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

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
NASA NTRS2000

Over-Expression, Purification and Crystallization of Human Dihydrolipoamide Dehydrogenase

Dehydrolipoamide dehydrogenase (E3; dihydrolipoan-tide:NAD+ oxidoreductase, EC 1.8.1.4) is a common catalytic component found in pyruvate dehydrogenase complex, alpha-ketoglutarate dehydrogenase complex, and branched-chain cc-keto acid dehydrogenase complex. E3 is also a component (referred to as L protein) of the glycine cleavage system in bacterial metabolism (2). Active E3 forms a homodimer with four distinctive subdomain structures (FAD binding, NAD+ binding, central and interface domains) with non-covalently but tightly bound FAD in the holoenzyme. Deduced amino acids from cloned full-length human E3 gene showed a total of 509 amino acids with a leader sequence (N-terminal 35 amino acids) that is excised (mature form) during transportation of expressed E3 into mitochondria membrane. So far, three-dimensional structure of human E3 has not been reported. Our effort to achieve the elucidation of the X-ray crystal structure of human E3 will be presented. Recombinant pPROEX-1 expression vector (from GIBCO BRL Life Technologies) having the human E3 gene without leader sequence was constructed by Polymerase Chain Reaction (PCR) and subsequent ligation, and cloned in E.coli XL1-Blue by transformation. Since pPROEX-1 vector has an internal His-tag (six histidine peptide) located at the upstream region of a multicloning site, one-step affinity purification of E3 using nickelnitriloacetic acid (Ni-NTA) agarose resin, which has a strong affinity to His-tag, was feasible. Also a seven-amino-acid spacer peptide and a recombinant tobacco etch virus protease recognition site (seven amino acids peptide) found between His-tag and first amino acid of expressed E3 facilitated the cleavage of His-tag from E3 after the affinity purification. By IPTG induction, ca. 15 mg of human E3 (mature form) was obtained from 1L LB culture with overnight incubation at 25C. Over 98% of purity of E3 from one-step Ni-NTA agarose affinity purification was confirmed by SDS-PAGE analysis. For crystallization, E3 samples were prepared with and without His-tag. To minimize the aggregation of E3, apo- and holo- forms of E3s were tested, as well as a mutated E3. Dynamic light scattering measurements revealed that the E3 preparations without His-tag and substrate are highly monodispersive with regard to homodimers. Consequent crystallization trials of this E3 preparation led to single crystals of E3 grown by the vapor diffusion method. Crystals were obtained within a few days from solution containing poly (ethylene glycol) monomethyl ether 5000 as a precipitant. Autoindexing and integration of the X-ray diffraction data showed that E3 crystals belong to an orthorhombic system with unit cell parameters a-- 123. 1, b= 165.3 and c=214.3A. Further optimization of protein preparation and crystallization experiments for the structural determination will be discussed.

Hong, Y. S.↗
DOE OSTI2025

Engineering a protease-stable, oral single-domain antibody to inhibit IL-23 signaling

Interleukin (IL)-23 is a validated therapeutic target in inflammatory bowel disease. While antibodies targeting IL23 demonstrate clinical efficacy, they face challenges such as high costs, safety risks, and the necessity of parenteral administration. Here, we present a workflow to simultaneously enhance the affinity and protease stability of an inhibitory anti-IL23R VHH for oral use. Cocrystal structure analysis reveals that the anti-IL23R VHH employs both CDR and framework residues to achieve picomolar affinity for IL23R. The engineered VHH remains stable for over 8 h in intestinal fluid and 24 h in fecal samples. Oral administration of this VHH achieves deep pathway inhibition in a murine colitis model. Furthermore, a single pill provides sustained IL23R inhibition in nonhuman primate blood for over 24 h. With high potency, gut stability, high production yield, and favorable drug-like properties, oral VHHs offer a promising approach for inflammatory bowel diseases.

