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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Influence of Potassium Metal‐Support Interactions on Dendrite Growth

Abstract Combined synchrotron X‐ray nanotomography imaging, cryogenic electron microscopy (cryo‐EM) and modeling elucidate how potassium (K) metal‐support energetics influence electrodeposit microstructure. Three model supports are employed: O‐functionalized carbon cloth (potassiophilic, fully‐wetted), non‐functionalized cloth and Cu foil (potassiophobic, nonwetted). Nanotomography and focused ion beam (cryo‐FIB) cross‐sections yield complementary three‐dimensional (3D) maps of cycled electrodeposits. Electrodeposit on potassiophobic support is a triphasic sponge, with fibrous dendrites covered by solid electrolyte interphase (SEI) and interspersed with nanopores (sub‐10 nm to 100 nm scale). Lage cracks and voids are also a key feature. On potassiophilic support, the deposit is dense and pore‐free, with uniform surface and SEI morphology. Mesoscale modeling captures the critical role of substrate‐metal interaction on K metal film nucleation and growth, as well as the associated stress state.

Liu, Pengcheng↗
DOE OSTI2023

Influence of Potassium Metal-Support Interactions on Dendrite Growth

We report combined synchrotron X-ray nanotomography imaging, cryogenic electron microscopy (cryo-EM) and modeling elucidate how potassium (K) metal-support energetics influence electrodeposit microstructure. Three model supports are employed: O-functionalized carbon cloth (potassiophilic, fully-wetted), non-functionalized cloth and Cu foil (potassiophobic, nonwetted). Nanotomography and focused ion beam (cryo-FIB) cross-sections yield complementary three-dimensional (3D) maps of cycled electrodeposits. Electrodeposit on potassiophobic support is a triphasic sponge, with fibrous dendrites covered by solid electrolyte interphase (SEI) and interspersed with nanopores (sub-10 nm to 100 nm scale). Lage cracks and voids are also a key feature. On potassiophilic support, the deposit is dense and pore-free, with uniform surface and SEI morphology. Mesoscale modeling captures the critical role of substrate-metal interaction on K metal film nucleation and growth, as well as the associated stress state.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Understanding Interfacial Electrochemical Reactions through in situ ec-STEM and IL-Cryo-STEM

A major criterion in the design of next generation materials for electrical energy storage applications is a comprehensive understanding of interfacial electrochemical reactions as well as correlating the structure and chemistry across site-specific electrode/electrolyte interfaces with electron, charge, and mass transport processes as they govern performance characteristics. Scanning transmission electron microscopy (STEM) based techniques have emerged as an indispensable materials characterization tool that provides high spatial resolution imaging and chemical analysis and has been effectively utilized to obtain an atomic to nanoscale view of the interfacial structure before and after electrochemical cycling. More recently, there have been several advances that now allows us to obtain more detailed mechanistic insight into evolving reactions through in situ ec-STEM and electrical biasing platforms such as in the understanding of the mechanisms of solid electrolyte interphase formation, lithium dendrite nucleation and growth mechanisms and ionic transport mechanisms within intercalation, conversion, and alloying electrode materials. Several major advantages of the in situ ec-STEM approach is the quantitative electrochemical measurement of charge passed during cycling with simultaneous analysis of the electrochemical processes with STEM imaging and diffraction. Here, while spectroscopic analysis of the electrochemical reactions products has been performed, there is the issue of beam sensitivity and therefore, Cryo-STEM imaging combined with electron energy loss spectroscopy (EELS) techniques have been employed to analyze the chemistry of the SEI and Li dendrites. In this talk, we discuss the potential for combining identical location (IL) STEM techniques with Cryo-EM. The advantage of using this approach is that the sample is placed on a conventional TEM grid and the exact same location of the specimen can be analyzed before and after quantitative electrochemical measurements. Moreover, since the sample is on the TEM grid, the grid itself can be prepared for further Cryo-TEM experiments by plunge freezing in liquid nitrogen then transferred to the Cryo-TEM under liquid nitrogen. Results obtain from these experiments can be used to enhance our scientific understanding of interfacial chemistry at electrode/electrolyte interfaces and may be useful in the design of new materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

ULK complex organization in autophagy by a C-shaped FIP200 N-terminal domain dimer

