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At least 271 records · Page 15

Cryo-FIB for TEM Investigation of Soft Matter and Beam Sensitive Energy Materials

Primarily driven by structural biology, the rapid advances in cryogenic electron microscopy techniques are now being adopted and applied by materials scientists. Samples that inherently have electron transparency can be rapidly frozen (vitrified) in amorphous ice and imaged directly on a cryogenic transmission electron microscopy (cryo-TEM), however this is not the case for many important materials systems, which can consist of layered structures, embedded architectures, or be contained within a device. Cryogenic focused ion beam (cryo-FIB) lift-out procedures have recently been developed to extract intact regions and interfaces of interest, that can then be thinned to electron transparency and transferred to the cryo-TEM for characterization. Several detailed studies have been reported demonstrating the cryo-FIB lift-out procedure, however due to its relative infancy in materials science improvements are still required to ensure the technique becomes more accessible and routinely successful. Here, we review recent results on the preparation of cryo-TEM lamellae using cryo-FIB and show that the technique is broadly applicable to a range of soft matter and beam sensitive energy materials. We then present a tutorial that can guide the materials scientist through the cryo-FIB lift-out process, highlighting recent methodological advances that address the most common failure points of the technique, such as needle attachment, lift-out and transfer, and final thinning.

36 MATERIALS SCIENCE↗

Cryo-FIB for TEM Investigation of Soft Matter and Beam Sensitive Energy Materials

Primarily driven by structural biology, the rapid advances in cryogenic electron microscopy techniques are now being adopted and applied by materials scientists. Samples that inherently have electron transparency can be rapidly frozen (vitrified) in amorphous ice and imaged directly on a cryogenic transmission electron microscopy (cryo-TEM), however this is not the case for many important materials systems, which can consist of layered structures, embedded architectures, or be contained within a device. Cryogenic focused ion beam (cryo-FIB) lift-out procedures have recently been developed to extract intact regions and interfaces of interest, that can then be thinned to electron transparency and transferred to the cryo-TEM for characterization. Several detailed studies have been reported demonstrating the cryo-FIB lift-out procedure, however due to its relative infancy in materials science improvements are still required to ensure the technique becomes more accessible and routinely successful. Here, we review recent results on the preparation of cryo-TEM lamellae using cryo-FIB and show that the technique is broadly applicable to a range of soft matter and beam sensitive energy materials. We then present a tutorial that can guide the materials scientist through the cryo-FIB lift-out process, highlighting recent methodological advances that address the most common failure points of the technique, such as needle attachment, lift-out and transfer, and final thinning.

36 MATERIALS SCIENCE↗

Spherical Cryogenic Hydrogen Tank Preliminary Design Trade Studies

A structural analysis, sizing optimization, and weight prediction study was performed by Collier Research Corporation and NASA Glenn on a spherical cryogenic hydrogen tank. The tank consisted of an inner and outer wall separated by a vacuum for thermal insulation purposes. HyperSizer (Collier Research and Development Corporation), a commercial automated structural analysis and sizing software package was used to design the lightest feasible tank for a given overall size and thermomechanical loading environment. Weight trade studies were completed for different panel concepts and metallic and composite material systems. Extensive failure analyses were performed for each combination of dimensional variables, materials, and layups to establish the structural integrity of tank designs. Detailed stress and strain fields were computed from operational temperature changes and pressure loads. The inner tank wall is sized by the resulting biaxial tensile stresses which cause it to be strength driven, and leads to an optimum panel concept that need not be stiffened. Conversely, the outer tank wall is sized by a biaxial compressive stress field, induced by the pressure differential between atmospheric pressure and the vacuum between the tanks, thereby causing the design to be stability driven and thus stiffened to prevent buckling. Induced thermal stresses become a major sizing driver when a composite or hybrid composite/metallic material systems are used for the inner tank wall for purposes such as liners to contain the fuel and reduce hydrogen permeation.

Arnold, Steven M.↗

Superplastic forming of Al-Li alloys for lightweight, low-cost structures

Superplastic forming of advanced aluminum alloys is being evaluated as an approach for fabricating low-cost, light-weight, cryogenic propellant tanks. Built-up structure concepts (with inherent reduced scrap rate) are under investigation to offset the additional raw material expenses incurred by using aluminum lithium alloys. This approach to fabrication offers the potential for significant improvements in both structural efficiency and overall manufacturing costs. Superplasticity is the ability of specially processed material to sustain very large forming strains without failure at elevated temperatures under controlled deformation conditions. It was demonstrated that superplastic forming technology can be used to fabricate complex structural components in a single operation and increase structural efficiency by as much as 60 percent compared to conventional configurations in skin-stiffened structures. Details involved in the application of this technology to commercial grade superplastic aluminum lithium material are presented. Included are identification of optimum forming parameters, development of forming procedures, and assessment of final part quality in terms of cavitation volume and thickness variation.

