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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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101 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT

Abstract Organisms have a myriad of strategies for sensing, responding to, and combating reactive oxygen species, which are unavoidable consequences of aerobic life. In the heterocystous cyanobacterium Nostoc sp. PCC 7120, one such strategy is the use of an ArsR-SmtB transcriptional regulator RexT that senses H 2 O 2 and upregulates expression of thioredoxin to maintain cellular redox homeostasis. Different from many other members of the ArsR-SmtB family which bind metal ions, RexT has been proposed to use disulfide bond formation as a trigger to bind and release DNA. Here, we present high-resolution crystal structures of RexT in the reduced and H 2 O 2 -treated states. These structures reveal that RexT showcases the ArsR-SmtB winged-helix-turn-helix fold and forms a vicinal disulfide bond to orchestrate a response to H 2 O 2 . The importance of the disulfide-forming Cys residues was corroborated using site-directed mutagenesis, mass spectrometry, and H 2 O 2 -consumption assays. Furthermore, an entrance channel for H 2 O 2 was identified and key residues implicated in H 2 O 2 activation were pinpointed. Finally, bioinformatics analysis of the ArsR-SmtB family indicates that the vicinal disulfide “redox switch” is a unique feature of cyanobacteria in the Nostocales order, presenting an interesting case where an ArsR-SmtB protein scaffold has been evolved to showcase peroxidatic activity and facilitate redox-based regulation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Cross-species analysis of FcγRIIa/b (CD32a/b) polymorphisms at position 131: structural and functional insights into the mechanism of IgG- mediated phagocytosis in human and macaque

Introduction Antibodies play a critical role in immunity in part by mediating clearance of pathogens and infected cells by antibody-dependent cellular phagocytosis (ADCP) through engagement of Fc gamma receptors (FcγRs) on innate immune cells. Among these, FcγRIIa (CD32a) is a key activating receptor expressed on macrophages, dendritic cells, and other antigen-presenting cells. Its affinity for IgG and ability to mediate ADCP is influenced by allelic polymorphisms. In humans, a single amino acid polymorphism at position 131, where histidine (H) is substituted with arginine (R), leads to decreased IgG1 and IgG2 subclass binding affinity and, consequently, lower efficiency of phagocytic responses. Rhesus macaques ( Macaca mulatta ), which are widely used as nonhuman primate models, exhibit a similar polymorphism at position 131 of FcγRIIa, but with arginine replaced by proline (P). Here, we investigated structure-function relationships associated with the FcγRIIa polymorphism at position 131 in both species, specifically with respect to IgG1 and IgG2. Methods We determined the structures of complexes formed by each variant with IgG1 Fc and those formed by the higher affinity variant with IgG2 Fc for both species by x-ray crystallography and linked these structures to affinity and activity using SPR and an ADCP assay. We also determined the structure of human inhibitory FcγRIIb (CD32b) in complex with IgG1 Fc by x-ray crystallography. Results Through analysis of these structures, our studies reveal that FcγRIIa engagement is minimally influenced by Fc glycan composition, distinguishing it from FcγRIIIa whose affinity is strongly influenced by glycan-composition. Comparative structures of human and macaque FcγRIIa variants demonstrate species- and allele-specific differences in Fc binding, but our functional assays showed only minimal allele-specific effects in humans. In contrast, allele-specific effects in macaques were highly significant; the macaque P 131 variant showing uniformly reduced IgG affinity. Conclusion These insights highlight fundamental interspecies and allelic distinctions that are critical for interpreting FcγRIIa-mediated effector functions in macaque models and for optimizing translational antibody and vaccine design.

Tolbert, William D.↗
DOE OSTI2026

Nonlinear viscoelastic response of silicone additively manufactured direct ink write (DIW) foams under repetitive compression

To investigate dynamic fatigue behavior of foam in military protective applications, such as helmets, additively manufactured (AM) foams were compressively strained into the plateau region using a reduced design of experiments. A simple power law was found to govern the decline in dynamic stiffness (complex modulus) as the foams underwent the purchase order requirement of 10,000 cycles of small deformation in the plateau region. This rate of decline was newly found to correlate with the degree of nonlinearity in the material’s deformation, quantified using total harmonic distortion. Materials with low nonlinearity exhibited relatively stable stiffness across cycles, while those with high nonlinearity experienced greater losses. The observed nonlinearity depended on both applied stress and strain rate. A strong linear correlation (R 2 = 0.78) was identified between second-order nonlinearity and the time-dependent stiffness response. Two lattice structures were examined: face-centered tetragonal (FCT) and simple cubic (SC). The SC material exhibited higher total harmonic distortion (5%) and lower stiffness retention than the FCT (2%). In conclusion, these results suggest that for cyclic compression applications in a wide variety of industries such as packaging, personal protective equipment, or aerospace, selecting materials with lower stress and greater structural uniformity can enhance the stability of dynamic performance.