Science & Technology - Other Topics↗
NASA NTRS1989

The search for and identification of amino acids, nucleobases and nucleosides in samples returned from Mars

An investigation of the returned Mars samples for biologically important organic compounds, with emphasis on amino acid, the puring and pyrimidine bases, and nucleosides is proposed. These studies would be conducted on subsurface samples obtained by drilling past the surface oxidizing layer with emphasis on samples containing the larges quantities of organic carbon as determined by the rover gas chromatographic mass spectrometer (GCMS). Extraction of these molecules from the returned samples will be performed using the hydrothermal extraction technique described by Cheng and Ponnamperuma. More rigorous extraction methods will be developed and evaluated. For analysis of the extract for free amino acids or amino acids present in a bound or peptidic form, aliquots will be analyzed by capillary GCMS both before and after hydrolysis with 6N hydrochloric acid. Establishment of the presence of amino acids would then lead to the next logical step which would be the use of chiral stationary gas chromatography phases to determine the enatiomeic composition of the amino acids present, and thus potentially establish their biotic or abiotic origin. Confirmational analyses for amino acids would include ion-exchange and reversed-phase liquid chromatographic analysis. For analyses of the returned Mars samples for nucleobases and nucleosides, affinity and reversed-phase liquid chromatography would be utilized. This technology coupled with scanning UV detection for identification, presents a powerful tool for nucleobase and nucleoside analysis. Mass spectrometric analysis of these compounds would confirm their presence in samples returned form Mars.

Gehrke, Charles W.↗
DOE OSTI2026

Affine Transformations to Correlate Experimental and Simulated EDS Spectra for Multi-Element Systems

Energy Dispersive X-ray Spectroscopy (EDS) is an essential technique for determining elemental concentrations and distributions within microstructures, critical for materials discovery, optimization, and qualification. However, most published EDS data is qualitative because current quantitative EDS analysis methods require extensive calibration and post-processing, limiting their practicality and widespread adoption. This work seeks to establish a framework for accelerated EDS characterization and spectrum analysis that can leverage ML to analyze correlations between various elemental compositions and resulting EDS spectra. The complex physics and data result in a high-dimensional problem that grows exponentially with the number of elements in the system and the complexity of the spectrum analysis. ML provides a way to compute and optimize the results of this highly dimensional problem in a flexible way to tailor it to the user’s specific needs and material system. However, the framework emphasizes transparency through a strictly mathematical affine transformation, so the analysis remains understandable and reviewable to facilitate adoption by the scientific community. While currently implemented methods are simplistic and unvalidated, further development and demonstration of this framework could enable high-throughput, accurate, and accessible EDS characterization.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
NASA NTRS1983

Complexes of polyadenylic acid and the methyl esters of amino acids

A study of amino acid methyl esters binding to polyadenylic acid supports the theory that the genetic code originated through weak but selective affinities between amino acids and nucleotides. NMR, insoluble complex analysis, and ultraviolet spectroscopy are used to illustrate a correlation between the hydrophybicities of A amino acids and their binding constants, which, beginning with the largest, are in the order of Phe (having nominally a hydrophobic AAA anticodon), Ile, Leu, Val and Gly (having a hydrophilic anticodon with no A). In general, the binding constants are twice the values by Reuben and Polk (1980) for monomeric AMP, which suggests that polymer amino acids are interacting with only one base. No real differences are found betwen poly A binding for free Phe, Phe methyl ester or Phe amide, except that the amide value is slightly lower.

Khaled, M. A.↗
NASA NTRS2009

Computational Study on Full-length Human Ku70 with Double Stranded DNA: Dynamics, Interactions and Functional Implications

The Ku70/80 heterodimer is the first repair protein in the initial binding of double-strand break (DSB) ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. In this study we constructed a full-length human Ku70 structure based on its crystal structure, and performed 20 ns conventional molecular dynamic (CMD) simulations on this protein and several other complexes with short DNA duplexes of different sequences. The trajectories of these simulations indicated that, without the topological support of Ku80, the residues in the bridge and C-terminal arm of Ku70 are more flexible than other experimentally identified domains. We studied the two missing loops in the crystal structure and predicted that they are also very flexible. Simulations revealed that they make an important contribution to the Ku70 interaction with DNA. Dislocation of the previously studied SAP domain was observed in several systems, implying its role in DNA binding. Targeted molecular dynamic (TMD) simulation was also performed for one system with a far-away 14bp DNA duplex. The TMD trajectory and energetic analysis disclosed detailed interactions of the DNA-binding residues during the DNA dislocation, and revealed a possible conformational transition for a DSB end when encountering Ku70 in solution. Compared to experimentally based analysis, this study identified more detailed interactions between DNA and Ku70. Free energy analysis indicated Ku70 alone is able to bind DNA with relatively high affinity, with consistent contributions from various domains of Ku70 in different systems. The functional implications of these domains in the processes of Ku heterodimerization and DNA damage recognition and repair can be characterized in detail based upon this analysis.