Hales, Stephen J.↗

Photogrammetric Metrology for the James Webb Space Telescope Integrated Science Instrument Module

The James Webb Space Telescope (JWST) is a 6.6m diameter, segmented, deployable telescope for cryogenic IR space astronomy (approximately 40K). The JWST Observatory architecture includes the Optical Telescope Element and the Integrated Science Instrument Module (ISIM) element that contains four science instruments (SI) including a Guider. The ISM optical metering structure is a roughly 2.2x1.7x2.2m, asymmetric frame that is composed of carbon fiber and resin tubes bonded to invar end fittings and composite gussets and clips. The structure supports the SIs, isolates the SIs from the OTE, and supports thermal and electrical subsystems. The structure is attached to the OTE structure via strut-like kinematic mounts. The ISIM structure must meet its requirements at the approximately 40K cryogenic operating temperature. The SIs are aligned to the structure's coordinate system under ambient, clean room conditions using laser tracker and theodolite metrology. The ISIM structure is thermally cycled for stress relief and in order to measure temperature-induced mechanical, structural changes. These ambient-to-cryogenic changes in the alignment of SI and OTE-related interfaces are an important component in the JWST Observatory alignment plan and must be verified. We report on the planning for and preliminary testing of a cryogenic metrology system for ISIM based on photogrammetry. Photogrammetry is the measurement of the location of custom targets via triangulation using images obtained at a suite of digital camera locations and orientations. We describe metrology system requirements, plans, and ambient photogrammetric measurements of a mock-up of the ISIM structure to design targeting and obtain resolution estimates. We compare these measurements with those taken from a well known ambient metrology system, namely, the Leica laser tracker system. We also describe the data reduction algorithm planned to interpret cryogenic data from the Flight structure. Photogrammetry was selected from an informal trade study of cryogenic metrology systems because its resolution meets sub-allocations to ISIM alignment requirements and it is a non-contact method that can in principle measure six degrees of freedom changes in target location. In addition, photogrammetry targets can be readily related to targets used for ambient surveys of the structure. By thermally isolating the photogrammetry camera during testing, metrology can be performed in situ during thermal cycling. Photogrammetry also has a small but significant cryogenic heritage in astronomical instrumentation metrology. It was used to validate the displacement/deformation predictions of the reflectors and the feed horns during thermal/vacuum testing (90K) for the Microwave Anisotropy Probe (MAP). It also was used during thermal vacuum testing (100K) to verify shape and component alignment at operational temperature of the High Gain Antenna for New Horizons. With tighter alignment requirements and lower operating temperatures than the aforementioned observatories, ISIM presents new challenges in the development of this metrology system.

Nowak, Maria↗

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro )

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M pro , is a promising target for the development of novel antiviral therapeutics. Previous X-ray crystal structures of M pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these data sets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a perturbation-dependent conformational landscape for M pro , including a mobile zinc ion interleaved between the catalytic dyad, mercurial conformational heterogeneity at various sites including a key substrate-binding loop, and a far-reaching intramolecular network bridging the active site and dimer interface. Our results may inspire new strategies for antiviral drug development to aid preparation for future coronavirus pandemics.

59 BASIC BIOLOGICAL SCIENCES↗

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↗

Lunar transfer vehicle studies

Lunar transportation architectures exist for several different mission scenarios. Direct flights from Earth are possible, as the Apollo program clearly demonstrated. Alternatively, a space transfer vehicle could be constructed in space by using the Space Station as a base of operations, or multiple vehicles could be launched from Earth and dock in LEO without using a space station for support. Similarly, returning personnel could proceed directly to Earth or rendezvous at the Space Station for a ride back home on the Space Shuttle. Multiple design concepts exist which are compatible with these scenarios and which can support requirements of cargo, personnel, and mission objectives. Regardless of the ultimate mission selected, some technologies will certainly play a key role in the design and operation of advanced lunar transfer vehicles. Current technologies are capable of delivering astronauts to the lunar surface, but improvements are needed to affordably transfer the material and equipment that will be needed for establishing a lunar base. Materials and structures advances, in particular, will enable the development of more capable cryogenic fluid management and propulsion systems, improved structures, and more efficient vehicle assembly, servicing and processing.