42 ENGINEERING↗
DOE OSTI2025

Identification and Exploration of a Series of SARS-Cov-2 M Pro Cyano-Based Inhibitors Revealing Ortho-Substitution Effects within the P3 Biphenyl Group

Starting from a simple scaffold hopping exercise based on our previous exploration of cysteine protease inhibitors against legumain, compound 6a was identified as a starting point for the development of a SARS-CoV-2 main protease (M Pro ) inhibitor. Compound 6a displayed submicromolar biochemical potency in the ultrasensitive assay developed by Drag and coworkers. Through an iterative structure−activity relationship campaign, we discovered an unexpected improvement in both biochemical and cellular potency through the incorporation of an ortho substituent within the P3 benzamide. X-ray crystallography revealed that incorporation of the ortho substituent caused a subtle but important binding enhancement of the P1 glutamate group within the M Pro S1 pocket. While incorporation of the ortho substituent improved the potency, the off-target selectivity against a panel of cysteine proteases and cell activity remained suboptimal. Further scanning of the P2 core revealed that incorporation of the 3.1.0 proline could address these issues and afford compound 22e, a highly potent and cellularly active M Pro inhibitor.

COVID-19 infection↗
DOE OSTI2025

Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H 2 O 2 and O 2 . This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Tulane virus protease as a structural surrogate for inhibitor screening of human norovirus proteases

Human norovirus (HuNoV) is a significant cause of gastroenteritis worldwide, affecting people of all age groups. There are currently no vaccines or drugs available, leaving susceptible populations vulnerable to severe or protracted illness. A HuNoV cultivation system is pivotal for screening norovirus antivirals. While the human intestinal enteroid cultivation system allows robust replication of multiple HuNoV strains, it presents technical and cost barriers. Tulane virus (TV), a surrogate for HuNoV, replicates well in monkey kidney cell lines and is closely related to norovirus in cellular biology. Here, we determined the structures of TV protease (TV-Pro) alone and in complex with rupintrivir, a picornavirus inhibitor that also inhibits HuNoV proteases (HuNoV-Pro). Our data validate TV as an efficient surrogate system for rapid screening of HuNoV protease inhibitors. The TV protease structure exhibits significant backbone similarity to the GI.1 HuNoV protease in the substrate-binding domain, with the BII-CII loop in an open conformation stabilized by hydrogen bonds as present in the GI.1 protease. Structural differences in the S2 pocket and two amino acid changes in the S4 pocket result in slightly altered P2 and P4 substrate and inhibitor conformations. Despite these differences, we confirm previous findings that the TV protease can cleave the GI.1 and GII HuNoV polyprotein substrates with high and moderate efficiency, respectively. We found that rupintrivir efficiently inhibits TV protease in vitro and inhibits TV replication in cell culture with similar efficacy in combination with P-glycoprotein efflux pump inhibitors. We conclude that TV is a valuable surrogate for HuNoV protease inhibitor screening and outline strategies to improve its compatibility as such.

crystal structures↗
DOE OSTI2025

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

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

09 BIOMASS FUELS↗
DOE OSTI2025

De Novo Design of High‐Affinity Miniprotein Binders Targeting Francisella Tularensis Virulence Factor

Abstract Francisella tularensis poses considerable public health risk due to its high infectivity and potential for bioterrorism. Francisella‐like lipoprotein (Flpp3), a key virulence factor unique to Francisella, plays critical roles in infection and immune evasion, making it a promising target for therapeutic development. However, the lack of well‐defined binding pockets and structural information on native interactions has hindered structure‐guided ligand discovery against Flpp3. Here, we used a combination of physics‐based and deep‐learning methods to design high‐affinity miniprotein binders targeting two distinct sites on Flpp3. We identified four binders for site I with binding affinities ranging between 24–110 nM. For the second site, an initial binder showed a dissociation constant ( K D ) of 81 nM, and subsequent site saturation mutagenesis yielded variants with sub‐nanomolar affinities. Circular dichroism confirmed the topology of designed miniproteins. The X‐ray crystal structure of Flpp3 in complex with a site I binder is nearly identical to the design model (Cα root‐mean‐square deviation (RMSD): 0.9 Å). These designed miniproteins provide research tools to explore the roles of Flpp3 in tularemia and should enable the development of new therapeutic candidates.

