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Results for “integrative structural biology”

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 OSTI2021

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current ‘state of the art’ from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of ‘soft recommendations’ about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage ‘open science’ practices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Processing of DNA single-strand breaks with oxidatively damaged ends by LIG1

Abstract DNA ligase 1 (LIG1) seals broken strand breaks by joining two adjacent ends during DNA replication and repair transactions. We previously reported atomic-level insight into the strategies that LIG1 uses to discriminate mismatches or ribonucleotides. However, how LIG1 processes strand breaks with oxidatively damaged ends in the absence and presence of a “wrong” sugar remains unknown. Here, we determined the crystal structures of LIG1/nick DNA complexes with 3′-8-oxodG and 3′-8-oxorG templating A or C during the pre- and post-catalytic steps of the ligation reaction. Our structures demonstrated differences in the distances at the +1 and +2 nucleotides relative to the 3′-end of the nick and a shift in the template base position to accommodate the oxidative lesion depending on the dual coding potential of 8-oxoG, which forms Hoogsteen or Watson–Crick base pairing in -syn or -anti conformation. Furthermore, these structural adjustments lead to mutagenic ligation or non-mutagenic end joining of the nick substrates. Overall, our findings provide mechanistic insight into how LIG1 processes nicks harboring oxidative damage and ribonucleotides to ensure fidelity at the final ligation step of DNA repair and replication to maintain genome integrity.

Balu, Kanal E [Department of Biochemistry and Mole↗
DOE OSTI2021

Metal Chalcogenides for Neuromorphic Computing: Emerging Materials and Mechanisms

The approaching end of Moore's Law scaling has significantly accelerated multiple fields of research including neuromorphic-, quantum-, and photonic computing, each of which possesses unique benefits unobtained through conventional binary computers. One of the most compelling arguments for neuromorphic computing systems is power consumption, noting that computations made in the human brain are approximately 106 times more efficient than conventional CMOS logic. This review article focuses on the materials science and physical mechanisms found in metal chalcogenides that are currently being explored for use in neuromorphic applications. We begin by reviewing the key biological signal generation and transduction mechanisms within neuronal components of mammalian brains and subsequently compare with observed experimental measurements in chalcogenides. With robustness and energy efficiency in mind, we will focus on short-range mechanisms such as structural phase changes and correlated electron systems that can be driven by low-energy stimuli, such as temperature or electric field. We aim to highlight fundamental materials research and existing gaps that need to be overcome to enable further integration or advancement of metal chalcogenides for neuromorphic systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Electrochemical reduction of ammonia-captured CO 2 to CO over a nickel single-atom catalyst

Carbon reactive capture and conversion offers a sustainable route to valuable chemicals and fuels while aiding Green House Gas (GHG) reduction. Direct electrochemical conversion of capture solutions like bicarbonate avoids the energy demands of conventional CO 2 regeneration. Ammonium bicarbonate (NH 4 HCO 3 ) is particularly attractive due to its low decomposition temperature and ability to supply in situ CO 2 from dilute sources without requiring purified CO 2 . Meanwhile, single-atom catalysts (SACs) with nitrogen-coordinated metal sites further enhance CO 2 reduction efficiency using Earth-abundant materials. In this study, we demonstrate a nickel single-atom catalyst (Ni-SAC)-based electrolyzer that utilizes NH 4 HCO 3 as the CO 2 source, achieving significantly improved CO production performance compared to the conventional silver cathodes used in the CO 2 reduction reaction (CO 2 RR) to produce CO. The Ni-SAC cathode exhibited a Faradaic efficiency of 60.1% for CO production at −200 mA cm −2 , while the silver cathode achieved a Faradaic efficiency of only 2%, likely due to ammonium-induced poisoning. Furthermore, the integration of a customized microporous layer onto the electrode significantly increased the Faradaic efficiency from 64% to 83% at −100 mA cm −2 , emphasizing the crucial role of electrode structure optimization in enhancing CO selectivity. These findings demonstrate a sustainable and economically viable strategy for green CO production directly from CO 2 capture solutions.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2024

Metasurface‐Based Mueller Matrix Microscope

In conventional optical microscopes, image contrast of objects mainly results from the differences in light intensity and/or color. Muller matrix optical microscopes (MMMs), on the other hand, can provide significantly enhanced image contrast and rich information about objects by analyzing their interactions with polarized light. However, state-of-the-art MMMs are fundamentally limited by bulky and slow polarization state generators and analyzers. Here, the study demonstrates a metasurface-based MMM, i.e., Meta-MMM, which is equipped with a chip-integrated, single-shot metasurface polarization state analyzer (Meta-PSA). The Meta-MMM is featured with high-speed measurement (≈2s per Muller matrix (MM) image), superior operation stability, dual-color operation, and high measurement accuracy (measurement error 1–2%) for MM imaging. The Meta-MMM is applied to nanostructure characterization, surface morphology analysis, and discovering birefringent structures in honeybee wings. As a result, the Meta-MMMs hold the promise to revolutionize various applications from biological imaging, medical diagnosis, and material characterization to industry inspection and space exploration.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Selection and development of aptamers for pyoverdine