The autophagy-initiating human ULK complex consists of the kinase ULK1/2, FIP200, ATG13, and ATG101. Hydrogen-deuterium exchange mass spectrometry was used to map their mutual interactions. The N-terminal 640 residues (NTD) of FIP200 interact with the C-terminal IDR of ATG13. Mutations in these regions abolish their interaction. Negative stain EM and multiangle light scattering showed that FIP200 is a dimer, while a single molecule each of the other subunits is present. The FIP200NTD is flexible in the absence of ATG13, but in its presence adopts the shape of the letter C ~20 nm across. The ULK1 EAT domain interacts loosely with the NTD dimer, while the ATG13:ATG101 HORMA dimer does not contact the NTD. Cryo-EM of the NTD dimer revealed a structural similarity to the scaffold domain of TBK1, suggesting an evolutionary similarity between the autophagy-initiating TBK1 kinase and the ULK1 kinase complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Exploring cryo-electron microscopy with molecular dynamics

Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low-resolution cryo-EM maps of large macromolecular complexes not amenable to crystallization. The connection between cryo-EM and MD evolved as cryo-EM maps improved in resolution, allowing advanced sampling algorithms to simultaneously refine backbone and sidechains. Moving beyond a single static snapshot, modern inferencing approaches integrate cryo-EM and MD to generate structural ensembles from cryo-EM map data or directly from the particle images themselves. We summarize the recent history of MD innovations in the area of cryo-EM modeling. The merits for the myriad of MD based cryo-EM modeling methods are discussed, as well as, the discoveries that were made possible by the integration of molecular modeling with cryo-EM. Lastly, current challenges and potential opportunities are reviewed.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Sub-Ångström-resolution MicroED Using a Direct Detection Camera

The recent development of microcrystal electron diffraction (MicroED) in electron cryo-microscopy (cryo-EM) has addressed many of the challenges of X-ray crystallography [1], filling a long-standing need in organic chemistry for rapid and accurate high-resolution structural characterization [2]. Like X-ray crystallography, this is also a diffraction technique requiring crystalline specimens, but because high energy electrons have a more favorable ration of elastic to inelastic scattering [3], MicroED can acquire data using crystals that are orders of magnitude smaller than those needed for X-ray crystallography—even as small as 50 nm in length [4]. Additionally, the instrumentation required for MicroED is readily available, as many chemistry and biology labs already have access to cryo-capable transmission electron microscopes (TEM).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structures of the mycobacterial membrane protein MmpL3 reveal its mechanism of lipid transport

The mycobacterial membrane protein large 3 (MmpL3) transporter is essential and required for shuttling the lipid trehalose monomycolate (TMM), a precursor of mycolic acid (MA)-containing trehalose dimycolate (TDM) and mycolyl arabinogalactan peptidoglycan (mAGP), in Mycobacterium species, including Mycobacterium tuberculosis and Mycobacterium smegmatis. However, the mechanism that MmpL3 uses to facilitate the transport of fatty acids and lipidic elements to the mycobacterial cell wall remains elusive. Here, we report 7 structures of the M. smegmatis MmpL3 transporter in its unbound state and in complex with trehalose 6-decanoate (T6D) or TMM using single-particle cryo-electron microscopy (cryo-EM) and X-ray crystallography. Combined with calculated results from molecular dynamics (MD) and target MD simulations, we reveal a lipid transport mechanism that involves a coupled movement of the periplasmic domain and transmembrane helices of the MmpL3 transporter that facilitates the shuttling of lipids to the mycobacterial cell wall.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Examining Bioethanol-Producing Ultrastructures with Electron Microscopy and Molecular Dynamics

A longstanding goal in the biofuel sector is to increase the efficiency of the circularization of the use of materials (1). One such instance is the degradation of plant material, such as cellulose, and converting it to biofuel via bacterial digestion (2). The bifunctional aldehyde-alcohol dehydrogenase (AdhE) from the anaerobic thermophile C. thermocellum seems to be vital for the production and cellular tolerance of bioethanol; however, it lacks the efficiency to produce ethanol at industry standards (3). Therefore, to understand how C. thermocellum AdhE functions, we used cryo-electron microscopy (cryo-EM) to obtain a 3.2 A structure of the AdhE complex. When compared to previously published structures from E. coli (4-6), we identified potential regions that control the native conformation of the ultrastructure, as well as located channels that isolate the intermediate aldehyde from the cellular milieu. This high-resolution structure, in combination with molecular dynamics simulations, provides insight into one example of substrate channeling and establishes a basis for future mutagenesis studies.

