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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Topological grain boundary segregation transitions

Engineering the structure of grain boundaries (GBs) by solute segregation is a promising strategy to tailor the properties of polycrystalline materials. Solute segregation triggering phase transitions at GBs has been suggested theoretically to offer different pathways to design interfaces, but an understanding of their intrinsic atomistic nature is missing. Here, we combined atomic resolution electron microscopy and atomistic simulations to discover that iron segregation to GBs in titanium stabilizes icosahedral units (“cages”) that form robust building blocks of distinct GB phases. Owing to their five-fold symmetry, the iron cages cluster and assemble into hierarchical GB phases characterized by a different number and arrangement of the constituent icosahedral units. Our advanced GB structure prediction algorithms and atomistic simulations validate the stability of these observed phases and the high excess of iron at the GB that is accommodated by the phase transitions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗
DOE OSTI2022

Sweep-tracing algorithm: in silico slip crystallography and tension-compression asymmetry in BCC metals

Abstract Direct Molecular Dynamics (MD) simulations are being increasingly employed to model dislocation-mediated crystal plasticity with atomic resolution. Thanks to the dislocation extraction algorithm (DXA), dislocation lines can be now accurately detected and positioned in space and their Burgers vector unambiguously identified in silico, while the simulation is being performed. However, DXA extracts static snapshots of dislocation configurations that by themselves present no information on dislocation motion. Referred to as a sweep-tracing algorithm (STA), here we introduce a practical computational method to observe dislocation motion and to accurately quantify its important characteristics such as preferential slip planes (slip crystallography). STA reconnects pairs of successive snapshots extracted by DXA and computes elementary slip facets thus precisely tracing the motion of dislocation segments from one snapshot to the next. As a testbed for our new method, we apply STA to the analysis of dislocation motion in large-scale MD simulations of single crystal plasticity in BCC metals. We observe that, when the crystal is subjected to uniaxial deformation along its [001] axis, dislocation slip predominantly occurs on the {112} maximum resolved shear stress plane under tension, while in compression slip is non-crystallographic (pencil) resulting in asymmetric mechanical response. The marked contrast in the observed slip crystallography is attributed to the twinning/anti-twinning asymmetry of shears in the {112} planes relatively favoring dislocation motion in the twinning sense while hindering dislocations from moving in the anti-twinning directions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure of BTK kinase domain with the second-generation inhibitors acalabrutinib and tirabrutinib

Bruton’s tyrosine kinase (BTK) is the target of the therapeutic agent, Ibrutinib, that treats chronic lymphocyte leukemia (CLL), mantle cell lymphoma (MCL) and other B cell malignancies. Ibrutinib is a first in class, covalent BTK inhibitor that limits B-cell survival and proliferation. Designing new inhibitors of BTK has been an important objective for advancing development of improved therapeutic agents against cancer and autoimmune disorders. Based on the success of Ibrutinib, several second-generation irreversible BTK inhibitors have been developed that exhibit fewer off-target effects. However, the binding-mode and their interaction with Btk have not been experimentally determined and evaluated at atomic resolution. Here we determined the first crystal structure of the BTK kinase domain in complex with acalabrutinib. In addition, we report a structure of the BTK/tirabrutinib complex and compare these structures with previously solved structures. The structures provide insight in the superior selectivity reported for acalabrutinb and guide future BTK inhibitor development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion

Varicella-zoster virus (VZV) is a medically important alphaherpesvirus that induces fusion of the virion envelope and the cell membrane during entry, and between cells to form polykaryocytes within infected tissues during pathogenesis. All members of the Herpesviridae , including VZV, have a conserved core fusion complex composed of glycoproteins, gB, gH and gL. The ectodomain of the primary fusogen, gB, has five domains, DI-V, of which DI contains the fusion loops needed for fusion function. We recently demonstrated that DIV is critical for fusion initiation, which was revealed by a 2.8Å structure of a VZV neutralizing mAb, 93k, bound to gB and mutagenesis of the gB-93k interface. To further assess the mechanism of mAb 93k neutralization, the binding site of a non-neutralizing mAb to gB, SG2, was compared to mAb 93k using single particle cryogenic electron microscopy (cryo-EM). The gB-SG2 interface partially overlapped with that of gB-93k but, unlike mAb 93k, mAb SG2 did not interact with the gB N-terminus, suggesting a potential role for the gB N-terminus in membrane fusion. The gB ectodomain structure in the absence of antibody was defined at near atomic resolution by single particle cryo-EM (3.9Å) of native, full-length gB purified from infected cells and by X-ray crystallography (2.4Å) of the transiently expressed ectodomain. Both structures revealed that the VZV gB N-terminus (aa72-114) was flexible based on the absence of visible structures in the cryo-EM or X-ray crystallography data but the presence of gB N-terminal peptides were confirmed by mass spectrometry. Notably, N-terminal residues 109 KSQD 112 were predicted to form a small α-helix and alanine substitution of these residues abolished cell-cell fusion in a virus-free assay. Importantly, transferring the 109 AAAA 112 mutation into the VZV genome significantly impaired viral propagation. These data establish a functional role for the gB N-terminus in membrane fusion broadly relevant to the Herpesviridae .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Resonant X-ray scattering of biological assemblies

