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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Conserved conformational dynamics determine enzyme activity

Homologous enzymes often exhibit different catalytic rates despite a fully conserved active site. The canonical view is that an enzyme sequence defines its structure and function and, more recently, that intrinsic protein dynamics at different time scales enable and/or promote catalytic activity. Here, we show that, using the protein tyrosine phosphatase PTP1B, residues surrounding the PTP1B active site promote dynamically coordinated chemistry necessary for PTP1B function. However, residues distant to the active site also undergo distinct intermediate time scale dynamics and these dynamics are correlated with its catalytic activity and thus allow for different catalytic rates in this enzyme family. We identify these previously undetected motions using coevolutionary coupling analysis and nuclear magnetic resonance spectroscopy. Our findings strongly indicate that conserved dynamics drives the enzymatic activity of the PTP family. Characterization of these conserved dynamics allows for the identification of novel regulatory elements (therapeutic binding pockets) that can be leveraged for the control of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Gcn2 structurally mimics and functionally repurposes the HisRS enzyme for the integrated stress response

Protein kinase Gcn2 attenuates protein synthesis in response to amino acid starvation while stimulating translation of a transcriptional activator of amino acid biosynthesis. Gcn2 activation requires a domain related to histidyl-tRNA synthetase (HisRS), the enzyme that aminoacylates tRNA His . While evidence suggests that deacylated tRNA binds the HisRS domain for kinase activation, ribosomal P-stalk proteins have been implicated as alternative activating ligands on stalled ribosomes. We report crystal structures of the HisRS domain ofChaetomium thermophilumGcn2 that reveal structural mimicry of both catalytic (CD) and anticodon-binding (ABD) domains, which in authentic HisRS bind the acceptor stem and anticodon loop of tRNA His . Elements for forming histidyl adenylate and aminoacylation are lacking, suggesting that Gcn2 HisRS was repurposed for kinase activation, consistent with mutations in the CD that dysregulate yeast Gcn2 function. Substituting conserved ABD residues well positioned to contact the anticodon loop or that form a conserved ABD–CD interface impairs Gcn2 function in starved cells. Mimicry in Gcn2 HisRS of two highly conserved structural domains for binding both ends of tRNA—each crucial for Gcn2 function—supports that deacylated tRNAs activate Gcn2 and exemplifies how a metabolic enzyme is repurposed to host new local structures and sequences that confer a novel regulatory function.

Science & Technology - Other Topics↗

DOE OSTI2020

Perovskite-Carbon Nanotube Light-Emitting Fibers

Active fibers with electro-optic functionalities are promising building blocks for the emerging and rapidly growing field of fiber and textile electronics. Yet, there remains significant challenges that require improved understanding of the principles of active fiber assembly to enable the development of fiber-shaped devices characterized by having a small diameter, being lightweight, and having high mechanical strength. To this end, the current frameworks are insufficient, and new designs and fabrication approaches are essential to accommodate this unconventional form factor. Here, we present a first demonstration of a pathway that effectively integrates the foundational components meeting such requirements, with the use of a flexible and robust conductive core carbon nanotube fiber and an organic–inorganic emissive composite layer as the two critical elements. We introduce an active fiber design that can be realized through an all solution-processed approach. In conclusion, we have implemented this technique to demonstrate a three- layered light-emitting fiber with a coaxially coated design.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Novel Anti-LY6G6D/CD3 T-Cell–Dependent Bispecific Antibody for the Treatment of Colorectal Cancer