AdhE↗
DOE OSTI2022

Structural basis of RNA conformational switching in the transcriptional regulator 7SK RNP

7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is hijacked by HIV-1 for viral transcription and replication. Methylphosphate capping enzyme (MePCE) and La-related protein 7 (Larp7) constitutively associate with 7SK to form a core RNP, while P-TEFb and other proteins dynamically assemble to form different complexes. Here, we present the cryo-EM structures of 7SK core RNP formed with two 7SK conformations, circular and linear, and uncover a common RNA-dependent MePCE-Larp7 complex. Further, together with NMR, biochemical, and cellular data, these structures reveal the mechanism of MePCE catalytic inactivation in the core RNP, unexpected interactions between Larp7 and RNA that facilitate a role as an RNP chaperone, and that MePCE-7SK-Larp7 core RNP serves as a scaffold for switching between different 7SK conformations essential for RNP assembly and regulation of P-TEFb sequestration and release.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes

Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9

Thermostable clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas9) enzymes could improve genome-editing efficiency and delivery due to extended protein lifetimes. However, initial experimentation demonstrated Geobacillus stearothermophilus Cas9 (GeoCas9) to be virtually inactive when used in cultured human cells. Laboratory-evolved variants of GeoCas9 overcome this natural limitation by acquiring mutations in the wedge (WED) domain that produce >100-fold-higher genome-editing levels. Cryoelectron microscopy (cryo-EM) structures of the wild-type and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome-editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome-editing activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

From cytoplasm to lumen—mapping the free pools of protein subunits of three photosynthetic complexes using quantitative mass spectrometry

The phycobilisome (PBS) captures light energy and transfers it to photosystem I (PSI) and photosystem II (PSII). Which and how many copies of protein subunits in PBSs, PSI, and PSII remain unbound in thylakoids are unknown. Here, quantitative mass spectrometry (QMS) was used to quantify substantial pools of free extrinsic subunits of PSII and PSI. Interestingly, the membrane intrinsic PsaL is 3-fold higher than PsaA/B. This scenario complements the static structures of these complexes as revealed by X-ray crystallography and cryo-EM. Furthermore, the ratios of ApcG and photoprotective OCP over PBS indicate a pool of extra ApcG. The 2.5 ratio of CpcG-PBS over CpcL-PBS improves our understanding of these light-harvesting complexes involved in energy capture and photoprotection in cyanobacteria.

cyanobacteria↗
DOE OSTI2021

A Sodium–Antimony–Telluride Intermetallic Allows Sodium-Metal Cycling at 100% Depth of Discharge and as an Anode-Free Metal Battery

In this work, repeated cold rolling and folding is employed to fabricate a metallurgical composite of sodium–antimony–telluride Na 2 (Sb 2/6 Te 3/6 Vac 1/6 ) dispersed in electrochemically active sodium metal, termed “NST-Na.” This new intermetallic has a vacancy-rich thermodynamically stable face-centered-cubic structure and enables state-of-the-art electrochemical performance in widely employed carbonate and ether electrolytes. NST-Na achieves 100% depth-of-discharge (DOD) in 1 m NaPF 6 in G2, with 15 mAh cm –2 at 1 mA cm –2 and Coulombic efficiency (CE) of 99.4%, for 1000 h of plating/stripping. Sodium-metal batteries (SMBs) with NST-Na and Na 3 V 2 (PO 4 ) 3 (NVP) or sulfur cathodes give significantly improved energy, cycling, and CE (>99%). An anode-free battery with NST collector and NVP obtains 0.23% capacity decay per cycle. Imaging and tomography using conventional and cryogenic microscopy (Cryo-EM) indicate that the sodium metal fills the open space inside the self-supporting sodiophilic NST skeleton, resulting in dense (pore-free and solid electrolyte interphase (SEI)-free) metal deposits with flat surfaces. The baseline Na deposit consists of filament-like dendrites and “dead metal”, intermixed with pores and SEI. Density functional theory calculations show that the uniqueness of NST lies in the thermodynamic stability of the Na atoms (rather than clusters) on its surface that leads to planar wetting, and in its own stability that prevents decomposition during cycling.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Fuel‐Driven π‐Conjugated Superstructures to Form Transient Conductive Hydrogels

Despite advances in creating dissipative materials with transient properties, such as hydrogels and active droplets, their application remains confined to temporal changes in structural properties. Developing out-of-equilibrium materials whose electronic functions are parameterized by a chemical reaction cycle is challenging. Yet, this class of materials is required to construct biomimetic materials. In contrast to traditional chemical reaction cycles that exploit molecularly dissolved building blocks at thermodynamic equilibrium, we show that fiber structures derived from reactive naphthalene diimide (NDI) building blocks can be used as resting states to form far-from-equilibrium conductive hydrogels after the addition of chemical fuels. Upon fueling the NDI-derived fibers, a dual-component activation and deactivation pathway is deduced by kinetic analysis and is absent when using a molecularly dissolved resting state. Investigating the solid-state morphologies of the structures formed throughout the fuel-driven reaction cycle using cryo-EM reveals that the resting thermodynamic fibers evolve to transient thicker fibrils and layered superstructures. We show that the transient redox-active hydrogels exhibit a nearly threefold increase in electrical conductivity upon fuel consumption before reverting to their original value over hours. In conclusion, these far-from-equilibrium materials are potential candidates in applications such as programmable biorobotics and chemical computing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A Hybrid Structural Method for Investigating Low Molecular Weight Oligomeric Structures of Amyloid Beta

