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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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif

Abstract The mechanochemical GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial and peroxisomal fission, but the regulatory mechanisms remain ambiguous. Here we find that a conserved, intrinsically disordered, six-residue Short Linear Motif at the extreme Drp1 C-terminus, named CT-SLiM, constitutes a critical allosteric site that controls Drp1 structure and function in vitro and in vivo. Extension of the CT-SLiM by non-native residues, or its interaction with the protein partner GIPC-1, constrains Drp1 subunit conformational dynamics, alters self-assembly properties, and limits cooperative GTP hydrolysis, surprisingly leading to the fission of model membranes in vitro. In vivo, the involvement of the native CT-SLiM is critical for productive mitochondrial and peroxisomal fission, as both deletion and non-native extension of the CT-SLiM severely impair their progression. Thus, contrary to prevailing models, Drp1-catalyzed membrane fission relies on allosteric communication mediated by the CT-SLiM, deceleration of GTPase activity, and coupled changes in subunit architecture and assembly-disassembly dynamics.

Science & Technology - Other Topics↗
DOE OSTI2024

Extending carbon chemistry at high-pressure by synthesis of CaC 2 and Ca 3 C 7 with deprotonated polyacene- and para-poly(indenoindene)-like nanoribbons

Metal carbides are known to contain small carbon units similar to those found in the molecules of methane, acetylene, and allene. However, for numerous binary systems ab initio calculations predict the formation of unusual metal carbides with exotic polycarbon units, [C 6 ] rings, and graphitic carbon sheets at high pressure (HP). Here we report the synthesis and structural characterization of a HP-CaC 2 polymorph and a Ca 3 C7 compound featuring deprotonated polyacene-like and para-poly(indenoindene)-like nanoribbons, respectively. We also demonstrate that carbides with infinite chains of fused [C6] rings can exist even at conditions of deep planetary interiors (~140 GPa and ~3300 K). Hydrolysis of high-pressure carbides may provide a possible abiotic route to polycyclic aromatic hydrocarbons in Universe.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Nucleic acid mediated activation of a short prokaryotic Argonaute immune system

A short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P) + hydrolysis, was recently identified in bacteria. We report the crystal structure of SPARTA heterodimer in the absence of guide-RNA/target-ssDNA (2.66 Å) and a cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA at nominal 3.15–3.35 Å resolution. The crystal structure provides a high-resolution view of SPARTA, revealing the APAZ domain as equivalent to the N, L1, and L2 regions of long pAgos and the MID domain containing a unique insertion (insert57). Cryo-EM structure reveals regions of the PIWI (loop10-9) and APAZ (helix αN) domains that reconfigure for nucleic-acid binding and decrypts regions/residues that reorganize to expose a positively charged pocket for higher-order assembly. The TIR domains amass in a parallel-strands arrangement for catalysis. We visualize SPARTA before and after RNA/ssDNA binding and uncover the basis of its active assembly leading to abortive infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cryo-EM captures the coordination of asymmetric electron transfer through a di-copper site in DPOR

Enzymes that catalyze long-range electron transfer (ET) reactions often function as higher order complexes that possess two structurally symmetrical halves. The functional advantages for such an architecture remain a mystery. Using cryoelectron microscopy we capture snapshots of the nitrogenase-like dark-operative protochlorophyllide oxidoreductase (DPOR) during substrate binding and turnover. DPOR catalyzes reduction of the C17 = C18 double bond in protochlorophyllide during the dark chlorophyll biosynthetic pathway. DPOR is composed of electron donor (L-protein) and acceptor (NB-protein) component proteins that transiently form a complex in the presence of ATP to facilitate ET. NB-protein is an α 2 β 2 heterotetramer with two structurally identical halves. However, our structures reveal that NB-protein becomes functionally asymmetric upon substrate binding. Asymmetry results in allosteric inhibition of L-protein engagement and ET in one half. Residues that form a conduit for ET are aligned in one half while misaligned in the other. An ATP hydrolysis-coupled conformational switch is triggered once ET is accomplished in one half. These structural changes are then relayed to the other half through a di-nuclear copper center at the tetrameric interface of the NB-protein and leads to activation of ET and substrate reduction. These findings provide a mechanistic blueprint for regulation of long-range electron transfer reactions.