Keeley, Joseph T.↗

Structural Characterization of TRAF6 N-Terminal for Therapeutic Uses and Computational Studies on New Derivatives

Tumor necrosis factor receptor-associated factors (TRAFs) are a protein family with a wide variety of roles and binding partners. Among them, TRAF6, a ubiquitin ligase, possesses unique receptor binding specificity and shows diverse functions in immune system regulation, cellular signaling, central nervous system, and tumor formation. TRAF6 consists of an N-terminal Really Interesting New Gene (RING) domain, multiple zinc fingers, and a C-terminal TRAF domain. TRAF6 is an important therapeutic target for various disorders and structural studies of this protein are crucial for the development of next-generation therapeutics. Here, we presented a TRAF6 N-terminal structure determined at the Turkish light source “Turkish DeLight” to be 3.2 Å resolution at cryogenic temperature (PDB ID: 8HZ2). This structure offers insight into the domain organization and zinc-binding, which are critical for protein function. Since the RING domain and the zinc fingers are key targets for TRAF6 therapeutics, structural insights are crucial for future research. Separately, we rationally designed numerous new compounds and performed molecular docking studies using this template (PDB ID:8HZ2). According to the results, 10 new compounds formed key interactions with essential residues and zinc ion in the N-terminal region of TRAF6. Molecular dynamic (MD) simulations were performed for 300 ns to evaluate the stability of three docked complexes (compounds 256, 322, and 489). Compounds 256 and 489 was found to possess favorable bindings with TRAF6. These new compounds also showed moderate to good pharmacokinetic profiles, making them potential future drug candidates as TRAF6 inhibitors.

60 APPLIED LIFE SCIENCES↗

Cryogenic Fracture Toughness Evaluation of an Investment Cast Al-Be Alloy for Structural Applications

Aluminum-Beryllium metal matrix composite materials are useful due to their desirable performance characteristics for aerospace applications. Desirable characteristics of this material includes light-weight, dimensional stability, stiffness, good vibration damping characteristics, low coefficient of thermal expansion, and workability, This material is 3.5 times stiffer and 22% lighter than conventional aluminum alloys. electro-optical systems, advanced sensor and guidance components for flight and satellite systems, components for light-weight high-performance aircraft engines, and structural components for helicopters. Aluminum-beryllium materials are now available in the form of near net shape investment castings. In this materials properties characterization study, the cryogenic tensile and fracture properties of an investment casting alloy, Beralcast 363, were determined. Tensile testing was performed at 21 C (70 F), -73.3 C (-100 F), -195.5 C (-320 F) and -252.8 C (-423 F), and fracture (K(sub lc) and da/dN) testing was performed at -73.3 C (-100 F), -195.5 C (-320 F) and -252.8 C (-423 F). Their use is attractive for weight critical structural applications such as advanced

Gamwell, W. R.↗

Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis

Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restrains for non-protein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in Chlorophyll (Chl) proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C 2 symmetry of Photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and Cryogenic electron microscopy (CryoEM) PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restrains play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested, from cyanobacteria to algae. Furthermore, these results highlight both the opportunities and limitations inherent in the structure-based analysis of the bioenergetic and optical properties of CPs and other protein-ligand complexes.

14 SOLAR ENERGY↗

Development of magnetostrictive active members for control of space structures

The goal of this Phase 2 Small Business Innovative Research (SBIR) project was to determine the technical feasibility of developing magnetostrictive active members for use as truss elements in space structures. Active members control elastic vibrations of truss-based space structures and integrate the functions of truss structure element, actively controlled actuator, and sensor. The active members must control structural motion to the sub-micron level and, for many proposed space applications, work at cryogenic temperatures. Under this program both room temperature and cryogenic temperature magnetostrictive active members were designed, fabricated, and tested. The results of these performance tests indicated that room temperature magnetostrictive actuators feature higher strain, stiffness, and force capability with lower amplifier requirements than similarly sized piezoelectric or electrostrictive active members, at the cost of higher mass. Two different cryogenic temperature magnetostrictive materials were tested at liquid nitrogen temperatures, both with larger strain capability than the room temperature magnetostrictive materials. The cryogenic active member development included the design and fabrication of a cryostat that allows operation of the cryogenic active member in a space structure testbed.