Abstract New therapeutics and combination regimens have led to marked clinical improvements for the treatment of a subset of colorectal cancer. Immune checkpoint inhibitors have shown clinical efficacy in patients with mismatch-repair–deficient or microsatellite instability–high (MSI-H) metastatic colorectal cancer (mCRC). However, patients with microsatellite-stable (MSS) or low levels of microsatellite instable (MSI-L) colorectal cancer have not benefited from these immune modulators, and the survival outcome remains poor for the majority of patients diagnosed with mCRC. In this article, we describe the discovery of a novel T-cell–dependent bispecific antibody (TDB) targeting tumor-associated antigen LY6G6D, LY6G6D-TDB, for the treatment of colorectal cancer. RNAseq analysis showed that LY6G6D was differentially expressed in colorectal cancer with high prevalence in MSS and MSI-L subsets, whereas LY6G6D expression in normal tissues was limited. IHC confirmed the elevated expression of LY6G6D in primary and metastatic colorectal tumors, whereas minimal or no expression was observed in most normal tissue samples. The optimized LY6G6D-TDB, which targets a membrane-proximal epitope of LY6G6D and binds to CD3 with high affinity, exhibits potent antitumor activity both in vitro and in vivo. In vitro functional assays show that LY6G6D-TDB–mediated T-cell activation and cytotoxicity are conditional and target dependent. In mouse xenograft tumor models, LY6G6D-TDB demonstrates antitumor efficacy as a single agent against established colorectal tumors, and enhanced efficacy can be achieved when LY6G6D-TDB is combined with PD-1 blockade. Our studies provide evidence for the therapeutic potential of LY6G6D-TDB as an effective treatment option for patients with colorectal cancer.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1987

Definition of tolerance to continuous hyperoxia in man - An abstract report of Predictive Studies V

The overall goals, design, and procedures of Predictive Studies V are discussed as well as the specific elements of neural effects produced by prolonged hyperoxia. It is noted that Predictive Studies V study of oxygen poisoning in normal men during uninterrupted exposures to oxygen over the range of hyperbaric oxygen exposure most useful in diving, the treatment of gas lesion diseases, and general hyperbaric medicine. It is found that, throughout the study, the most striking observations were related to effects on visual function, on the lung, and the probable interactions of preconvulsive neural activity with effects on cardiovascular and respiratory-pulmonary functions.

Lambertsen, C. J.↗

NASA NTRS1993

Evaluation of two January - June 1992 ERS-1 AMI wind vector data sets

A Jan. - Jun. 1992 10 m height wind vector field was computed with the CMOD2 model function. Freilich and Dunbar used ESA measurements of AMI (Active Microwave Instrument) sigma-naught to derive a refined model function and to produce an alternate Jan. - Jun. 1992 10 m height wind vector field, named FD data. The ESA and FD model functions and algorithms were substantially different. The FD wind vectors were in better agreement with the climatological mean wind field and with moored buoy wind measurements. The average correlation coefficients between monthly mean and daily averaged FD and moored buoy matchups of the Cartesian wind components were 0.84 and 0.74, respectively. The average root mean square differences between the monthly mean and daily averaged FD and moored buoy matchups of the Cartesian wind components were 1.25 and 3.0 m/s, respectively.

Halpern, D.↗

NASA NTRS1980

Functional stability of cerebral circulatory system

The functional stability of the cerebral circulation system seems to be based on the active mechanisms and on those stemming from specific of the biophysical structure of the system under study. This latter parameter has some relevant criteria for its quantitative estimation. The data obtained suggest that the essential part of the mechanism for active responses of cerebral vessels which maintains the functional stability of this portion of the vascular system, consists of a neurogenic component involving central nervous structures localized, for instance, in the medulla oblongata.

Moskalenko, Y. Y.↗

DOE OSTI2026

Regional specialization in prefrontal cortex manifests in the reliability of task progression codes

The brain has the remarkable ability to guide the performance of complex tasks. Distinct prefrontal cortical areas make specific contributions to this ability, with the orbitofrontal cortex (OFC) critical for processing information related to trial outcomes and the dorsomedial prefrontal cortex (dmPFC) critical for sustained effort and selecting the right action at the right time. Yet, in both areas, neural activity represents both outcome- and action-related quantities. How similar neural representations support different functions remains unclear. Here, we compared OFC and dmPFC activity in rats performing a spatial alternation task. We show that, in contrast to other task-related variables, task progression is represented in both areas, but with distinct patterns of across-trial reliability that match each area’s previously documented functional specialization. Our results indicate that the engagement of reliable, task-phase-specific activity patterns differs across prefrontal regions in a manner well suited to engage different computations at different times.