Understanding the relationship between structure and function for biological assemblies can guide identification of new therapeutics, design of biomaterials, and development of biotechnological processes. Resonant X-ray scattering provides a chemically-specific approach to characterize complex biological structures based on anomalous or resonant scattering from a specific element or chemical moiety. Anomalous or resonant diffraction can provide structural details with high atomic resolution, while resonant X-ray scattering can provide structural details with lower resolution through tender or soft X-rays. Furthermore, we review applications, challenges, and opportunities for resonant X-ray scattering in the field of structural biology.

36 MATERIALS SCIENCE↗
NASA NTRS1986

Base pairing and base mis-pairing in nucleic acids

In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

Wang, A. H. J.↗
NASA NTRS1998

Modeling the Growth Rates of Tetragonal Lysozyme Crystal Faces

The measured macroscopic growth rates of the (110) and (101) faces of tetragonal lysozyme show an unexpectedly complex dependence on the supersaturation. The growth rates decay asymptotically to zero when the supersaturation is lowered to zero and increase rapidly when the supersaturation is increased. When supersaturations are increased still further the growth rates attain a maximum before starting to decrease. However, growth of these crystals is known to proceed by the classical dislocation and 2D nucleation growth mechanisms. This anomaly can be explained if growth is assumed to occur not by monomer units but by lysozyme aggregates. Analysis of the molecular packing of these crystals revealed that they were constructed of strongly bonded 4(sub 3) helices, while weaker bonds were responsible for binding the helices to each other. It follows that during crystal growth the stronger bonds are formed before the weaker ones. Thus, the growth of these crystals could be viewed as a two step process: aggregate growth units corresponding to the 4(sub 3) helix are first formed in the bulk solution by stronger intermolecular bonds and then attached to the crystal face by weaker bonds on dislocation hillocks or 2D islands. This will lead to a distribution of aggregates in the solution with monomers and lower order aggregates being predominant at low supersaturations and higher order aggregates being predominant at high supersaturations. If the crystal grows mostly by higher order aggregates, such as tetramers and octamers, it would explain the anomalous dependence of the growth rates on the supersaturation. Besides the analysis of molecular packing, a comprehensive analysis of the measured (110) and (101) growth rates was also undertaken in this study. The distribution of aggregates in lysozyme nutrient solutions at various solution conditions were determined from reversible aggregation reactions at equilibrium. The supersaturation was defined for each aggregate species with respect to its concentration at saturation in order to apply growth rate models to this process. The measured growth rates were then compared with the predicted ones from several dislocation and 2D nucleation growth models, employing tetramer and octamer growth units in polydisperse solutions and monomer units in monodisperse solutions. For the (110) face, the calculations consistently showed that the measured growth rates followed the expected model relations with octamer growth units. For the (101) face, it is not possible to obtain a clear agreement between the predicted and measured growth rates for a single growth unit as done for the (110) face. However, the calculations do indicate that the average size of the growth unit is between a tetramer and an octamer. This suggests that tetramers, octamers and other intermediate size growth units all participate in the growth process for this face. These calculations show that it is possible to model the macroscopic protein crystal growth rates if the molecular level processes can be account for, particularly protein aggregation processes in the bulk solution. Our recent investigations of tetragonal lysozyme crystals employing high resolution atomic force microscopy scans have further confirmed the growth of these crystals by aggregate growth units corresponding to 4(sub 3) helices.

Li, Meirong↗
NASA NTRS2003

Which Strategy for a Protein Crystallization Project?

