted to address this shortcoming through using dynamic conditions and chemical precursor materials. Here, we report on an approach to create unusual crystal structures deep in the bulk of a silicon crystal by irradiating it with a laser pulse at ultrarelativistic intensity of up to 7.5 × 10 19 W/ c m 2 . Laser-generated electrons with MeV energy swiftly penetrate the target with speed close to the speed of light and deposit their energy into a large volume across the whole thickness of the sample. The relativistic electron current creates, via branching propagation and ionization, high-energy-density conditions for thermodynamically nonequilibrium phase transformation paths into new crystal polymorphs. X-ray microdiffraction and synchrotron x-ray diffraction analyses indicate, along with conventional dc-Si, the presence of exotic silicon structures in the bulk of the laser intact target volume. These structures are identified as body-centered bc8-Si, rhombohedral r8-Si, hexagonal-diamond hd-Si, and the tetragonal Si-VIII, all phases of Si that have previously been made through static techniques. Additionally, simple-tetragonal st12-Si and body-centered tetragonal bt8-Si were observed along with signatures of not yet identified diffraction spots. Both st12-Si and bt8-Si have only been observed in ultrafast laser microexplosion conditions at much lower laser intensity ∼ 10 14 W/ c m 2 and within a micron-thin surface layer. The findings here are supported by direct observation of nanoparticles with high-resolution transmission electron microscopy and corresponding fast Fourier transform analysis of their interatomic distances. The presented analyses of absorbed laser energy, generation of the MeV electron current, and deposition of energy across the whole target thickness provide a solid basis for drawing the conclusion that the observed silicon polymorphs were produced because of laser-generated high-energy electrons fast-penetrating deeply into the bulk of silicon. In contrast to solid-solid transformations, the plasma-solid transitions offer a paradigm for the creation of exotic, high-energy density materials inside the bulk of the sample by using laser pulses at relativistic intensities. Published by the American Physical Society 2024

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Definitive Mineralogical Analysis of Martian Rocks and Soil Using the CheMin XRD/XRF Instrument and the USDC Sampler

The search for evidence of extant or extinct life on Mars will initially be a search for evidence of present or past conditions supportive of life (e.g., evidence of water), not for life itself. Definitive evidence of past or present water activity lies in the discovery of: * Hydrated minerals: The "rock type" hosting the hydrated minerals could be igneous, metamorphic, or sedimentary, with only a minor hydrated mineral phase. Therefore, the identification of minor phases is important. * Clastic sediments: Clastic sediments are commonly identified by the fact that they contain minerals of disparate origin that could only have come together as a mechanical mixture. Therefore, the identification of all minerals present in a mixture to ascertain mineralogical source regions is important. * Hydrothermal precipitates and chemical sediments: Some chemical precipitates are uniquely identified only by their structure. For example, Opal A, Opal CT, tridymite, crystobalite, high and low Quartz all have the same composition (SiO2) but different crystal structures indicative of different environments - from hydrothermal hydrothermal formation to low temperature precipitation. Other silica types such as stishovite can provide evidence of shock metamorphism. Therefore, identification of crystal structures and structural polymorphs is important. The elucidation of the nature of the Mars soil will require the identification of mineral components that can unravel its history and the history of the Mars atmosphere.

D F Blake↗

Structure-Spin-Transport Anomaly in Quasi-One-Dimensional Ba9Fe3Te15 under High Pressure

Recently, a series of novel compounds Ba3MX5 (M= Fe, Ti, V; X=Se, Te) with hexagonal crystal structures composed of quasi-1-dimensional (1D) magnetic chains has been synthesized by our research team using high-pressure and high-temperature methods. The initial hexagonal phases persist to the maximum achievable pressure, while spin configurations and magnetic interactions may change dramatically as a result of considerable reductions in interchain separations upon pressurization. These compounds therefore offer unique possibilities for studying the evolution of intrinsic electronic structures in quasi-1D magnetic systems. Here we present a systematic investigation of Ba9Fe3Te15, in which the interchain separations between trimerized 1D chains (~10.2 Å) can be effectively modulated by external high pressure. The crystal structure especially along the 1D chains exhibits an abnormal expansion at ~5GPa, which accompanies trimerization entangled anomalous mixed-high-low spin transition. An insulator-metal transition has been observed under high pressure as a result of charge-transfer gap closing. Pressure-induced superconductivity emerges at 26GPa, where the charge-transfer gap fully closes, 3D electronic configuration forms and local spin fully collapses.

Zhang, Jun↗

Structures of Astromaterials Revealed by EBSD

Groups at the Johnson Space Center and the University of Tokyo have been using electron back-scattered diffraction (EBSD) to reveal the crystal structures of extraterrestrial minerals for many years. Even though we also routinely use transmission electron microscopy, synchrotron X-ray diffraction (SXRD), and conventional electron diffraction, we find that EBSD is the most powerful technique for crystal structure elucidation in many instances. In this talk I describe a few of the cases where we have found EBSD to provide crucial, unique information. See attachment.