The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescensPf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA and 2’ F-Y-RNA aptamers with specificity for pyoverdine over other siderophores. Pyoverdines from various strains possess a conserved chromophore along with strain-specific peptide chain. Some of the isolated aptamers bind to chromophore of pyoverdine. These will identify pyoverdines from a variety of pseudomonads. Identification of aptamers that selectively bind the peptide portion of pyoverdine Pf-5 is underway. The identified aptamers that are broadly and narrowly specific for pyoverdines or Pf-5 will be optimized for integration into an electrochemical biosensor to track, in real time, P fluorescens activity and other pseudomonads in and around the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Nanoscale chemical imaging with structured X-ray illumination

High-resolution imaging with compositional and chemical sensitivity is crucial for a wide range of scientific and engineering disciplines. Although synchrotron X-ray imaging through spectromicroscopy has been tremendously successful and broadly applied, it encounters challenges in achieving enhanced detection sensitivity, satisfactory spatial resolution, and high experimental throughput simultaneously. In this work, based on structured illumination, we develop a single-pixel X-ray imaging approach coupled with a generative image reconstruction model for mapping the compositional heterogeneity with nanoscale resolvability. This method integrates a full-field transmission X-ray microscope with an X-ray fluorescence detector and eliminates the need for nanoscale X-ray focusing and raster scanning. We experimentally demonstrate the effectiveness of our approach by imaging a battery sample composed of mixed cathode materials and successfully retrieving the compositional variations of the imaged cathode particles. Bridging the gap between structural and chemical characterizations using X-rays, this technique opens up vast opportunities in the fields of biology, environmental, and materials science, especially for radiation-sensitive samples.

Li, Jizhou↗
DOE OSTI2025

Conformation-specific synthetic intrabodies modulate mTOR signaling with subcellular spatial resolution

Subcellular compartmentalization is integral to the spatial regulation of mechanistic target of rapamycin (mTOR) signaling. However, the biological outputs associated with location-specific mTOR signaling events are poorly understood and challenging to decouple. Here, we engineered synthetic intracellular antibodies (intrabodies) that are capable of modulating mTOR signaling with genetically programmable spatial resolution. Epitope-directed phage display was exploited to generate high affinity synthetic antibody fragments (Fabs) against the FKBP12–Rapamycin binding site of mTOR (mTOR FRB ). We determined high-resolution crystal structures of two unique Fabs that discriminate distinct conformational states of mTOR FRB through recognition of its substrate recruitment interface. By leveraging these conformation-specific binders as intracellular probes, we uncovered the structural basis for an allosteric mechanism governing mTOR complex 1 (mTORC1) stability mediated by subtle structural adjustments within mTOR FRB . Furthermore, our results demonstrated that synthetic binders emulate natural substrates by employing divergent yet complementary hydrophobic residues at defined positions, underscoring the broad molecular recognition capability of mTOR FRB . Intracellular signaling studies showed differential time-dependent inhibition of S6 kinase 1 and Akt phosphorylation by genetically encoded intrabodies, thus supporting a mechanism of inhibition analogous to the natural product rapamycin. Finally, we implemented a feasible approach to selectively modulate mTOR signaling in the nucleus through spatially programmed intrabody expression. These findings establish intrabodies as versatile tools for dissecting the conformational regulation of mTORC1 and should be useful to explore how location-specific mTOR signaling influences disease progression.

Science & Technology - Other Topics↗
NASA NTRS1996

The calculation of radial dose from heavy ions: predictions of biological action cross sections