Gokce‐Alpkilic, Gizem [Molecular Engineering and S↗
DOE OSTI2020

Assembly of Building Blocks by Double-End-Anchored Polymers in the Dilute Regime Mediated by Hydrophobic Interactions at Controlled Distances

Hierarchical assembly of building blocks via competing, orthogonal interactions is a hallmark of many of nature’s composite materials that do not require highly specific ligand-receptor interactions. To mimic this assembly mechanism requires the development of building blocks capable of tunable interactions. In the present work, we explored the interplay between repulsive (steric and electrostatic) and attractive hydrophobic forces. The designed building blocks allow hydrophobic forces to effectively act at controlled, large distances, to create and tune the assembly of membrane-based building blocks under dilute conditions and affect their interactions with cellular membranes via physical cross-bridges. Specifically, we employed double-end-anchored poly(ethylene glycol)s (DEA-PEGs)—hydrophilic PEG tethers with hydrophobic tails on both ends. Using differential-interference-contrast optical microscopy, synchrotron small angle X-ray scattering (SAXS), and cryogenic electron microscopy, we investigated the ability of DEA-PEGs to mediate assembly in the dilute regime on multiple length scales and on practical time scales. The PEG length, anchor hydrophobicity, and molar fraction of DEA-PEG molecules within a membrane strongly affect the assembly properties. Additional tuning of the intermembrane interactions can be achieved by adding repulsive interactions via PEG-lipids (steric) or cationic lipids to the DEA-PEG-mediated attractions. Further, while the optical and electron microscope imaging methods provided qualitative evidence of the ability of DEA-PEGs to assemble liposomes, the SAXS measurements and quantitative line-shape analysis in dilute preparations demonstrated that the ensemble average of loosely organized liposomal assemblies maintains DEA-PEG concentration-dependent tethering on defined nanometer length scales. For cationic liposome–DNA nanoparticles (CL–DNA NPs), aggregation induced by DEA-PEGs decreased internalization of NPs by cells, but tuning the DEA-PEG-induced attractions by adding repulsive steric interactions via PEG-lipids limited aggregation and increased NP uptake. However, confocal microscopy imaging together with colocalization studies with Rab11 and LysoTracker as markers of intracellular pathways showed that modifying CL–DNA NPs with DEA-PEGs alters their interactions with the plasma and endosomal membranes.

- x-ray scattering↗
DOE OSTI2020

Conformation-specific inhibitors of activated Ras GTPases reveal limited Ras dependency of patient-derived cancer organoids

The small GTPases H, K, and NRAS are molecular switches indispensable for proper regulation of cellular proliferation and growth. Several mutations in the genes encoding members of this protein family are associated with cancer and result in aberrant activation of signaling processes caused by a deregulated recruitment of downstream effector proteins. In this study, we engineered variants of the Ras-binding domain (RBD) of the C-Raf proto-oncogene, Ser/Thr kinase (CRAF). These variants bound with high affinity with the effector-binding site of Ras in an active conformation. Structural characterization disclosed how the newly identified RBD mutations cooperate and thereby enhance affinity with the effector-binding site in Ras compared with WT RBD. The engineered RBD variants closely mimicked the interaction mode of naturally occurring Ras effectors and acted as dominant-negative affinity reagents that block Ras signal transduction. We report experiments with cancer cells showed that expression of these RBD variants inhibits Ras signaling, reducing cell growth and inducing apoptosis. Using these optimized RBD variants, we stratified patient-derived colorectal cancer organoids with known Ras mutational status according to their response to Ras inhibition. These results revealed that the presence of Ras mutations was insufficient to predict sensitivity to Ras inhibition, suggesting that not all of these tumors required Ras signaling for proliferation. In summary, by engineering the Ras/Raf interface of the CRAF-RBD, we identified potent and selective inhibitors of Ras in its active conformation that outcompete binding of Ras-signaling effectors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Dynamic crushing of metal lattice metamaterials: Shock mode diagrams and transition to topology-independent compaction regime

Additively manufactured lattice metamaterials offer design versatility in strength and energy absorption and provide an additional degree of freedom through the selection of the lattice topology. Under quasistatic loading, the unit cell structure can strongly affect the stiffness, yield, and post-yield behavior, but whether and to what degree the effect of lattice topology persists into dynamic loading scenarios, up to the compaction shock regime, has not been established. LLNL’ s ALE3D hydrocode was used to perform a computational investigation of dynamic loading in multiple lattice types, including the gyroid, octet, Schwarz D, and rhombic dodecahedron, under impact velocities from 0.25 to 2.25 km/s. Shock Hugoniots for each lattice topology are generated and compared, suggesting that above a critical velocity, distinctions between architectures may not persevere and compacted lattices behave similarly. Here, to investigate the transition between topology-dependent quasistatic compression and the topology-independent regime above the critical velocity, a one-dimensional elastic-linear hardening plasticity-densified solid (E-LHP-DS) shock model for lattice materials was developed that relies upon confined compression to link the quasistatic and shock mechanics. Unlike similar works, the model does not assume rigid behavior prior to yield or locking behavior at densification, allowing a richer exploration of lattice mechanics. With only six parameters, the analytical model simultaneously fit quasistatic confined compression simulations for relative densities 0.1 $≤ \bar{ρ} ≤$ 0.9 and predicted dynamic compaction behavior to traverse several distinct shock modes, each defined by a critical impact speed (equivalently, critical stresses). Comparing the numerical results to the one-dimensional E-LHP-DS shock model predictions suggests that the topology-independence under strong shocks is linked to the onset of densification, which can be predicted based on quasistatic confined compression results.

Cellular material↗