Biological and medical sciences↗

DOE OSTI2020

Combining Computational Modeling with Reaction Kinetics Experiments for Elucidating the In Situ Nature of the Active Site in Catalysis

Microkinetic modeling based on density functional theory (DFT) derived energetics is important for addressing fundamental questions in catalysis. The quantitative fidelity of microkinetic models (MKMs), however, is often insufficient to conclusively infer the mechanistic details of a specific catalytic system. Here, this can be attributed to a number of factors such as an incorrect model of the active site for which DFT calculations are performed, deficiencies in the hypothesized reaction mechanism, inadequate consideration of the surface environment under reaction conditions, and intrinsic errors in the DFT exchange-correlation functional. Despite these limitations, we aim at developing a rigorous understanding of the reaction mechanism and of the nature of the active site for heterogeneous catalytic chemistries under reaction conditions. By achieving parity between experimental and modeling outcomes through robust parameter estimation and by ensuring coverage-consistency between DFT calculations and MKM predictions, it is possible to systematically refine the mechanistic model and, thereby, our understanding of the catalytic active site in situ.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1996

On the Reaction of FNO2 with CH3, t-butyl, and C13H21

Theoretical studies are reported for the reaction of FN02 with the radicals CH3, t-butyl, and C13H21, which are templates for the radical site of a hydrogenated diamond surface. All structures axe fully optimized using density functional theory (DFT) based on the B3LYP functional. Calibration calculations axe performed for CH3 + FNO2 using the coupled cluster approach, the the internally contracted multireference configuration. interaction method, and second order perturbation theory based upon complete active space SCF (CASSCF) reference wave function. These calibration calculations support the B3LYP approach for the calculation of bond energies, but show the B3LYP barrier is too low. Combining the calibration calculations with the larger clusters yields our best estimate of a barrier of about 10 kcal/mol. for the reaction of FNO2 with a radical site on hydrogenated diamond.

Thuemmel, H. T.↗

DOE OSTI2025

Cryogenic thermal modeling of microwave high density signaling

Superconducting quantum computers require microwave control lines running from room temperature to the mixing chamber of a dilution refrigerator. Adding more lines without preliminary thermal modeling to make predictions risks overwhelming the cooling power at each thermal stage. In this paper, we investigate the thermal load of SC-086/50-SCN-CN semi-rigid coaxial cable, which is commonly used for the control and readout lines of a superconducting quantum computer, as we increase the number of lines to a quantum processor. We investigate the makeup of the coaxial cables, verify the materials and dimensions, and experimentally measure the total thermal conductivity of a single cable as a function of the temperature from cryogenic to room temperature values. We also measure the cryogenic DC electrical resistance of the inner conductor as a function of temperature, allowing for the calculation of active thermal loads due to Ohmic heating. Fitting this data produces a numerical thermal conductivity function used to calculate the static heat loads due to thermal transfer within the wires resulting from a temperature gradient. The resistivity data is used to calculate active heat loads, and we use these fits in a cryogenic model of a superconducting quantum processor in a typical Bluefors XLD1000-SL dilution refrigerator, investigating how the thermal load increases with processor sizes ranging from 100 to 225 qubits. We conclude that the theoretical upper limit of the described architecture is approximately 200 qubits. However, including an engineering margin in the cooling power and the available space for microwave readout circuitry at the mixing chamber, the practical limit is approximately 140 qubits.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS2022

Structural Shape Sensing from Strain Data Using the Basis Function Method

An aircraft shape must be measured during flight to implement an active trim shape control, such as an active dihedral control for a highly flexible aircraft with a high-aspect-ratio wing, and an active sonic boom control for a supersonic transport aircraft. A basis function method for linear as well as geometrically nonlinear structural shape sensing is proposed in this study. Basis functions can be mode shapes, linear static deformation shapes, or geometrically nonlinear static deformation shapes. The proposed basis function method is validated using a high-aspect-ratio wing, a swept test plate, and the National Aeronautics and Space Administration Low Boom Flight Demonstration mission X-59 Quiet Supersonic Technology (QueSST) aircraft (Lockheed Martin, Bethesda, Maryland). A large structural deformation of a high-aspect-ratio wing is successfully captured using the proposed basis function method with less than 0.3-percentprediction error at the wing-tip section. The basis function method gives excellent deformation prediction, even with stress concentration. Performance of the basis functions is compared using the X-59 stabilator sample case. In most of the sample load cases, static deformations give a better correlation with the target deformation than do mode shapes. Wing shape sensing with sparse strain data is also demonstrated in this study using the X-59 QueSST aircraft. Predicted structural deformations match reasonably with the target deformations even without strain gauges on some structural components. The predicted deformations have a good match with the target deformations.

