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Results for “cryoelectron microscopy”

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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121 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation

Functional crosstalk between DNA methylation, histone H3 lysine-9 trimethylation (H3K9me3) and heterochromatin protein 1 (HP1) is essential for proper heterochromatin assembly and genome stability. However, how repressive chromatin cues guide DNA methyltransferases for region-specific DNA methylation remains largely unknown. Here, we report structure-function characterizations of DNA methyltransferase Defective-In-Methylation-2 (DIM2) in Neurospora . The DNA methylation activity of DIM2 requires the presence of both H3K9me3 and HP1. Our structural study reveals a bipartite DIM2-HP1 interaction, leading to a disorder-to-order transition of the DIM2 target-recognition domain that is essential for substrate binding. Furthermore, the structure of DIM2-HP1-H3K9me3-DNA complex reveals a substrate-binding mechanism distinct from that for its mammalian orthologue DNMT1. In addition, the dual recognition of H3K9me3 peptide by the DIM2 RFTS and BAH1 domains allosterically impacts the DIM2-substrate binding, thereby controlling DIM2-mediated DNA methylation. Together, this study uncovers how multiple heterochromatin factors coordinately orchestrate an activity-switching mechanism for region-specific DNA methylation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structure of a biohybrid photosystem I-platinum nanoparticle solar fuel catalyst

Biohybrid solar fuel catalysts leverage natural light-driven enzymes to produce valuable fuel products. One useful biological platform for such a system is photosystem I, a pigment-protein complex that captures sunlight and converts it into chemical energy with near unity quantum efficiency, which generates low potential reducing equivalents for metabolism. Realizing and understanding the molecular basis for an approach that utilizes those electrons and stores solar energy as a fuel is therefore appealing. Here, we report the 2.27-Å global resolution cryo-EM structure of a photosystem I complex with bound platinum nanoparticles that catalyzes light-driven H 2 production. The platinum nanoparticle binding sites and possible stabilizing interactions are described. Overall, the investigation reveals a direct structural look at a photon-to-fuels photosynthetic biohybrid system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural diversity and clustering of bacterial flagellar outer domains

Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we report atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii , Stenotrophomonas maltophilia , and Geovibrio thiophilus . Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyze all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a distinct cluster, indicating additional opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.

Science & Technology - Other Topics↗
DOE OSTI2025

A family of tubular pili from harmful algal bloom forming cyanobacterium Microcystis aeruginosa

Cyanobacteria are vital photosynthetic prokaryotes, but some form harmful algal blooms (cyanoHABs) that disrupt ecosystems and produce toxins. The mechanisms by which these blooms form have yet to be fully understood, particularly the role of extracellular components. Here, we present a 2.4 Å cryo-EM structure of a pilus, termed the cyanobacterial tubular (CT) pilus, found in the cyanoHAB-forming Microcystis aeruginosa. The pilin exhibits a unique protein fold, forming a tubular pilus structure with tight, double-layer anti-parallel β-sheet interactions. We show that CT pili are essential for buoyancy by facilitating the formation of micro-colonies, which increases drag force and prevents sinking. The CT pilus surface is heavily glycosylated with ten monosaccharide modifications per pilin. Furthermore, CT pili can enrich microcystin, potentially enhancing cellular resilience, and co-localize with iron-enriched extracellular matrix components. Thus, we propose that this pilus plays an important role in the proliferation of cyanoHABs. This just discovered pilus family appears to be widely distributed across several cyanobacterial orders. Our structural and functional characterization of CT pili provide insights into cyanobacterial cell morphology, physiology, and toxin interactions, and identify potential targets for disrupting bloom formation.