Hu, Shaowen↗
DOE OSTI2021

The efficacy of Lewis affinity scale metrics to represent solvent interactions with reagent salts in all-inorganic metal halide perovskite solutions

Solvents employed in the solution processing of metal halide perovskites are known to play a key role in defining the morphology and properties of the resulting thin film, and thus the performance of perovskite solar cell devices. Accurate metrics are needed that are capable of differentiating among candidates, finding solvents that adequately solubilize the various precursor species in solution and facilitate the nucleation and growth of these materials. Existing metrics such as the unsaturated Mayer bond order (UMBO) and the Gutmann donor number (DN) have been tested for lead iodide perovskite systems; but there has yet to be a comprehensive study on their transferability to lead-free perovskite solutions. Here, we use ab initio methods (density functional theory) and regression analysis tools to study the usefulness of DN and BF 3 affinity scales in this regard. We compared the relative effectiveness of these scales to describe interactions between solvents and BXn perovskite salts of lead (Pb 2+ ), tin (Sn 2+ and Sn 4+ ), germanium (Ge 2+ ), bismuth (Bi 3+ ), and antimony (Sb 3+ and Sb 5+ ). The DN proved to be a better representation than the BF 3 of such interactions, reflecting the closer similarity of these species to the “parent” SbCl 5 Lewis acid than to BF 3 . In addition, we have uncovered the usefulness of the lithium cation affinity metric (LCA) to describe the strength of interactions between solvents and A-site cations (e.g. Na + , K + , Rb + and Cs + ) in all-inorganic metal halide perovskite solutions. We find that the coordination strengths of solvents towards species in all-inorganic metal halide perovskite solutions are best described by two different metrics with distinct modes of action: DN differentiates among BX n salt complexes, and LCA among A-site cation species. This revelation can help guide the choice of solvent to optimize processing conditions. It also emphasizes the importance of selecting solvents whose DN and LCA optimize coordination to key Lewis acid species in all-inorganic perovskite solutions.

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

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. In this study, we aim to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2

COVID-19 is a highly infectious respiratory disease caused by the novel coronavirus SARS-CoV-2. It has become a global pandemic and its frequent mutations may pose new challenges for vaccine design. During viral infection, the Spike RBD of SARS-CoV-2 binds the human host cell receptor ACE2, enabling the virus to enter the host cell. Both the Spike and ACE2 are densely glycosylated, and it is unclear how distinctive glycan types may modulate the interaction of RBD and ACE2. Detailed understanding of these determinants is key for the development of novel therapeutic strategies. To this end, we perform extensive all-atom simulations of the (i) RBD-ACE2 complex without glycans, (ii) RBD-ACE2 with oligomannose MAN9 glycans in ACE2, and (iii) RBD-ACE2 with complex FA2 glycans in ACE2. These simulations identify the key residues at the RBD-ACE2 interface that form contacts with higher probabilities, thus providing a quantitative evaluation that complements recent structural studies. Notably, we find that this RBD-ACE2 contact signature is not altered by the presence of different glycoforms, suggesting that RBD-ACE2 interaction is robust. Applying our simulated results, we illustrate how the recently prevalent N501Y mutation may alter specific interactions with host ACE2 that facilitate the virus-host binding. Furthermore, our simulations reveal how the glycan on Asn90 of ACE2 can play a distinct role in the binding and unbinding of RBD. Finally, an energetics analysis shows that MAN9 glycans on ACE2 decrease RBD-ACE2 affinity, while FA2 glycans lead to enhanced binding of the complex. Together, our results provide a more comprehensive picture of the detailed interplay between virus and human receptor, which is much needed for the discovery of effective treatments that aim at modulating the physical-chemical properties of this virus.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2019

Template Matching Used for Small Body Optical Navigation with Poorly Detailed Objects

Object and template matching becomes difficult when an image lacks detail. This is particularly worrisome when typical matching techniques, cross-correlation, log-polar mapping, and key point matching fail. Work herein describes a formulation that identifies objects of interest, estimates the affine transformation between a template object and scene using Principal Component Analysis (PCA), and provides a fit value for the objects and template incorporating Hu's Moments. The algorithm presented is tested on synthetic images and images obtained from the OSIRIS-REx mission while the spacecraft was approaching its target, Bennu. Results for the current formulation show that, with the presence of large-scale variations and rotation, the fitting scheme performs well when compared with other techniques.

