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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM

The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20–30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

CryoTEN: efficiently enhancing cryo-EM density maps using transformers

Abstract Motivation Cryogenic electron microscopy (cryo-EM) is a core experimental technique used to determine the structure of macromolecules such as proteins. However, the effectiveness of cryo-EM is often hindered by the noise and missing density values in cryo-EM density maps caused by experimental conditions such as low contrast and conformational heterogeneity. Although various global and local map-sharpening techniques are widely employed to improve cryo-EM density maps, it is still challenging to efficiently improve their quality for building better protein structures from them. Results In this study, we introduce CryoTEN—a 3D UNETR++ style transformer to improve cryo-EM maps effectively. CryoTEN is trained using a diverse set of 1295 cryo-EM maps as inputs and their corresponding simulated maps generated from known protein structures as targets. An independent test set containing 150 maps is used to evaluate CryoTEN, and the results demonstrate that it can robustly enhance the quality of cryo-EM density maps. In addition, automatic de novo protein structure modeling shows that protein structures built from the density maps processed by CryoTEN have substantially better quality than those built from the original maps. Compared to the existing state-of-the-art deep learning methods for enhancing cryo-EM density maps, CryoTEN ranks second in improving the quality of density maps, while running >10 times faster and requiring much less GPU memory than them. Availability and implementation The source code and data are freely available at https://github.com/jianlin-cheng/cryoten.

Biochemistry & Molecular Biology↗
DOE OSTI2023

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.

42 ENGINEERING↗
DOE OSTI2026

Freeze It or Leave It? Evaluating the Role of Cryo-Electron Microscopy in Battery Research

Cryogenic electron microscopy (cryo-EM) continues to gain prominence in materials science, particularly in battery research where it has enabled high-resolution, multimodal characterization of electrode materials and interfaces that otherwise degrade quickly under electron beam irradiation. But as anyone who has attempted cryo-EM techniques knows, freezing comes at a cost; cryo-EM experiments are time-consuming, highly sensitive, and carry an increased risk of artifacts due to issues such as frost contamination. Thus, when planning new characterization of battery materials or other beam-sensitive samples, it is critical to consider whether (and which) cryo-EM techniques are appropriate, based on study goals and an understanding of electron beam-sample interactions. Here we review such considerations for battery materials to elucidate the questions of when, why, and how to freeze to achieve high-quality characterization.

25 ENERGY STORAGE↗
DOE OSTI2025

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↗
DOE OSTI2023

Monomer and dimer structures of cytochrome bo 3 ubiquinol oxidase from Escherichia coli

Abstract The Escherichia coli cytochrome bo 3 ubiquinol oxidase is a four‐subunit heme‐copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it is unclear whether this ubiquinol oxidase functions as a monomer, or as a dimer in a manner similar to its eukaryotic counterparts—the mitochondrial electron transport complexes. In this study, we determined the monomeric and dimeric structures of the E. coli cytochrome bo 3 ubiquinol oxidase reconstituted in amphipol by cryogenic electron microscopy single particle reconstruction (cryo‐EM SPR) to a resolution of 3.15 and 3.46 Å, respectively. We have discovered that the protein can form a dimer with C2 symmetry, with the dimerization interface maintained by interactions between the subunit II of one monomer and the subunit IV of the other monomer. Moreover, the dimerization does not induce significant structural changes in the monomers, except the movement of a loop in subunit IV (residues 67–74).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins

Structural studies of membrane proteins by cryogenic electron microscopy (cryo-EM) often require antibody fragments (Fabs) to facilitate particle alignments and achieve high resolution. While conformational nanobodies have been developed to lock specific states of many membrane proteins, they only add 15 kDa of mass to the complex. We developed a synthetic Fab (NabFab) that rigidly binds the conserved scaffold of nanobodies, providing a universally applicable fiducial for cryo-EM studies of protein–nanobody complexes. Additionally, we demonstrate the concept by determining two high-resolution structures of membrane proteins bound to specific nanobodies and NabFab. As the structural epitope for NabFab can be incorporated into the scaffold of virtually any nanobody, this raises the prospect of facile structure determination of many nanobody–protein complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges

Abstract Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling the determination of high-resolution 3-Dimensional (3D) structures of large biological macromolecules. Protein particle picking, the process of identifying individual protein particles in cryo-EM micrographs for building protein structures, has progressed from manual and template-based methods to sophisticated artificial intelligence (AI)-driven approaches in recent years. This review critically examines the evolution and current state of cryo-EM particle picking methods, with an emphasis on the impact of AI. We conducted a comparative evaluation of popular AI-based particle picking methods, using both general machine learning metrics and specific cryo-EM structure determination metrics. This analysis involved constructing the 3D density map from the picked protein particles and assessing the obtained resolution and particle orientation diversity, underscoring the significant impact of AI on cryo-EM particle picking. Despite the advancements, we also identified key obstacles, such as handling complex micrographs with small proteins. The analysis provides insights into the future development of more sophisticated and fully automated AI methods in cryo-EM particle recognition.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Two datasets are better than one: method of double moments for 3D reconstruction in cryo-EM

Cryo-electron microscopy is a powerful imaging technique for reconstructing three-dimensional molecular structures from noisy tomographic projection images of randomly oriented particles. We introduce a new data fusion framework, termed the method of double moments, which reconstructs molecular structures from two instances of the second-order moment of projection images obtained under distinct orientation distributions: one uniform, the other non-uniform and unknown. We prove that these moments generically uniquely determine the underlying structure, up to a global rotation and reflection, and we develop a convex-relaxation-based algorithm that achieves accurate recovery using only second-order statistics. Our results demonstrate the advantage of collecting and modeling multiple datasets under different experimental conditions, illustrating that leveraging dataset diversity can substantially enhance reconstruction quality in computational imaging tasks.

Kam’s method↗
DOE OSTI2022

Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia

Cryogenic electron microscopy (cryo-EM) has emerged as a viable structural tool for molecular therapeutics development against human diseases. However, it remains a challenge to determine structures of proteins that are flexible and smaller than 30 kDa. The 11 kDa KIX domain of CREB-binding protein (CBP), a potential therapeutic target for acute myeloid leukemia and other cancers, is a protein which has defied structure-based inhibitor design. Here, we develop an experimental approach to overcome the size limitation by engineering a protein double-shell to sandwich the KIX domain between apoferritin as the inner shell and maltose-binding protein as the outer shell. To assist homogeneous orientations of the target, disulfide bonds are introduced at the target–apoferritin interface, resulting in a cryo-EM structure at 2.6 Å resolution. We used molecular dynamics simulations to design peptides that block the interaction of the KIX domain of CBP with the intrinsically disordered pKID domain of CREB. The double-shell design allows for fluorescence polarization assays confirming the binding between the KIX domain in the double-shell and these interacting peptides. Further cryo-EM analysis reveals a helix–helix interaction between a single KIX helix and the best peptide, providing a possible strategy for developments of next-generation inhibitors.

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

Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution

Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution1,2,3. However, cryo-EM studies of protein-free RNA are in their early days. The Tetrahymena thermophila group I self-splicing intron was the first ribozyme to be discovered and has been a prominent model system for the study of RNA catalysis and structure–function relationships4, but its full structure remains unknown. Here we report cryo-EM structures of the full-length Tetrahymena ribozyme in substrate-free and bound states at a resolution of 3.1 Å. Additionally, newly resolved peripheral regions form two coaxially stacked helices; these are interconnected by two kissing loop pseudoknots that wrap around the catalytic core and include two previously unforeseen (to our knowledge) tertiary interactions. The global architecture is nearly identical in both states; only the internal guide sequence and guanosine binding site undergo a large conformational change and a localized shift, respectively, upon binding of RNA substrates. These results provide a long-sought structural view of a paradigmatic RNA enzyme and signal a new era for the cryo-EM-based study of structure–function relationships in ribozymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures

The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. Cryo2StructData is larger than existing, publicly available datasets for training AI methods to build atomic protein structures from cryo-EM density maps. We trained and tested deep learning models on Cryo2StructData to validate its quality showing that it is ready for being used to train and test AI methods for building atomic models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation

Imaging scaffolds composed of designed protein cages fused to designed ankyrin repeat proteins (DARPins) have enabled the structure determination of small proteins by cryogenic electron microscopy (cryo-EM). One particularly well characterized scaffold type is a symmetric tetrahedral assembly composed of 24 subunits, 12 A and 12 B, which has three cargo-binding DARPins positioned on each vertex. Here, the X-ray crystal structure of a representative tetrahedral scaffold in the apo state is reported at 3.8 Å resolution. The X-ray crystal structure complements recent cryo-EM findings on a closely related scaffold, while also suggesting potential utility for crystallographic investigations. As observed in this crystal structure, one of the three DARPins, which serve as modular adaptors for binding diverse `cargo' proteins, present on each of the vertices is oriented towards a large solvent channel. The crystal lattice is unusually porous, suggesting that it may be possible to soak crystals of the scaffold with small (≤30 kDa) protein cargo ligands and subsequently determine cage–cargo structures via X-ray crystallography. The results suggest the possibility that cryo-EM scaffolds may be repurposed for structure determination by X-ray crystallography, thus extending the utility of electron-microscopy scaffold designs for alternative structural biology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Operando Freezing Cryogenic Electron Microscopy of Active Battery Materials

Abstract Understanding structural and chemical evolution of battery materials during operation is critical to achieving safe, efficient, and long-lasting energy storage. Cryogenic electron microscopy (cryo-EM) has become a valuable tool in battery characterization, leveraging low temperatures to improve stability of sensitive materials under electron beam irradiation. However, typical cryo-EM sample preparations leave extended time between the electrochemical point of interest and ex situ freezing of samples, during which active structures may relax, degrade, or otherwise evolve. Here, we detail a method for operando freezing cryo-EM to preserve and characterize native electrode and interfacial structures that arise during battery cycling, based on an operando plunge freezer and cold sample removal process. We validate the method on multiple electrode materials and quantify and discuss the freezing rate achieved. Operando freezing cryo-EM can be used to directly visualize transient features that arise at active electrochemical interfaces, to enable deeper understanding of structural evolution and interfacial chemistry in batteries and other electrochemical systems.

25 ENERGY STORAGE↗
DOE OSTI2021

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Quantitative Modeling of High-Energy Electron Scattering in Thick Samples Using Monte Carlo Techniques

Cryo-electron microscopy (cryo-EM) is a powerful tool for imaging biological samples but is typically limited by sample thickness, which is restricted to a few hundred nanometers depending on the electron energy. However, there is a growing need for imaging techniques capable of studying biological samples up to 10 µm in thickness while maintaining nanoscale resolution. This need motivates the use of mega-electron-volt scanning transmission electron microscopy (MeV-STEM), which leverages the high penetration power of MeV electrons to generate high-resolution images of thicker samples. In this study, we employ Monte Carlo simulations to model electron–sample interactions and explore the signal decay of imaging electrons through thick specimens. By incorporating material properties, interaction cross-sections for energy loss, and experimental parameters, we investigate the relationship between the incident and transmitted beam intensities. Key factors such as detector collection angle, convergence semi-angle, and the material properties of samples were analyzed. Our results demonstrate that the relationship between incident and transmitted beam intensities follows the Beer–Lambert law over thicknesses ranging from a few microns to several tens of microns, depending on material composition, electron energy, and collection angles. The linear depth of silicon dioxide reaches 3.9 µm at 3 MeV, about 6 times higher than that at 300 keV. Meanwhile, the linear depth of amorphous ice reaches 17.9 µm at 3 MeV, approximately 11.5 times higher than that at 300 keV. These findings are crucial for advancing the study of thick biological and semiconductor samples using MeV-STEM.

36 MATERIALS SCIENCE↗
DOE OSTI2024

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net

Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step in the cryo-EM-based structure determination. However, existing methods trained on a limited amount of cryo-EM data still cannot accurately pick protein particles from noisy cryo-EM images. The general foundational artificial intelligence–based image segmentation model such as Meta’s Segment Anything Model (SAM) cannot segment protein particles well because their training data do not include cryo-EM images. Here, we present a novel approach (CryoSegNet) of integrating an attention-gated U-shape network (U-Net) specially designed and trained for cryo-EM particle picking and the SAM. The U-Net is first trained on a large cryo-EM image dataset and then used to generate input from original cryo-EM images for SAM to make particle pickings. CryoSegNet shows both high precision and recall in segmenting protein particles from cryo-EM micrographs, irrespective of protein type, shape and size. On several independent datasets of various protein types, CryoSegNet outperforms two top machine learning particle pickers crYOLO and Topaz as well as SAM itself. The average resolution of density maps reconstructed from the particles picked by CryoSegNet is 3.33 Å, 7% better than 3.58 Å of Topaz and 14% better than 3.87 Å of crYOLO. It is publicly available at https://github.com/jianlin-cheng/CryoSegNet

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

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.↗