Cryoelectron microscopy↗
DOE OSTI2025

PhaseT3M: 3D imaging at 1.6 Å resolution via electron cryo-tomography with nonlinear phase retrieval

Electron cryo-tomography (cryo-ET) enables 3D imaging of complex, radiation-sensitive structures with molecular detail. However, image contrast from the interference of scattered electrons is nonlinear with atomic density and multiple scattering further complicates interpretation. These effects degrade resolution, particularly in conventional reconstruction algorithms, which assume linearity. Particle averaging can reduce such issues but is unsuitable for heterogeneous or dynamic samples ubiquitous in biology, chemistry, and materials sciences. Here, we develop a phase retrieval-based cryo-ET method, PhaseT3M. We experimentally demonstrate its application to an approximately 7 nm Co3O4 nanoparticle on an approximately 30 nm carbon substrate, achieving a maximum resolution of 1.6 Å, surpassing conventional limits using standard cryo-TEM equipment. PhaseT3M uses a multislice model for multiple scattering and Bayesian optimization for alignment and computational aberration correction, with a positivity constraint to recover ‘missing wedge’ information. Applied directly to biological particles, it enhances reconstruction quality and reduces artifacts, establishing a standard for routine 3D imaging with phase contrast.

Biophysics↗
DOE OSTI2025

How short peptides disassemble tau fibrils in Alzheimer’s disease

Reducing fibrous aggregates of the protein tau is a possible strategy for halting the progression of Alzheimer’s disease (AD). Previously, we found that in vitro, the d-enantiomeric peptide (D-peptide) D-TLKIVWC disassembles ultra-stable tau fibrils extracted from the autopsied brains of individuals with AD (hereafter, these tau fibrils are referred to as AD-tau) into benign segments, with no energy source other than ambient thermal agitation. To consider D-peptide-mediated disassembly as a potential route to therapeutics for AD, it is essential to understand the mechanism and energy source of the disassembly action. Here, in this work, we show that the assembly of D-peptides into amyloid-like (‘mock-amyloid’) fibrils is essential for AD-tau disassembly. These mock-amyloid fibrils have a right-handed twist but are constrained to adopt a left-handed twist when templated in complex with AD-tau. The release of strain that accompanies the conversion of left-twisted to right-twisted, relaxed mock-amyloid produces a torque that is sufficient to break the local hydrogen bonding between tau molecules, and leads to the fragmentation of AD-tau. This strain-relief mechanism seems to operate in other examples of amyloid fibril disassembly, and could inform the development of first-in-class therapeutics for amyloid diseases.

Alzheimer's disease↗
DOE OSTI2023

Brominated lipid probes expose structural asymmetries in constricted membranes

Lipids in biological membranes are thought to be functionally organized, but few experimental tools can probe nanoscale membrane structure. Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane-remodeling system composed of human CHMP1B and IST1, we observed leaflet-level and protein-localized structural lipid patterns within highly constricted and thinned membrane nanotubes. These nanotubes differed markedly from protein-free, flat bilayers in leaflet thickness, lipid diffusion rates and lipid compositional and conformational asymmetries. Simulations and cryo-EM imaging of brominated stearoyl-docosahexanenoyl-phosphocholine showed how a pair of phenylalanine residues scored the outer leaflet with a helical hydrophobic defect where polyunsaturated docosahexaenoyl tails accumulated at the bilayer surface. Combining cryo-EM of halogenated lipids with molecular dynamics thus enables new characterizations of the composition and structure of membranes on molecular length scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Control of transcription elongation and DNA repair by alarmone ppGpp

Second messenger (p)ppGpp (collectively guanosine tetraphosphate and guanosine pentaphosphate) mediates bacterial adaptation to nutritional stress by modulating transcription initiation. More recently, ppGpp has been implicated in coupling transcription and DNA repair; however, the mechanism of ppGpp engagement remained elusive. Here we present structural, biochemical and genetic evidence that ppGpp controls Escherichia coli RNA polymerase (RNAP) during elongation via a specific site that is nonfunctional during initiation. Structure-guided mutagenesis renders the elongation (but not initiation) complex unresponsive to ppGpp and increases bacterial sensitivity to genotoxic agents and ultraviolet radiation. Thus, ppGpp binds RNAP at sites with distinct functions in initiation and elongation, with the latter being important for promoting DNA repair. Our data provide insights on the molecular mechanism of ppGpp-mediated adaptation during stress, and further highlight the intricate relationships between genome stability, stress responses and transcription.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Architecture, catalysis and regulation of methylthio-alkane reductase for bacterial sulfur acquisition from volatile organic compounds