Chan-gi Pak↗

DOE OSTI2021

Facile Synthesis of Palladium-Based Nanocrystals with Different Crystal Phases and a Comparison of Their Catalytic Properties

A relatively unexplored aspect of noble-metal nanomaterials is polymorphism, or their ability to crystallize in different crystal phases. Here, in this work, a method is reported for the facile synthesis of Ru@Pd core–shell nanocrystals featuring polymorphism, with the core made of hexagonally close-packed (hcp)-Ru while the Pd shell takes either an hcp or face-centered cubic (fcc) phase. The polymorphism shows a dependence on the shell thickness, with shells thinner than ≈1.4 nm taking the hcp phase whereas the thicker ones revert to fcc. The injection rate provides an experimental knob for controlling the phase, with one-shot and drop-wise injection of the Pd precursor corresponding to fcc-Pd and hcp-Pd shells, respectively. When these nanocrystals are tested as catalysts toward formic acid oxidation, the Ru@Pd hcp nanocrystals outperform Ru@Pd fcc in terms of both specific activity and peak potential. Density functional theory calculations are also performed to elucidate the origin of this performance enhancement.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Selective Enrichment Coupled with Proteomics to Identify S-Acylated Plasma Membrane Proteins in Arabidopsis

Protein S-acylation, predominately in the form of palmitoylation, is a reversible lipid post-translational modification (PTM) on cysteines that plays important roles in protein localization, trafficking, activity, and complex assembly. The functions and regulatory mechanisms of Sacylation have been extensively studied in mammals, owing to remarkable development of the high-resolution proteomics and the discovery of the S-acylation-related enzymes. However, the advance of S-acylation studies in plants lags farther behind than that in mammals, mainly due to the lack of knowledge about proteins responsible for this process, such as protein acyltransferases (PATs) and their substrates. In this article, a systematic protocol to study global S-acylation in Arabidopsis seedlings is described. The procedures are presented in detail, including preparation of Arabidopsis seedlings, enrichment of plasma membrane (PM) proteins, followed by enrichment of S-acylated proteins/peptides based on the acyl-biotin exchange (ABE) method, and large-scale identification of S-acylated proteins/peptides via mass spectrometry. This approach enables researchers to study S-acylation of PM proteins in plants in a systematic and straightforward way. Basic protocol 1: Preparation of Arabidopsis seedling materials Basic protocol 2: Isolation and enrichment of plasma membrane proteins Support protocol 1: Determination of protein concentration using BCA assay Basic Protocol 3: Enrichment of S-acylated proteins by ABE method Support protocol 2: Protein precipitation by methanol/chloroform method Basic Protocol 4: Trypsin digestion and proteomic analysis Alternate protocol 1: Pre-resin digestion and peptide level enrichment.

S-acylation, palmitoylation, plasma membrane prote↗

DOE OSTI2022

Uncompetitive, adduct-forming SARM1 inhibitors are neuroprotective in preclinical models of nerve injury and disease

Axon degeneration is an early pathological event in many neurological diseases. The identification of the nicotinamide adenine dinucleotide (NAD) hydrolase SARM1 as a central metabolic sensor and axon executioner presents an exciting opportunity to develop novel neuroprotective therapies that can prevent or halt the degenerative process, yet limited progress has been made on advancing efficacious inhibitors. Here we describe a class of NAD-dependent active-site SARM1 inhibitors that function by intercepting NAD hydrolysis and undergoing covalent conjugation with the reaction product adenosine diphosphate ribose (ADPR). The resulting small-molecule ADPR adducts are highly potent and confer compelling neuroprotection in preclinical models of neurological injury and disease, validating this mode of inhibition as a viable therapeutic strategy. Additionally, we show that the most potent inhibitor of CD38, a related NAD hydrolase, also functions by the same mechanism, further underscoring the broader applicability of this mechanism in developing therapies against this class of enzymes.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Galectin-1 secreted by bone marrow-derived mesenchymal stem cells mediates anti-inflammatory responses in acute airway disease