Computational biophysics↗
DOE OSTI2025

Translocation mechanism of xeroderma pigmentosum group D protein on single-stranded DNA and genetic disease etiology

Abstract XPD is a key nucleotide excision repair (NER) protein whose function is vital for genome integrity. During NER, XPD serves as a 5′−3′ single-strand DNA translocase that enables lesion scanning and verification in genomic DNA. Yet, its translocation mechanism is incompletely understood. Here we use molecular simulations and chain-of-replicas path optimization methods to model the ATP-driven translocation mechanisms of XPD and its bacterial homolog DinG, revealing all on-path metastable intermediates and corresponding kinetic rates. We identify the XPD(DinG) global domain motions that modulate the strength of DNA association at the opposing ends of the DNA-binding groove. During the ATP hydrolysis cycle, alternating weak and strong interactions at two defined groove constrictions enable DNA reptation and forward displacement of the ATPase. Moreover, we show that DNA- or ATP-binding residues directly involved in translocation are hotspots for genetic disease mutations. Thus, our findings shed light on the etiology of XPD-associated genetic syndromes.

Paul, Tanmoy↗
DOE OSTI2023

On the effect of Al on alumino-borosilicate glass chemical durability

The chemical durability of borosilicate glass used to confine nuclear wastes is known to vary nonlinearly with their composition, making glass dissolution rate predictions difficult. Here, we focus on the effect of Al, an important oxide of these materials. The initial and residual glass dissolution rates were investigated through experiments conducted at 90 °C and pH 9. Our results show that low Al content glasses dissolve initially faster than glasses with higher Al content, but quickly achieve a lower residual rate due to the rapid formation of a more passivating gel. Nevertheless, the high Al content gel will eventually achieve passivation with a slower reorganization. The strengthening effect of Al on the Si-O bond hydrolysis will result in more stable gels, suggesting that slightly higher Al content in the gel will improve nuclear high-level waste glass durability in geological disposal conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Hybrid organic–inorganic two-dimensional metal carbide MXenes with amido- and imido-terminated surfaces

Two-dimensional (2D) transition-metal carbides and nitrides (MXenes) combine the electronic and mechanical properties of 2D inorganic crystals with chemically modifiable surfaces, which provides an ideal platform for both fundamental and applied studies of interfaces. Good progress has been achieved in the functionalization of MXenes with small inorganic ligands, but relatively little work has been reported on the covalent bonding of various organic groups to MXene surfaces. Here we synthesize a family of hybrid MXenes (h-MXenes) that incorporate amido- and imido-bonding between organic and inorganic parts by reacting halogen-terminated MXenes with deprotonated organic amines. The resulting hybrid structures unite tailorability of organic molecules with electronic connectivity and other properties of inorganic 2D materials. Describing the structure of h-MXene necessitates the integration of concepts from coordination chemistry, self-assembled monolayers and surface science. The optical properties of h-MXenes reveal coherent coupling between the organic and inorganic constituents. Further, h-MXenes also exhibit superior stability against hydrolysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences

Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. Furthermore, these results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Carotenoid cleavage enzymes evolved convergently to generate the visual chromophore

The retinal light response in animals originates from the photoisomerization of an opsin-coupled 11-cis-retinaldehyde chromophore. This visual chromophore is enzymatically produced through the action of carotenoid cleavage dioxygenases. Vertebrates require two carotenoid cleavage dioxygenases, β-carotene oxygenase 1 and retinal pigment epithelium 65 (RPE65), to form 11-cis-retinaldehyde from carotenoid substrates, whereas invertebrates such as insects use a single enzyme known as Neither Inactivation Nor Afterpotential B (NinaB). RPE65 and NinaB couple trans–cis isomerization with hydrolysis and oxygenation, respectively, but the mechanistic relationship of their isomerase activities remains unknown. Here we report the structure of NinaB, revealing details of its active site architecture and mode of membrane binding. Structure-guided mutagenesis studies identify a residue cluster deep within the NinaB substrate-binding cleft that controls its isomerization activity. Our data demonstrate that isomerization activity is mediated by distinct active site regions in NinaB and RPE65—an evolutionary convergence that deepens our understanding of visual system diversity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Generalized enzymatic mechanism of catalysis by tetrameric L -asparaginases from mesophilic bacteria