Lyzhoft, Joshua R.↗
DOE OSTI2026

Directed evolution of a stem-helix–targeting antibody enables MERS-CoV cross-neutralization through enhanced binding affinity

Broadly neutralizing antibodies (bnAbs) targeting conserved regions of the betacoronavirus spike are important for pan-betacoronavirus protection and pandemic preparedness. Here, we report the isolation of a human monoclonal antibody, CC65.1, from a SARS-CoV-2 convalescent donor that targets the conserved S2 stem helix region. CC65.1 neutralizes various sarbecoviruses, including SARS-CoV-2, and binds to the MERS-CoV spike but lacks MERS-CoV-neutralizing activity due to insufficient binding affinity. We utilized directed evolution to enhance the binding affinity of CC65.1 for the MERS-CoV S2 stem helix, yielding engineered antibody variants with newly acquired MERS-CoV-neutralizing activity. High-resolution structural analysis reveals key paratope mutations that enhance binding and stabilize epitope engagement. Our findings demonstrate the potential of in vitro affinity maturation to expand the neutralization breadth of stem-helix-targeting antibodies across divergent betacoronaviruses. This work supports the development of engineered bnAbs for broadly protective betacoronavirus countermeasures and provides a strategy for achieving cross-lineage neutralization.

Zhou, Panpan↗
DOE OSTI2025

The evolution of analytical techniques for multiplex analysis of protein biomarkers

Introduction: The landscape of biomarker development has evolved with advanced analytical technologies, particularly affinity- and mass spectrometry-based techniques. These advancements have deepened our understanding of disease mechanisms, enabling the development of precise diagnostic tools and personalized medicine. Protein biomarkers, which play pivotal roles in biological processes, have become invaluable in diagnosing and monitoring diseases, aided by their presence in various biological samples and the availability of established detection methods. Areas covered: This review covers the role of protein biomarkers in clinical practice, the development and dimensionality of protein biomarkers, advancements in detection technologies, a comparison of these technologies, and future directions in biomarker discovery and disease mechanism elucidation. Expert opinion: Advances in biomarker technologies have the potential to transform diagnostics and personalized treatment but face challenges such as high costs and technical complexity. Enhancing reproducibility and integrating multi-omics approaches may offer better insights. In conclusion, the field should evolve toward high-throughput, automated methods, continuously adapting research, and clinical practices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Data-Driven Insights into the Structural Essence of Plasticity in High-Entropy Alloys

The heterogeneous mechanical response of a crystalline alloy with multiple principal elements was investigated using molecular dynamics simulations. The local configuration of the alloy in its quiescent state was characterized by the variables derived from the gyration tensor and the atomic electronegativity. A multivariate analysis identified the geometric and chemical factors that influenced the atomic packing variations. Further, upon straining, the non-affine displacement exhibited spatial heterogeneity. A statistical correlation was established between the local yield events and the specific features of the local configuration. Our findings, validated by the performance metrics analysis, provided a structural criterion for the instability mechanisms in high-entropy alloys (HEAs) and enhanced the understanding of their plasticity.

36 MATERIALS SCIENCE↗
NASA NTRS1993

Exploiting structure: Introduction and motivation

Research activities performed during the period of 29 June 1993 through 31 Aug. 1993 are summarized. The Robust Stability of Systems where transfer function or characteristic polynomial are multilinear affine functions of parameters of interest in two directions, Algorithmic and Theoretical, was developed. In the algorithmic direction, a new approach that reduces the computational burden of checking the robust stability of the system with multilinear uncertainty is found. This technique is called 'Stability by linear process.' In fact, the 'Stability by linear process' described gives an algorithm. In analysis, we obtained a robustness criterion for the family of polynomials with coefficients of multilinear affine function in the coefficient space and obtained the result for the robust stability of diamond families of polynomials with complex coefficients also. We obtained the limited results for SPR design and we provide a framework for solving ACS. Finally, copies of the outline of our results are provided in the appendix. Also, there is an administration issue in the appendix.

Xu, Zhong Ling↗
NASA NTRS2001

Expression of extracellular calcium-sensing receptor in human osteoblastic MG-63 cell line

We have previously shown the expression of the extracellular calcium (Ca2+o)-sensing receptor (CaR) in osteoblast-like cell lines, and others have documented its expression in sections of murine, bovine, and rat bone. The existence of the CaR in osteoblasts remains controversial, however, since some studies have failed to document its expression in the same osteoblast-like cell lines. The goals of the present study were twofold. 1) We sought to determine whether the CaR is expressed in the human osteoblast-like cell line, MG-63, which has recently been reported by others not to express this receptor. 2) We investigated whether the CaR, if present in MG-63 cells, is functionally active, since most previous studies have not proven the role of the CaR in mediating known actions of Ca2+o on osteoblast-like cells. We used immunocytochemistry and Western blotting with the specific, affinity-purified anti-CaR antiserum 4637 as well as Northern blot analysis and RT-PCR using a riboprobe and PCR primers specific for the human CaR, respectively, to show readily detectable CaR protein and mRNA expression in MG-63 cells. Finally, we employed the patch-clamp technique to show that an elevation in Ca2+o as well as the specific, allosteric CaR activator NPS R-467 (0.5 microM), but not its less active stereoisomer NPS S-467 (0.5 microM), activate an outward K+ channel in MG-63 cells, strongly suggesting that the CaR in MG-63 cells is not only expressed but is functionally active.