Zolensky, M.↗

Synthesis and properties of anhydrous rare-earth phosphates, monazite and xenotime: a review

The synthesis methods, crystal structures, and properties of anhydrous monazite and xenotime (REPO 4 ) crystalline materials are summarized within this review. For both monazite and xenotime, currently available Inorganic Crystal Structure Database data were used to study the effects of incorporating different RE cations on the unit cell parameters, cell volumes, densities, and bond lengths. Domains of monazite-type and xenotime-type structures and other AXO4 compounds (A = RE; X = P, As, V) are discussed with respect to cation sizes. Reported chemical and radiation durabilities are summarized. Different synthesis conditions and chemicals used for single crystals and polycrystalline powders, as well as first-principles calculations of the structures and thermophysical properties of these minerals are also provided.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography

The genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus has a capping modification at the 5'-untranslated region (UTR) to prevent its degradation by host nucleases. These modifications are performed by the Nsp10/14 and Nsp10/16 heterodimers using S-adenosylmethionine as the methyl donor. Nsp10/16 heterodimer is responsible for the methylation at the ribose 2'-O position of the first nucleotide. To investigate the conformational changes of the complex during 2'-O methyltransferase activity, we used a fixed-target serial synchrotron crystallography method at room temperature. We determined crystal structures of Nsp10/16 with substrates and products that revealed the states before and after methylation, occurring within the crystals during the experiments. Here we report the crystal structure of Nsp10/16 in complex with Cap-1 analog ( m7 GpppA m2'-O ). Inhibition of Nsp16 activity may reduce viral proliferation, making this protein an attractive drug target.

59 BASIC BIOLOGICAL SCIENCES↗

A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models

Interactions between WD40 repeat domain protein 5 (WDR5) and its various partners such as mixed lineage leukemia (MLL) and c-MYC are essential for sustaining oncogenesis in human cancers. However, inhibitors that block protein-protein interactions (PPIs) between WDR5 and its binding partners exhibit modest cancer cell killing effects and lack in vivo efficacy. Here, we present pharmacological degradation of WDR5 as a promising therapeutic strategy for treating WDR5-dependent tumors and report two high-resolution crystal structures of WDR5-degrader-E3 ligase ternary complexes. We identified an effective WDR5 degrader via structure-based design and demonstrated its in vitro and in vivo antitumor activities. On the basis of the crystal structure of an initial WDR5 degrader in complex with WDR5 and the E3 ligase von Hippel–Lindau (VHL), we designed a WDR5 degrader, MS67, and demonstrated the high cooperativity of MS67 binding to WDR5 and VHL by another ternary complex structure and biophysical characterization. MS67 potently and selectively depleted WDR5 and was more effective than WDR5 PPI inhibitors in suppressing transcription of WDR5-regulated genes, decreasing the chromatin-bound fraction of MLL complex components and c-MYC, and inhibiting the proliferation of cancer cells. In addition, MS67 suppressed malignant growth of MLL-rearranged acute myeloid leukemia patient cells in vitro and in vivo and was well tolerated in vivo. Collectively, our results demonstrate that structure-based design can be an effective strategy to identify highly active degraders and suggest that pharmacological degradation of WDR5 might be a promising treatment for WDR5-dependent cancers.

99 GENERAL AND MISCELLANEOUS↗

Fundamentals and emerging optical applications of hexagonal boron nitride: a tutorial

Hexagonal boron nitride (hBN), also known as white graphite, is a transparent layered crystal with a wide bandgap. Its crystal structure resembles graphite, featuring layers composed of honeycomb lattices held together through van der Waals forces. The layered crystal structure of hBN facilitates exfoliation into thinner flakes and makes it highly anisotropic in in-plane and out-of-plane directions. Unlike graphite, hBN is both insulating and transparent, making it an ideal material for isolating devices from the environment and acting as a waveguide. As a result, hBN has found extensive applications in optical devices, electronic devices, and quantum photonic devices. This comprehensive tutorial aims to provide readers with a thorough understanding of hBN, covering its synthesis, lattice and spectroscopic characterization, and various applications in optoelectronic and quantum photonic devices. This tutorial is designed for both readers without prior experience in hBN and those with expertise in specific fields seeking to understand its relevance and connections to others.

36 MATERIALS SCIENCE↗

Deep Optical Switching on Subpicosecond Timescales in an Amorphous Ge Metamaterial

Active nanostructured optical components show promise as potential building blocks for novel light-based computing and data processing architectures. However, nanoscale all-optical switches that have low activation powers and high-contrast ultrafast switching have been elusive so far. Here, pump–probe measurements performed on amorphous-Ge-based micro-resonator metasurfaces that exhibit strong resonant modes in the mid-infrared are reported. Relative change is observed in transmittance of ΔT/T ≈ 1 with picosecond (down to τ ≈ 0.5 ps) free carrier relaxation rates, obtained with very low pump fluences of 50 μJ cm –2 . In this work, these observations are attributed to efficient free carrier promotion, affecting light transmittance via high quality-factor optical resonances, followed by an increased electron–phonon scattering of free carriers due to the amorphous crystal structure of Ge. Full-wave simulations based on a permittivity model that describes free-carrier damping through crystal structure disorder find excellent agreement with the experimental data. These findings offer an efficient and robust platform for all-optical switching at the nanoscale.

36 MATERIALS SCIENCE↗