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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 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA

Abstract In selected Campylobacter species, the biosynthesis of N‐linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane‐associated GT‐B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N ‐acetylgalatosamine (GalNAc) from uridine 5′‐diphospho‐ N ‐acetylgalactosamine (UDP‐GalNAc) to undecaprenyl‐diphospho‐ N , N ′‐diacetylbacillosamine (UndPP‐diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane‐embedded acceptor and the structural analysis of the complex together with bioinformatics and site‐directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″‐OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate‐specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.

Vuksanovic, Nemanja↗
DOE OSTI2025

The structural basis for the broad aldehyde specificity of the aminoaldehyde dehydrogenase PauC from the human pathogen Pseudomonas aeruginosa

Abstract Despite significant differences in size and formal charge, the aldehyde dehydrogenasePaPauC (PA5312) fromPseudomonas aeruginosaPAO1 efficiently catalyzes the NAD + ‐dependent oxidation of the aminoaldehydes formed in polyamines degradation. We report here thatPaPauC also oxidizes 4‐guanidinebutyraldehyde, formed in one arginine degradation pathway, trimethylaminobutyraldehyde, of unknown metabolic origin, and indole‐3‐acetaldehyde, a precursor of the plant growth‐promoting hormone indoleacetic acid.PaPauC has been proposed as a potential target for combatingP. aeruginosa. However, understanding its structure–function relationships, crucial for developing specific inhibitors, is lacking. Using X‐ray crystallography, we identified the structural characteristics that determinePaPauC broad aldehyde specificity: a spacious aldehyde‐entrance tunnel and six active‐site residues. Docking simulations, site‐directed mutagenesis, and kinetic analyses support the interactions of Lys479 with glutamylated aminoaldehydes; Phe169, Trp176, and Phe467 with amino and guanidinium groups through cation–π interactions and with the indole group via NH–π and CH–π interactions; Asp459 with amino and indole groups; and Thr303 with amide and guanidinium groups. Exploiting the distinctive structural features of thePaPauC active site could aid in developing specific inhibitors to combatP. aeruginosainfections in humans and animals, as well as in preventing its colonization of plants, which are abundantP. aeruginosareservoirs and, therefore, a significant source of human infections.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Molecular basis and biological relevance of bacterial and plant pinoresinol/lariciresinol reductase specificities

A bacterial pinoresinol/lariciresinol reductase (PLR) homolog named NrPinZ was obtained from a Novosphingobium rhizosphaerae sp. LY bacterial strain, with NrPinZ being part of its 5-step biochemical system catabolizing pinoresinol into coniferyl aldehyde and vanillin. Recombinant NrPinZ reduces racemic 8–8′ furanofuran lignans [(±)-pinoresinols, medioresinols, and syringaresinols] with similar overall catalytic efficiencies. In those reductions, only one of the two furan ring systems is reduced. Two other bacterial PLR homologs, NaPinZ and SlPinZ, from N. aromaticivorans F199 and Sphingobium lignivorans SYK-6, respectively, had comparable substrate versatilities and catalytic efficacies. Plant PLR homologs, by comparison, are either enantiospecific, enantioselective, or variants thereof, being able to reduce either one or both furan rings. For example, a recombinant enantioselective PLR (PLR_Tp2) from western red cedar (Thuja plicata) preferentially reduces both (+)-pinoresinol furan rings to afford (−)-secoisolariciresinol. BoltZ-2 modeling of NrPinZ and PLR_Tp2, together with substrate docking of (+)- and (−)-pinoresinols, medioresinols, and syringaresinols, was very instructive. The NrPinZ active site P1/P2 sub-pockets allow for both racemic forms to be catabolized. Conversely, the smaller P1 pocket in PLR_Tp2 preferentially positions (+)-pinoresinol for downstream metabolism into (−)-secoisolariciresinol, thereby providing a biochemical explanation for the different stereochemical outcomes. NrPinZ, NaPinZ, and SlPinZ, catalyzing substrate versatile catabolism of both racemic forms, may have important ramifications for gymnosperm and angiosperm lignin and lignan biodegradation, including its evolutionary significance and potential in enzyme engineering.