The track structure model of heavy ion cross sections was developed by Katz and co-workers in the 1960s. In this model the action cross section is evaluated by mapping the dose-response of a detector to gamma rays (modeled from biological target theory) onto the radial dose distribution from delta rays about the path of the ion. This is taken to yield the radial distribution of probability for a "hit" (an interaction leading to an observable end-point). Radial integration of the probability yields the cross section. When different response from ions of different Z having the same stopping power is observed this model may be indicated. Since the 1960s there have been several developments in the computation of the radial dose distribution, in the measurement of these distributions, and in new radiobiological data against which to test the model. The earliest model, by Butts and Katz made use of simplified delta ray distribution functions, of simplified electron range-energy relations, and neglected angular distributions. Nevertheless it made possible the calculation of cross sections for the inactivation of enzymes and viruses, and allowed extension to tracks in nuclear emulsions and other detectors and to biological cells. It set the pattern for models of observable effects in the matter through which the ion passed. Here we outline subsequent calculations of radial dose which make use of improved knowledge of the electron emission spectrum, the electron range-energy relation, the angular distribution, and some considerations of molecular excitation, of particular interest both close to the path of the ion and the outer limits of electron penetration. These are applied to the modeling of action cross sections for the inactivation of several strains of E-coli and B. subtilis spores where extensive measurements in the "thin-down" region have been made with heavy ion beams. Such calculations serve to test the radial dose calculations at the outer limit of electron penetration. We lack data from which to test these calculations in regions close to the path of the ion aside from our earliest work on latent tracks in plastics, though it appears that the criterion then suggested for the threshold of track formation, of a minimal dose at a minimal distance (of about 20 angstroms, in plastics), remains valid.

NASA Discipline Radiation Health↗
DOE OSTI2021

A quantitative model for a nanoscale switch accurately predicts thermal actuation behavior

Manipulation of temperature can be used to actuate DNA origami nano-hinges containing gold nanoparticles. We develop a physical model of this system that uses partition function analysis of the interaction between the nano-hinge and nanoparticle to predict the probability that the nano-hinge is open at a given temperature. The model agrees well with experimental data and predicts experimental conditions that allow the actuation temperature of the nano-hinge to be tuned over a range of temperatures from 30 °C to 45 °C. Additionally, the model identifies microscopic interactions that are important to the macroscopic behavior of the system, revealing surprising features of the system. This combination of physical insight and predictive potential is likely to inform future designs that integrate nanoparticles into dynamic DNA origami structures or use strand binding interactions to control dynamic DNA origami behavior. Furthermore, our modeling approach could be expanded to consider the incorporation, stability, and actuation of other types of functional elements or actuation mechanisms integrated into nucleic acid devices.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Cytochrome P450–catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass ( Panicum virgatum L.)

Specialized diterpenoid metabolites are important mediators of plant-environment interactions in monocot crops. To understand metabolite functions in plant environmental adaptation that ultimately can enable crop improvement strategies, a deeper knowledge of the underlying species-specific biosynthetic pathways is required. Furthermore, we report the genomics-enabled discovery of five cytochrome P450 monooxygenases (CYP71Z25-CYP71Z29) that form previously unknown furanoditerpenoids in the monocot bioenergy crop Panicum virgatum (switchgrass). Combinatorial pathway reconstruction showed that CYP71Z25-CYP71Z29 catalyze furan ring addition directly to primary diterpene alcohol intermediates derived from distinct class II diterpene synthase products. Transcriptional co-expression patterns and the presence of select diterpenoids in switchgrass roots support the occurrence of P450-derived furanoditerpenoids in planta. Integrating molecular dynamics, structural analysis and targeted mutagenesis identified active site determinants that contribute to the distinct catalytic specificities underlying the broad substrate promiscuity of CYP71Z25-CYP71Z29 for native and non-native diterpenoids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study

Abstract Atomic-level three-dimensional (3D) structure data for biological macromolecules often prove critical to dissecting and understanding the precise mechanisms of action of cancer-related proteins and their diverse roles in oncogenic transformation, proliferation, and metastasis. They are also used extensively to identify potentially druggable targets and facilitate discovery and development of both small-molecule and biologic drugs that are today benefiting individuals diagnosed with cancer around the world. 3D structures of biomolecules (including proteins, DNA, RNA, and their complexes with one another, drugs, and other small molecules) are freely distributed by the open-access Protein Data Bank (PDB). This global data repository is used by millions of scientists and educators working in the areas of drug discovery, vaccine design, and biomedical and biotechnology research. The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides an integrated portal to the PDB archive that streamlines access for millions of worldwide PDB data consumers worldwide. Herein, we review online resources made available free of charge by the RCSB PDB to basic and applied researchers, healthcare providers, educators and their students, patients and their families, and the curious public. We exemplify the value of understanding cancer-related proteins in 3D with a case study focused on human papillomavirus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Array of Graphene Variable Capacitors on 100 mm Silicon Wafers for Vibration-Based Applications