Bacteria utilize methylthio-alkane reductase (MAR) to acquire sulfur from volatile organic sulfur compounds. Reductive cleavage of methylthio-ethanol and dimethylsulfide liberates methanethiol for methionine synthesis and concomitantly releases ethylene and methane, respectively. Here we show that the native MAR of Rhodospirillum rubrum is a two-component system composed of a MarH ATP-dependent reductase and a MarDK catalytic core, whose architecture parallels nitrogenase. MarS complexes with MarDK to downregulate MAR activity during cellular sulfate influx, based on chromatographic and activity analyses. MarDK possesses complex metallocofactors resembling, but not identical to, nitrogenase P- and iron-only M-clusters, designated as mar1 and mar2 clusters based on metal, spectroscopic and mutagenesis analyses. They exhibit electronic features similar to the iron-only nitrogenase under turnover and, remarkably, are matured by MarB or nitrogenase NifB, resulting in maturase-dependent activity profiles. Altogether, this suggests a broader scope of reactivity, mechanisms and regulation in microbial metabolism for the nitrogenase-like family of enzymes than previously considered.

09 BIOMASS FUELS↗
DOE OSTI2022

Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state

Abstract AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of membrane-anchored AAA+ proteases essential for membrane protein quality control. Although a spiral staircase rotation mechanism for substrate translocation across the FtsH pore has been proposed, the detailed conformational changes among various states have not been clear due to absence of FtsH structures in these states. We report here the cryo-EM structure for Thermotoga maritima FtsH ( Tm FtsH) in a fully ADP-bound symmetric state. Comparisons of the ADP-state structure with its apo-state and a substrate-engaged yeast YME1 structure show conformational changes in the ATPase domains, rather than the protease domains. A reconstruction of the full-length Tm FtsH provides structural insights for the dynamic transmembrane and the periplasmic domains. Our structural analyses expand the understanding of conformational switches between different nucleotide states in ATP hydrolysis by FtsH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mechanism of allosteric inhibition of human p97/VCP ATPase and its disease mutant by triazole inhibitors

Human p97 ATPase is crucial in various cellular processes, making it a target for inhibitors to treat cancers, neurological, and infectious diseases. Triazole allosteric p97 inhibitors have been demonstrated to match the efficacy of CB-5083, an ATP-competitive inhibitor, in cellular models. However, the mechanism is not well understood. This study systematically investigates the structures of new triazole inhibitors bound to both wild-type and disease mutant forms of p97 and measures their effects on function. These inhibitors bind at the interface of the D1 and D2 domains of each p97 subunit, shifting surrounding helices and altering the loop structures near the C-terminal α2 G helix to modulate domain-domain communications. A key structural moiety of the inhibitor affects the rotameric conformations of interacting side chains, indirectly modulating the N-terminal domain conformation in p97 R155H mutant. The differential effects of inhibitor binding to wild-type and mutant p97 provide insights into drug design with enhanced specificity, particularly for oncology applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

The XLZD Design Book: towards the next-generation liquid xenon observatory for dark matter and neutrino physics

This report describes the experimental strategy and technologies for XLZD, the next-generation xenon observatory sensitive to dark matter and neutrino physics. In the baseline design, the detector will have an active liquid xenon target of 60 tonnes, which could be increased to 80 tonnes if the market conditions for xenon are favorable. It is based on the mature liquid xenon time projection chamber technology used in current-generation experiments, LZ and XENONnT. The report discusses the baseline design and opportunities for further optimization of the individual detector components. The experiment envisaged here has the capability to explore parameter space for Weakly Interacting Massive Particle (WIMP) dark matter down to the neutrino fog, with a 3σ evidence potential for WIMP-nucleon cross sections as low as 3 x 10 –49 cm 2 (at 40 GeV/c 2 WIMP mass). The observatory will also have leading sensitivity to a wide range of alternative dark matter models. It is projected to have a 3σ observation potential of neutrinoless double beta decay of 136 Xe at a half-life of up to 5.7 x 10 27 years. Additionally, it is sensitive to astrophysical neutrinos from the sun and galactic supernovae.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Real-time 3D analysis during electron tomography using tomviz

The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high-quality tomogram is available within 30 minutes. Real-time tomography is integrated into tomviz, an open-source and cross-platform 3D data analysis tool that contains intuitive graphical user interfaces (GUI), to enable any scientist to characterize biological and material structure in 3D.

36 MATERIALS SCIENCE↗