The mechanism of catalysis by the L -glutaminase-asparaginase from Pseudomonas 7A (PGA) was investigated using structural, mass spectrometry, and kinetic data. We had previously proposed mechanism of hydrolysis of L -Asn by the type II L-asparaginase from E. coli (EcAII), but that work was limited to just one enzyme. Based on results presented in this report, we postulate that all homotetrameric L -asparaginases from mesophilic bacteria utilize a common ping-pong mechanism of catalysis consisting of two subsequent nucleophilic substitutions. Several new structures of non-covalent complexes of PGA with different substrates, as well as structures of covalent acyl-enzyme intermediates of PGA with canonical substrates ( L -Asp and L -Glu) and an opportunistic ligand, a citrate anion, were determined. The results of kinetic experiments monitored by high-resolution LC/MS, when combined with new structural data, clearly show that the reaction catalyzed by L -glutaminase-asparaginases proceeds through formation of a covalent intermediate, as observed previously for EcAII. Additionally, by showing that the same mechanism applies to L -Asn and L -Gln, we postulate that it is common for all these structurally related enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Fungal hyphae develop where titanomagnetite inclusions reach the surface of basalt grains

Nutrient foraging by fungi weathers rocks by mechanical and biochemical processes. Distinguishing fungal-driven transformation from abiotic mechanisms in soil remains a challenge due to complexities within natural field environments. We examined the role of fungal hyphae in the incipient weathering of granulated basalt from a three-year field experiment in a mixed hardwood-pine forest (S. Carolina) to identify alteration at the nanometer to micron scales based on microscopy-tomography analyses. Investigations of fungal-grain contacts revealed (i) a hypha-biofilm-basaltic glass interface coinciding with titanomagnetite inclusions exposed on the grain surface and embedded in the glass matrix and (ii) native dendritic and subhedral titanomagnetite inclusions in the upper 1–2 µm of the grain surface that spanned the length of the fungal-grain interface. We provide evidence of submicron basaltic glass dissolution occurring at a fungal-grain contact in a soil field setting. An example of how fungal-mediated weathering can be distinguished from abiotic mechanisms in the field was demonstrated by observing hyphal selective occupation and hydrolysis of glass-titanomagnetite surfaces. We hypothesize that the fungi were drawn to basaltic glass-titanomagnetite boundaries given that titanomagnetite exposed on or very near grain surfaces represents a source of iron to microbes. Furthermore, glass is energetically favorable to weathering in the presence of titanomagnetite. Our observations demonstrate that fungi interact with and transform basaltic substrates over a three-year time scale in field environments, which is central to understanding the rates and pathways of biogeochemical reactions related to nuclear waste disposal, geologic carbon storage, nutrient cycling, cultural artifact preservation, and soil-formation processes.

58 GEOSCIENCES↗
DOE OSTI2022

Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors

Targeted covalent inhibition represents one possible strategy to block the function of SARS-CoV-2 Main Protease (M PRO ), an enzyme that plays a critical role in the replication of the novel SARS-CoV-2. Toward the design of covalent inhibitors, we built a covalent inhibitor dataset using deep learning models followed by high throughput virtual screening of these candidates against M PRO . Two top-ranking inhibitors were selected for mechanistic investigations—one with an activated ester warhead that has a piperazine core and the other with an acrylamide warhead. Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. Simulations show that both candidates form more stable enzyme-inhibitor (E-I) complexes than the chosen NSP. It was found that both the NSP fragment and the activated ester inhibitor react with CYS145 of M PRO in a concerted manner, whereas the acrylamide inhibitor follows a stepwise mechanism. Most importantly, the reversible reaction and the subsequent hydrolysis reaction from E-I complexes are less probable when compared to the reactions with an NSP fragment, showing promise for these candidates to be the base for efficient M PRO inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Benzyl trichloroacetimidates as derivatizing agents for phosphonic acids related to nerve agents by EI-GC-MS during OPCW proficiency test scenarios