Spurred in part by the failure of recent therapeutics targeting amyloid β plaques in Alzheimer's Disease (AD), attention is increasingly turning to the oligomeric forms of this peptide that form early in the aggregation process. However, while numerous amyloid β fibril structures have been characterized, primarily by NMR spectroscopy and cryo-EM, obtaining structural information on the low molecular weight forms of amyloid β that presumably precede and/or seed fibril formation has proved challenging. Furthermore, these transient forms are heterogeneous, and depend heavily on experimental conditions such as buffer, temperature, concentration, and degree of quiescence during measurement. Here, we present the concept for a new approach to delineating structural features of early-stage low molecular weight amyloid β oligomers, using a solvent accessibility assay in conjunction with simultaneous fluorescence measurements.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS‐CoV‐2

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) enters the host cell by binding to angiotensin‐converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across various species and differential interactions with Spike (S) glycoproteins of SARS‐CoV‐2 viruses impact species specificity. Reverse zoonoses led to SARS‐CoV‐2 outbreaks on multiple American mink (Mustela vison) farms during the pandemic and gave rise to mink‐associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio‐layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink‐derived S glycoproteins of SARS‐CoV‐2 and their respective ACE2 receptors. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo‐electron microscopy (cryo‐EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 receptor is bound to the receptor‐binding domain (RBD) of the S glycoprotein in a “down” position, approximately 34° lower than previously reported “up” RBD. Finally, we compared residue interactions in the S‐ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS‐CoV‐2 entry.

Virology↗
DOE OSTI2025

Detection of non‐native species formed during fibrillization of the myocilin olfactomedin domain

Abstract Glaucoma is a group of neurodegenerative diseases that together are the leading cause of irreversible blindness worldwide. Myocilin‐associated glaucoma is an inherited form of this disease, caused by intracellular aggregation of misfolded mutant myocilin. In vitro, the myocilin C‐terminal olfactomedin domain (OLF), the relevant domain for glaucoma pathogenesis, can be driven to form amyloid‐like fibrils under mild conditions. Here we characterize a species present during in vitro fibrillization. Purified OLF was subjected to fibrillization at concentrations required for downstream electron microscopy imaging and NMR spectroscopy. Additional biophysical techniques, including analytical ultracentrifugation and X‐ray crystallography, were employed to further characterize the multicomponent mixture. Negative stain transmission electron microscopy (TEM) shows a non‐native species reminiscent of known prefibrillar oligomers from other amyloid systems, NMR indicates a minor population of partially misfolded species is present in solution, and cryo‐EM imaging shows two‐dimensional protein arrays. The predominant soluble species remaining in solution after the fibril reaction is natively folded, as evidenced by X‐ray crystallography. In summary, after incubating OLF under fibrillization‐promoting conditions, there is a heterogeneous mixture consisting of soluble folded protein, mature amyloid‐like fibrils, and partially misfolded intermediate species that at present belie additional molecular detail. The characterization of OLF fibrillar species illustrates the challenges associated with developing a comprehensive understanding of the fibrillization process for large, non‐model amyloidogenic proteins.

Scelsi, Hailee F. [School of Chemistry and Biochem↗
DOE OSTI2020

A comparative look at structural variation among RC–LH1 ‘Core’ complexes present in anoxygenic phototrophic bacteria

All purple photosynthetic bacteria contain RC–LH1 ‘Core’ complexes. The structure of this complex from Rhodobacter sphaeroides, Rhodopseudomonas palustris and Thermochromatium tepidum has been solved using X-ray crystallography. Recently, the application of single particle cryo-EM has revolutionised structural biology and the structure of the RC–LH1 ‘Core’ complex from Blastochloris viridis has been solved using this technique, as well as the complex from the non-purple Chloroflexi species, Roseiflexus castenholzii. It is apparent that these structures are variations on a theme, although with a greater degree of structural diversity within them than previously thought. Furthermore, it has recently been discovered that the only phototrophic representative from the phylum Gemmatimonadetes, Gemmatimonas phototrophica, also contains a RC–LH1 ‘Core’ complex. At present only a low-resolution EM-projection map exists but this shows that the Gemmatimonas phototrophica complex contains a double LH1 ring. This short review compares these different structures and looks at the functional significance of these variations from two main standpoints: energy transfer and quinone exchange.

59 BASIC BIOLOGICAL SCIENCES↗