The three-dimensional, atomic-resolution protein structures produced by X-ray crystallography over the past 50+ years have led to tremendous chemical understanding of fundamental biochemical processes. The pace of discovery in protein crystallography has increased greatly with advances in molecular biology, crystallization techniques, cryo-crystallography, area detectors, synchrotrons and computing. While the methods used to produce single, well-ordered crystals have also evolved over the years in response to increased understanding and advancing technology, crystallization strategies continue to be rooted in trial-and-error approaches. This review summarizes the current approaches in protein crystallization and surveys the first results to emerge from the structural genomics efforts.

Kundrot, Craig E.↗
NASA NTRS2004

Life in the Fast Lane for Protein Crystallization and X-Ray Crystallography

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today s high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Pusey, Marc L.↗
NASA NTRS2004

Which strategy for a protein crystallization project?

The three-dimensional, atomic-resolution protein structures produced by X-ray crystallography over the past 50+ years have led to tremendous chemical understanding of fundamental biochemical processes. The pace of discovery in protein crystallography has increased greatly with advances in molecular biology, crystallization techniques, cryocrystallography, area detectors, synchrotrons and computing. While the methods used to produce single, well-ordered crystals have also evolved over the years in response to increased understanding and advancing technology, crystallization strategies continue to be rooted in trial-and-error approaches. This review summarizes the current approaches in protein crystallization and surveys the first results to emerge from the structural genomics efforts.

Review↗
NASA NTRS2000

Database of non-canonical base pairs found in known RNA structures

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

NASA Discipline Exobiology↗
NASA NTRS2005

Life in the fast lane for protein crystallization and X-ray crystallography

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Review↗
NASA NTRS2007

Novel Nanotube Manufacturing Streamlines Production

Nanotubes have novel qualities that make them uniquely qualified for a plethora of uses, including applications in electronics, optics, and other scientific and industrial fields. The NASA process for creating these nanostructures involves using helium arc welding to vaporize an amorphous carbon rod and then form nanotubes by depositing the vapor onto a water-cooled carbon cathode, which then yields bundles, or ropes, of single-walled nanotubes at a rate of 2 grams per hour using a single setup. This eliminates costs associated with the use of metal catalysts, including the cost of product purification, resulting in a relatively inexpensive, high-quality, very pure end product. While managing to be less expensive, safer, and simpler, the process also increases the quality of the nanotubes. Goddard's Innovative Partnerships Program (IPP) Office promoted the technology, and in 2005, Boise-based Idaho Space Materials Inc. (ISM) was formed and applied for a nonexclusive license for the single-walled carbon nanotube (SWCNT) manufacturing technology. ISM commercialized its products, and the inexpensive, robust nanotubes are now in the hands of the scientists who will create the next generation of composite polymers, metals, and ceramics that will impact the way we live. In fact, researchers are examining ways for these newfound materials to be used in the manufacture of transistors and fuel cells, large screen televisions, ultra-sensitive sensors, high-resolution atomic force microscopy probes, supercapacitors, transparent conducting films, drug carriers, catalysts, and advanced composite materials, to name just a few of the myriad technologies to benefit.

Source record↗
NASA NTRS2017

The Evolution of the Deformation Substructure in a Ni-Co-Cr Equiatomic Solid Solution Alloy

The equiatomic NiCoCr alloy exhibits an excellent combination of strength and ductility, even greater than the FeNiCrCoMn high entropy alloy, and also displays a simultaneous increase in strength and ductility with decreasing the testing temperature. To systemically investigate the origin of the exceptional properties of NiCoCr alloy, which are related to the evolution of the deformation substructure with strain, interrupted tensile testing was conducted on the equiatomic NiCoCr single-phase solid solution alloy at both cryogenic and room temperatures at five different plastic strain levels of 1.5%, 6.5%, 29%, 50% and 70%. The evolution of deformation substructure was examined using electron backscatter diffraction (EBSD), transmission Kikuchi diffraction (TKD), conventional transmission electron microscopy (CTEM), diffraction contrast imaging using STEM (DCI-STEM) and atomic resolution scanning transmission electron microscopy. While the deformation substructure mainly consisted of planar dislocation slip and the dissociation of dislocations into stacking faults at small strain levels (≤6.5%), at larger strain levels, additional substructures including nanotwins and a new phase with hexagonal close packed (HCP) lamellae also appeared. The volume fraction of the HCP lamellae increases with increasing deformation, especially at cryogenic temperature. First principles calculations at 0 K indicate that the HCP phase is indeed energetically favorable relative to FCC for this composition. The effects of the nanotwin and HCP lamellar structures on hardening rate and ductility at both cryogenic and room temperature are qualitatively discussed.