Abstract The use of benzyl trichloroacetimidates for the benzylation of phosphonic acid nerve agent markers under neutral, basic, and slightly acidic conditions is presented. The benzyl-derived phosphonic acids were detected and analyzed by Electron Ionization Gas Chromatography–Mass Spectrometry (EI-GC–MS). The phosphonic acids used in this work included ethyl-, cyclohexyl- and pinacolyl methylphosphonic acid, first pass hydrolysis products from the nerve agents ethyl N -2-diisopropylaminoethyl methylphosphonothiolate (VX), cyclosarin (GF) and soman (GD) respectively. Optimization of reaction parameters for the benzylation included reaction time and solvent, temperature and the effect of the absence or presence of catalytic acid. The optimized conditions for the derivatization of the phosphonic acids specifically for their benzylation, included neutral as well as catalytic acid (< 5 mol%) and benzyl 2,2,2-trichloroacetimidate in excess coupled to heating the mixture to 60 °C in acetonitrile for 4 h. While the neutral conditions for the method proved to be efficient for the preparation of the p -methoxybenzyl esters of the phosphonic acids, the acid-catalyzed process appeared to provide much lower yields of the products relative to its benzyl counterpart. The method’s efficiency was tested in the successful derivatization and identification of pinacolyl methylphosphonic acid (PMPA) as its benzyl ester when present at a concentration of ~ 5 μg/g in a soil matrix featured in the Organisation for the Prohibition of Chemical Weapons (OPCW) 44th proficiency test (PT). Additionally, the protocol was used in the detection and identification of PMPA when spiked at ~ 10 μg/mL concentration in a fatty acid-rich liquid matrix featured during the 38 th OPCW-PT. The benzyl derivative of PMPA was partially corroborated with the instrument's internal NIST spectral library and the OPCW central analytical database (OCAD v.21_2019) but unambiguously identified through comparison with a synthesized authentic standard. The method’s MDL (LOD) values for the benzyl and the p -methoxybenzyl pinacolyl methylphosphonic acids were determined to be 35 and 63 ng/mL respectively, while the method’s Limit of Quantitation (LOQ) was determined to be 104 and 189 ng/mL respectively in the OPCW-PT soil matrix evaluated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structural and functional analyses of the echinomycin resistance conferring protein Ecm16 from Streptomyces lasalocidi

Echinomycin is a natural product DNA bisintercalator antibiotic. The echinomycin biosynthetic gene cluster in Streptomyces lasalocidi includes a gene encoding the self-resistance protein Ecm16. Here, we present the 2.0 Å resolution crystal structure of Ecm16 bound to adenosine diphosphate. The structure of Ecm16 closely resembles that of UvrA, the DNA damage sensor component of the prokaryotic nucleotide excision repair system, but Ecm16 lacks the UvrB-binding domain and its associated zinc-binding module found in UvrA. Mutagenesis study revealed that the insertion domain of Ecm16 is required for DNA binding. Furthermore, the specific amino acid sequence of the insertion domain allows Ecm16 to distinguish echinomycin-bound DNA from normal DNA and link substrate binding to ATP hydrolysis activity. Expression of ecm16 in the heterologous host Brevibacillus choshinensis conferred resistance against echinomycin and other quinomycin antibiotics, including thiocoraline, quinaldopeptin, and sandramycin. Our study provides new insight into how the producers of DNA bisintercalator antibiotics fend off the toxic compounds that they produce.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Reactive transport modeling of organic carbon degradation in marine methane hydrate systems