Johnson, Bruce G.↗

Cryo-EM structures of DNA-free and DNA-bound BsaXI: architecture of a Type IIB restriction–modification enzyme

Abstract We have determined multiple cryogenic electron microscopy (cryo-EM) structures of the Type IIB restriction–modification enzyme BsaXI. Such enzymes cleave DNA on both sides of their recognition sequence and share features of Types I, II, and III restriction systems. BsaXI forms a heterotrimeric (RM)2S assemblage in the presence and absence of bound DNA. Two unique structural motifs—a multi-helical “knob” and a long antiparallel double-helical “paddle”—are involved in DNA binding and cleavage. Binding of the DNA target triggers a large conformational change from an ‘open’ to ‘closed’ configuration, resulting in a mixture of two different conformations with respect to the positioning of the S subunit and its target recognition domains on the enzyme’s bipartite DNA target site. Structure-guided mutagenesis studies implicated two clusters of residues in the RM subunit as being critical for DNA cleavage, both are located proximal to a DNA cleavage site. One corresponds to a canonical PD-(D/E)xK endonuclease site in the N-terminal endonuclease domain, while the other corresponds to residues clustered within the paddle motif (near to the C-terminal end of the RM subunit). This analysis facilitates a comparison of three potential mechanisms by which such enzymes cleave DNA on each side of the bound target.

Shen, Betty W.↗

X-ray crystallographic and hydrogen deuterium exchange studies confirm alternate kinetic models for homolog insulin monomers

Despite the crucial role of various insulin analogs in achieving satisfactory glycemic control, a comprehensive understanding of their in-solution dynamic mechanisms still holds the potential to further optimize rapid insulin analogs, thus significantly improving the well-being of individuals with Type 1 Diabetes. Here, we employed hydrogen-deuterium exchange mass spectrometry to decipher the molecular dynamics of newly modified and functional insulin analog. A comparative analysis of H/D dynamics demonstrated that the modified insulin exchanges deuterium atoms faster and more extensively than the intact insulin aspart. Additionally, we present new insights derived from our 2.5 Å resolution X-ray crystal structure of modified hexamer insulin analog at ambient temperature. Furthermore, we obtained a distinctive side-chain conformation of the Asn3 residue on the B chain (AsnB3) by operating a comparative analysis with a previously available cryogenic rapid-acting insulin structure (PDB_ID: 4GBN). The experimental conclusions have demonstrated compatibility with modified insulin’s distinct cellular activity, comparably to aspart. Additionally, the hybrid structural approach combined with computational analysis employed in this study provides novel insight into the structural dynamics of newly modified and functional insulin vs insulin aspart monomeric entities. It allows further molecular understanding of intermolecular interrelations driving dissociation kinetics and, therefore, a fast action mechanism.

59 BASIC BIOLOGICAL SCIENCES↗

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

Abstract As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

Burley, Stephen K. (ORCID:0000000224879713)↗

Cryo-EM Visualization of Intermolecular π-Electron Interactions within π-Conjugated Peptidic Supramolecular Polymers

The self-assembly of “π-peptides” – molecules with π-electron cores substituted with two or more oligopeptide chains – brings organic electronic function into biologically relevant nanomaterials. π-Peptides assemble into fibrillar nanomaterials as driven by enthalpic peptide-based hydrogen bonding networks and pi-core-based quadrupolar interactions. A large body of spectroscopic, morphological and computational studies informs on the nature of the self-assembly process and the resulting nanostructures, but detailed structural information has remained elusive. Here, inspired by the recent use of cryogenic electron microscopy (cryo-EM) to provide high-resolution structures for synthetic peptide nanomaterials, we present here the use of cryo-EM to offer ca. 3 Å resolution of π-peptide nanomaterial assemblies, visualizing for the first time the nature of the intermolecular π-core electronic interactions responsible for energy transport through these supramolecular materials.

Group theory↗

Facesheet Delamination of Composite Sandwich Materials at Cryogenic Temperatures

The next generation of space transportation vehicles will require advances in lightweight structural materials and related design concepts to meet the increased demands on performance. One potential source for significant structural weight reduction is the replacement of traditional metallic cryogenic fuel tanks with new designs for polymeric matrix composite tanks. These new tank designs may take the form of thin-walled sandwich constructed with lightweight core and composite facesheets. Life-time durability requirements imply the materials must safely carry pressure loads, external structural loads, resist leakage and operate over an extremely wide temperature range. Aside from catastrophic events like tank wall penetration, one of the most likely scenarios for failure of a tank wall of sandwich construction is the permeation of cryogenic fluid into the sandwich core and the subsequent delamination of the sandwich facesheet due to the build-up of excessive internal pressure. The research presented in this paper was undertaken to help understand this specific problem of core to facesheet delamination in cryogenic environments and relate this data to basic mechanical properties. The experimental results presented herein provide data on the strain energy release rate (toughness) of the interface between the facesheet and the core of a composite sandwich subjected to simulated internal pressure. A unique test apparatus and associated test methods are described and the results are presented to highlight the effects of cryogenic temperature on the measured material properties.

Gates, Thomas S.↗