NASA Discipline Regulatory Physiology↗
DOE OSTI2020

Synchrotron x-ray fluorescence analysis reveals diagenetic alteration of fossil melanosome trace metal chemistry

A key feature of the pigment melanin is its high binding affinity for trace metal ions. In modern vertebrates trace metals associated with melanosomes, melanin-rich organelles, can show tissue-specific and taxon-specific distribution patterns. Such signals preserve in fossil melanosomes, informing on the anatomy and phylogenetic affinities of fossil vertebrates. Fossil and modern melanosomes, however, often differ in trace metal chemistry; in particular, melanosomes from fossil vertebrate eyes are depleted in Zn and enriched in Cu relative to their extant counterparts. Whether these chemical differences are biological or taphonomic in origin is unknown, limiting our ability to use melanosome trace metal chemistry to test palaeobiological hypotheses. Here, we use maturation experiments on eye melanosomes from extant vertebrates and synchrotron rapid scan-x-ray fluorescence analysis to show that thermal maturation can dramatically alter melanosome trace element chemistry. In particular, maturation of melanosomes in Cu-rich solutions results in significant depletion of Zn, probably due to low pH and competition effects with Cu. These results confirm fossil melanosome chemistry is susceptible to alteration due to variations in local chemical conditions during diagenesis. Maturation experiments can provide essential data on melanosome chemical taphonomy required for accurate interpretations of preserved chemical signatures in fossils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A Rhodopseudomonas strain with a substantially smaller genome retains the core metabolic versatility of its genus

ABSTRACT Rhodopseudomonas are a group of phototrophic microbes with a marked metabolic versatility and flexibility that underpins their potential use in the production of value-added products, bioremediation, and plant growth promotion. Members of this group have an average genome size of about 5.5 Mb, but two closely related strains have genome sizes of about 4.0 Mb. To identify the types of genes missing in a reduced genome strain, we compared strain DSM127 with other Rhodopseudomonas isolates at the genomic and phenotypic levels. We found that DSM127 can grow as well as other members of the Rhodopseudomonas genus and retains most of their metabolic versatility, but it has many fewer genes associated with high-affinity transport of nutrients, iron uptake, nitrogen metabolism, and biodegradation of aromatic compounds. This analysis indicates genes that can be deleted in genome reduction campaigns and suggests that DSM127 could be a favorable choice for biotechnology applications using Rhodopseudomonas or as a strain that can be engineered further to reside in a specialized natural environment. IMPORTANCE Rhodopseudomonas are a cohort of phototrophic bacteria with broad metabolic versatility. Members of this group are present in diverse soil and water environments, and some strains are found associated with plants and have plant growth-promoting activity. Motivated by the idea that it may be possible to design bacteria with reduced genomes that can survive well only in a specific environment or that may be more metabolically efficient, we compared Rhodopseudomonas strains with typical genome sizes of about 5.5 Mb to a strain with a reduced genome size of 4.0 Mb. From this, we concluded that metabolic versatility is part of the identity of the Rhodopseudomonas group, but high-affinity transport genes and genes of apparent redundant function can be dispensed with.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Streptavidin Affinity Grids for the Preparation of Biological Samples for Cryogenic Electron Microscopy (CRADA Final Report)

Currently, cryo-EM is the most powerful tool for structural analysis of large biomacromolecules, but there are still problems in that biomacromolecules are denatured at the air-interface and their orientations are limited in a specific orientation. We solved this problem at LBL by developing a streptavidin-coated EM grid. Use of such affinity-binding grids can minimize exposure to air-interface by keeping biomacromolecules bound to streptavidin. It is urgently needed to make such grids readily available to the cryo-EM community, but they are somewhat difficult to make. The goal of the CRADA with Hummingbird company was to mass-produce the streptavidin grids so that they would become readily available to the cryo-EM community. Our contribution to the CRADA was to first help Hummingbird to replicate the manual process that we use, and this was completed successfully.

59 BASIC BIOLOGICAL SCIENCES↗