The hallmarks of allergic airway disease (AAD) include infiltration of inflammatory cells into the bronchoalveolar space. Bone marrow derived mesenchymal stem cells (BMSCs) show anti-inflammatory properties in AAD. In addition, galectin-1 (Gal-1) is a lectin significantly upregulated upon inflammation and is also known to mediate potential anti-inflammatory responses. We hypothesized that BMSCs regulated inflammatory responses by secretion of Gal-1 during AAD pathogenesis. BMSCs were isolated from murine femurs and tibiae and adoptively transferred into an ovalbumin-induced AAD mouse model. Knockdown of Gal-1 in BMSCs was performed using shRNA. Flow cytometry, ELISAs, and immunohistology were performed to analyze inflammatory responses in mice, and a Transwell system was used to establish an in vitro co-culture system of lung epithelial cells (MLE-12) and BMSCs. Administration of BMSCs significantly upregulated Gal-1 expression upon inflammation and decreased infiltration of inflammatory cells and secretion of proinflammatory cytokines in vivo. In addition, we showed that this function was mediated by reduced activation of the MAPK p38 signaling pathway. Similar observations were found using an in vitro lipopolysaccharide-induced model when MLE-12 cells were co-cultured with BMSCs. Gal-1 secretion by BMSCs alleviated inflammatory responses observed in AAD and hence provides a promising therapeutic alternative to AAD patients insensitive to conventional drug treatments.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Identifying the Molecular Edge Termination of Exfoliated Hexagonal Boron Nitride Nanosheets with Solid-State NMR Spectroscopy and Plane-Wave DFT Calculations

Hexagonal boron nitride nanosheets (h-BNNS), the isoelectronic analog to graphene, have received interest over the past decade due to their high thermal oxidative resistance, high bandgap, catalytic activity, and low cost. The functional groups that terminate boron and nitrogen zigzag and/or armchair edges directly affect their chemical, physical, and electronic properties. However, an understanding of the molecular edge termination present in h-BNNS is lacking. Here, high-resolution magic-angle spinning (MAS) solid-state NMR (SSNMR) spectroscopy, and plane-wave density-functional theory (DFT) calculations are used to determine the molecular edge termination in exfoliated h-BNNS. 1 H → 11 B cross-polarization MAS (CPMAS) SSNMR spectra of h-BNNS revealed multiple hydroxyl/oxygen coordinated boron edge sites that were not detectable in direct excitation experiments. A dynamic nuclear polarization (DNP)-enhanced 1 H → 15 N CPMAS spectrum of h-BNNS displayed four distinct 15 N resonances while a 2D 1 H{ 14 N} dipolar-HMQC spectrum acquired with fast MAS revealed three distinct 14 N environments. Plane-wave DFT calculations were used to construct model edge structures and predict the corresponding 11 B, 14 N and 15 N SSNMR spectra. Comparison of the experimental and predicted SSNMR spectra confirms that zigzag and armchair edges with both amine and boron hydroxide/oxide termination are present. The detailed characterization of h-BNNS molecular edge termination will prove useful for many material science applications. The techniques outlined here should also be applicable to understand the molecular edge terminations in other 2D materials

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Advancing the Performance of Lithium-Rich Oxides in Cooperation with Inherent Complexities: Engineering Domain Structure

The nanodomain structure of lithium- and manganese-rich, composite cathode materials has been systematically altered through synthesis conditions while keeping larger-scale morphological differences to a minimum. Clear changes in electrochemical performance across the samples studied are observed, especially with respect to the anomalous impedance at low states-of-charge. Atomic-scale modeling, coupled to electrochemical measurements and physical characterization, reveals the local consequences of the high-voltage activation charge process as a function of specific domain structures. Furthermore, the results explain the influence of different postactivation structures on the insertion of Li-ions and the associated impedance during discharge. This work adds to our series of studies on lithium- and manganese-rich oxides, demonstrating that the inherent performance of LMRs can be greatly enhanced through rational, highly controlled synthetic strategies based on an understanding of synthesis–structure–property relationships across length scales.

25 ENERGY STORAGE↗