Abstract Natural methane hydrate has often been observed in sand layers that contain no particulate organic carbon (POC), but are surrounded by organic-rich, fine-grained marine muds. In this paper, we develop a reactive transport model (RTM) of a microbially-mediated set of POC degradation reactions, including hydrolysis of POC driven by extracellular enzymes, fermentation of the resulting high-molecular weight dissolved organic carbon (HMW-DOC), and methanogenesis that consumes low-molecular weight dissolved organic carbon (LMW-DOC). These processes are mediated by two groups of microbes, fermenters and methanogens that are heterogeneously distributed in different lithologies, with the largest numbers of microbes in the large pores of coarse-grained layers. We find that the RTM can reproduce methane hydrate occurrences observed in two different geological environments, at Walker Ridge Site 313-H (Gulf of Mexico) and IODP Site U1325 (Cascadia Margin). We also find that microbes can degrade POC even if they are physically separated, as extracellular enzymes and DOC can diffuse away from where they are produced by microbes. Microbial activity is highest at relatively early times after burial at shallow depths and near lithological boundaries, where concentration gradients transport solutes to intervals that contain the most microbes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Unlocking soybean meal pectin recalcitrance using a multi-enzyme cocktail approach

Pectin is a complex plant heteropolysaccharide whose structure and function differ depending on its source. In animal feed, breaking down pectin is essential, as its presence increases feed viscosity and reduces nutrient absorption. Soybean meal, a protein-rich poultry feed ingredient, contains significant amounts of pectin, the structure of which remains unclear. Consequently, the enzyme activities required to degrade soybean meal pectin and how they interact are still open questions. In this study, we produced 15 recombinant fungal carbohydrate-active enzymes (CAZymes) identified from fungal secretomes acting on pectin. After observing that these enzymes were not active on soybean meal pectin when used alone, we developed a semi-miniaturized method to evaluate their effect as multi-activity cocktails. We designed and tested 12 enzyme pools, containing up to 15 different CAZymes, using several hydrolysis markers. Thanks to our multiactivity enzymatic approach combined with a Pearson correlation matrix, we identified 10 fungal CAZymes efficient on soybean meal pectin, 9 of which originate from Talaromyces versatilis. Based on enzyme specificity and linkage analysis, we propose a structural model for soybean meal pectin. Our findings underscore the importance of combining CAZymes to improve the degradation of agricultural co-products.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Depolymerization of polyesters by a binuclear catalyst for plastic recycling

Plastics play an essential role in modern society, however, the relentless growth of their production is threatening both human health and ecosystems. As a result, there are intensive efforts in developing recycling technologies to repurpose waste plastics into the building blocks for valuable materials. Here we show a binuclear complex that can catalyze the degradation of polyethylene terephthalate (PET)-the most widely used polyester globally-and a wide spectrum of other plastics including polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), polycaprolactone (PCL), polyurethane (PU) and Nylon 66. Inspired by hydrolases, the group of enzymes that catalyze bond cleavages with water, the present catalyst design features biomimetic Zn-Zn sites which activate the plastic, stabilize the key intermediate, and enable intramolecular hydrolysis. This synthetic catalyst delivers activities of 36 mg PET d -1 g catal -1 toward PET depolymerization at pH 8 and 40 oC, and of 577 g PET d -1 g catal -1 at pH 13 and 90 oC for scalable PET recycling. We further demonstrate the closed-loop production of a bottle-grade PET. This work presents a practical and viable solution to the sustainable management of plastics waste.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner

The reduction of dinitrogen to ammonia catalyzed by nitrogenase involves a complex series of events, including ATP hydrolysis, electron transfer, and activation of metal clusters for N 2 reduction. Early evidence shows that an essential part of the mechanism involves transducing information between the nitrogenase component proteins through conformational dynamics. Here, millisecond time-resolved hydrogen-deuterium exchange mass spectrometry was used to unravel peptide-level protein motion on the time scale of catalysis of Mo-dependent nitrogenase from Azotobacter vinelandii. Normal mode analysis calculations complemented this data, providing insights into the specific signal transduction pathways that relay information across protein interfaces at distances spanning 100 Å. Together, these results show that conformational changes induced by protein docking are rapidly transduced to the active site, suggesting a specific mechanism for activating the metal cofactor in the enzyme active site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