Highly flexible, electrically conductive freestanding graphene membranes hold great promise for vibration-based applications. This study focuses on their integration into mainstream semiconductor manufacturing methods. We designed a two-mask lithography process that creates an array of freestanding graphene-based variable capacitors on 100 mm silicon wafers. The first mask forms long trenches terminated by square wells featuring cone-shaped tips at their centers. The second mask fabricates metal traces from each tip to its contact pad along the trench and a second contact pad opposite the square well. A graphene membrane is then suspended over the square well to form a variable capacitor. The same capacitor structures were also built on 5 mm by 5 mm bare dies containing an integrated circuit underneath. We used atomic force microscopy, optical microscopy, and capacitance measurements in time to characterize the samples.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Scaling Field-Theoretic Simulation for Multicomponent Mixtures with Neural Operators

Multicomponent polymer mixtures are ubiquitous in biological self-organization but are notoriously difficult to study computationally. Plagued by both slow single molecule relaxation times and slow equilibration within dense mixtures, molecular dynamics simulations are typically infeasible at the spatial scales required to study the stability of mesophase structure. Polymer field theories offer an attractive alternative, but analytical calculations are only tractable for mean-field theories and nearby perturbations, constraints that become especially problematic for fluctuation-induced effects such as coacervation. Here, we show that a recently developed technique for obtaining numerical solutions to partial differential equations based on operator learning, neural operators, lends itself to a highly scalable training strategy by parallelizing per-species operator maps. We illustrate the efficacy of our approach on six-component mixtures with randomly selected compositions and that it significantly outperforms the state-of-the-art pseudospectral integrators for field-theoretic simulations, especially as polymer lengths become long.

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

Accurate prediction of protein structures and interactions using a three-track neural network

DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryo–electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. Here, we make the method available to the scientific community to speed biological research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural mechanism for modulation of functional amyloid and biofilm formation by Staphylococcal Bap protein switch

The Staphylococcal Bap proteins sense environmental signals (such as pH, [Ca 2+ ]) to build amyloid scaffold biofilm matrices via unknown mechanisms. We here report the crystal structure of the aggregation-prone region of Staphylococcus aureus Bap which adopts a dumbbell-shaped fold. The middle module (MM) connecting the N-terminal and C-terminal lobes consists of a tandem of novel double-Ca 2+ -binding motifs involved in cooperative interaction networks, which undergoes Ca 2+ -dependent order-disorder conformational switches. The N-terminal lobe is sufficient to mediate amyloid aggregation through liquid-liquid phase separation and maturation, and subsequent biofilm formation under acidic conditions. Such processes are promoted by disordered MM at low [Ca 2+ ] but inhibited by ordered MM stabilized by Ca 2+ binding, with inhibition efficiency depending on structural integrity of the interaction networks. Furthermore, these studies illustrate a novel protein switch in pathogenic bacteria and provide insights into the mechanistic understanding of Bap proteins in modulation of functional amyloid and biofilm formation, which could be implemented in the anti-biofilm drug design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Saccharomyces cerevisiae CellWall Remodeling in the Absence of Knr4 and Kre6 Revealed by Nano-FourierTransform Infrared Spectroscopy

The cell wall integrity (CWI) signaling pathway regulates yeast cell wall biosynthesis, cell division, and responses to external stress. The cell wall, comprised of a dense network of chitin, β-1,3- and β-1,6- glucans, and mannoproteins, is very thin, <100 nm. Alterations in cell wall composition may activate the CWI pathway. Saccharomyces cerevisiae, a model yeast, was used to study the role of individual wall components in altering the structure and biophysical properties of the yeast cell wall. Near-field Fourier transform infrared spectroscopy (nano-FT-IR) was used for the first direct, spectrochemical identification of cell wall composition in a background (wild-type) strain and two deletion mutants from the yeast knock-out collection: kre6Δ and knr4Δ. Killer toxin resistant 6 (Kre6) is an integral membrane protein required for biosynthesis of β-1,6-glucan, while Knr4 is a cell signaling protein involved in the control of cell wall biosynthesis, in particular, biosynthesis and deposition of chitin. Complementary spectral data were obtained with far-field (FF)-FT-IR, in transmission, and with attenuated total reflectance (ATR) spectromicroscopy with 3 –10 μm wavelength-dependent spatial resolution. The FF-FT-IR spectra of cells and spectra of isolated cell wall components showed that components of the cell body dominated transmission spectra and were still evident in ATR spectra. In contrast, the nano-FT-IR at ~25 nm spatial resolution could be used to characterize the yeast wall chemical structure. Our results show that the β-1,6-glucan content is decreased in kre6Δ, while all glucan content is decreased in the knr4Δ cell wall. The latter may be thinner than in wild type, since not only are mannan and chitin detectable by nano-FT-IR, but also lipid membranes and protein, indicative of cell interior.

59 BASIC BIOLOGICAL SCIENCES↗