Twinning↗
NASA NTRS2019

Complex Intergrowths of Non-Stoichiometric Defect-Structured Hibonite and Al-Rich Spinel in an Allende Ca-Al-Rich Inclusion

Hibonite is a primary ultra-refractory mineral occurring in many Ca-Al-rich inclusions (CAIs) and is predicted to condense as the second major phase from a cooling gas of solar composition. Our previous microstructural studies of hibonite in carbonaceous chondrites revealed its unique microstructures consisting of numerous defects that contain Mg-enriched, wider spinel blocks in stoichiometric hibonite. Han, J. et al. [2 items] demonstrated experimentally that defect-structured hibonites can grow easily in the presence of minor Mg and are kinetically more stable than equilibrium assemblages predicted by thermodynamic calculations. However, a thermo-dynamic vs. structural stability of defect-structured hibonite relative to other early-condensed Al-rich phases such as corundum, grossite, and spinel remains poorly constrained. Here, we present the results of atomic resolution TEM (Transmission Electron Microscopy) imaging of hibonite in a compact Type A CAI in the Allende CV3 chondrite in order to better understand the crystal structure and chemistry of defect-structured hibonite and its associated Al-rich phases, especially non-stoichiometric, Al-rich spinel, in the context of the formation of first refractory solids in the early solar nebula.

Han, J.↗
DOE OSTI2023

Structure and Electronic Properties of Mesopores in Si PV Devices with PLEO Contacts

All current state-of-the-art silicon photovoltaic (PV) devices employ some flavor of passivating contact structure to minimize detrimental recombination while providing good conductivity. These properties are most often provided by a dielectric layer (SiNx, Al2O3, or SiOx) that is in contact with the crystalline silicon (c-Si) substrate. The effectiveness of these layers is heavily dependent on the nanoscale structure of both the dielectric layers and the crystalline silicon interface. As an example, the tunneling probability for charge carriers across thin SiOx layers, a process that is critical to maintain high conductivity, is extremely sensitive to the SiOx thickness. SiOx with a thickness below 2 nm readily allows charge carrier tunneling, whereas it is impeded for greater thicknesses. In the latter case it has been shown that modifications to the thermal processing schedule can induce disruptions, or pinholes, in thick SiOx layers that allow transport of charge carriers while maintaining excellent passivation. However, this requires higher temperatures processes that may inhibit widespread adoption by industry. Recently, another option has been presented that may circumvent the necessity for high temperature processing, namely metal assisted chemical etching (MACE). MACE relies on deposition of Ag nanoparticles onto the SiOx layers with subsequent electroless etching to form mesopores in the SiOx layers that are analogous to the pinholes created with high temperature processing. The size and density can be controlled based on the Ag nanoparticle deposition conditions. The resulting contact structure is known as polysilicon on locally etched oxide (PLEO) contacts. The nanoscale structure of the mesopores in PLEO contacts define the device level observables such as recombination current (Jo) and junction resistance. In this work we present atomic resolution transmission electron microscopy (TEM) analysis of mesopores in PLEO contacts formed with a different processing conditions to connect provide insight into how the nanoscale structure of the SiOx layer influences PV device properties. Additionally, we have previously used electron beam induced current (EBIC) to probe local transport properties in Si PV devices with a SiOx layer containing pinholes due to high temperature processing. Using EBIC we were able to directly show the enhance charge carrier transport through the pinholes. Here we also employ EBIC to study non-uniformities in charge carrier recombination and transport associated with mesopores in PLEO contacts and compare these results with our previous work on devices with pinholes in the SiOx formed through high temperature processes. The products of this work provide critical information that is required to both further optimize performance of Si PV devices with PLEO contact and to drive future adoption of this technology by industry.

ENGINEERING,SOLAR ENERGY↗
DOE OSTI2023

Gas delivery system for environmental transmission electron microscope

A portable, compact gas delivery system can support an environmental transmission electron microscope. Environment transmission electron microscopy provides researchers a unique capability of assessing a material's surface conditions at atomic resolution in a variety of reactive and oxidizing environments. The ability to precisely control the analysis chamber's environmental conditions over time is key to the success of a typical surface analysis. The gas delivery system provides the correct balance or pressure delivery precision, contamination control, and gas isolation.

Nogan, John Joseph↗