Boltz-2 molecular modeling↗
DOE OSTI2026

Predicting compatibility between ferredoxins and the Fe protein of nitrogenase using in silico protein modeling

Biological nitrogen fixation is the process by which certain bacteria and archaea use the enzyme nitrogenase to reduce atmospheric nitrogen into bioavailable ammonium. Engineering non‐nitrogen‐fixing organisms, like plants, to use nitrogenase could reduce dependency on synthetic fertilizer and mitigate the environmental impacts of industrial fertilizer production. However, nitrogenase activity requires delivery of reducing power by small electron carrying proteins known as ferredoxins and flavodoxins, and successfully engineering nitrogenase into new systems will require a mechanistic understanding of electron delivery by these proteins. Most organisms often have multiple ferredoxins, raising the question of which ferredoxin can support nitrogenase activity. The purpose of this study is to gain insight into how we can predict which ferredoxin is compatible with the Fe protein, the component of nitrogenase that interacts with ferredoxin or flavodoxin. Our in silico protein–protein docking simulations reveal that most ferredoxins and flavodoxins involved in nitrogen fixation have the shortest distance (≤10 Å) between their redox cofactor and the [4Fe‐4S] cluster of the Fe protein. We found shorter cofactor distance contributes to faster intermolecular electron tunneling rates. Bacterial ferredoxins that play a role in nitrogen fixation also exhibit more complementary interactions with the Fe protein than bacterial and plant ferredoxins not involved in this process. Heterologous expression of a set of ferredoxins from both nitrogen‐fixing and non‐nitrogen‐fixing bacteria in the diazotroph Rhodopseudomonas palustris supports our model‐derived prediction that shorter distances between the electron‐carrying cofactors favor nitrogenase compatibility. These findings offer a framework to predict and potentially enhance ferredoxin–nitrogenase compatibility, which will help to improve our ability to engineer nitrogen fixation into non‐nitrogen‐fixing organisms like plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The crystal structure of Klebsiella pneumoniae FeoA reveals a site for protein-protein interactions

In order to establish infection, pathogenic bacteria must obtain essential nutrients such as iron. Under acidic and/or anaerobic conditions, most bacteria utilize the Feo system in order to acquire ferrous iron (Fe 2+ ) from their host environment. The mechanism of this process, including its regulation, remains poorly understood. In this work, we have determined the crystal structure of FeoA from the nosocomial agent Klebsiella pneumoniae (KpFeoA). Our structure reveals an SH3-like domain that mediates interactions between neighboring polypeptides via hydrophobic intercalations into a Leu-rich surface ridge. Using docking of a small peptide corresponding to a postulated FeoB partner binding site, we demonstrate that KpFeoA can assume both “open” and “closed” conformations, controlled by binding at this Leu-rich ridge. We propose a model in which a “C-shaped” clamp along the FeoA surface mediates interactions with its partner protein, FeoB. Overall, these findings are the first to demonstrate atomic-level details of FeoA-based protein-protein interactions and provide a framework for testing FeoA-FeoB interactions, which could be exploited for future antibiotic developments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV -2 spike receptor binding domain ( RBD )

The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods for the design of potentially neutralizing antibodies (Abs) to counter immune evasion by the virus. Here, we report on the de novo computational design of high-affinity Ab variable regions (Fv) through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike receptor binding domain (RBD) protein using the software tool OptMAVEn-2.0. Subsequently, we carried out computational affinity maturation of the designed variable regions through amino acid substitutions for improved binding with the target epitope. Immunogenicity of designs was restricted by preferring designs that match sequences from a 9-mer library of “human Abs” based on a human string content score. We generated 106 different antibody designs and reported in detail on the top five that trade-off the greatest computational binding affinity for the RBD with human string content scores. We further describe computational evaluation of the top five designs produced by OptMAVEn-2.0 using a Rosetta-based approach. We used Rosetta SnugDock for local docking of the designs to evaluate their potential to bind the spike RBD and performed “forward folding” with DeepAb to assess their potential to fold into the designed structures. Ultimately, our results identified one designed Ab variable region, P1.D1, as a particularly promising candidate for experimental testing. This effort puts forth a computational workflow for the de novo design and evaluation of Abs that can quickly be adapted to target spike epitopes of emerging SARS-CoV-2 variants or other antigenic targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Zeolite Nanosheets Stabilize Catalyst Particles to Promote the Growth of Thermodynamically Unfavorable, Small–Diameter Carbon Nanotubes

A challenge in the synthesis of single–wall carbon nanotubes (SWCNTs) is the lack of control over the formation and evolution of catalyst nanoparticles and the lack of control over their size or chirality. Here, zeolite MFI nanosheets (MFI–Ns) are used to keep cobalt (Co) nanoparticles stable during prolonged annealing conditions. Environmental transmission electron microscopy (ETEM) shows that the MFI–Ns can influence the size and shape of nanoparticles via particle/support registry, which leads to the preferential docking of nanoparticles to four or fewer pores and to the regulation of the SWCNT synthesis products. The resulting SWCNT population exhibits a narrow diameter distribution and SWCNTs of nearly all chiral angles, including sub–nm zigzag (ZZ) and near–ZZ tubes. Theoretical simulations reveal that the growth of these unfavorable tubes from unsupported catalysts leads to the rapid encapsulation of catalyst nanoparticles bearing them; their presence in the growth products suggests that the MFI–Ns prevent nanoparticle encapsulation and prologue ZZ and near–ZZ SWCNT growth. Furthermore, these results thus present a path forward for controlling nanoparticle formation and evolution, for achieving size– and shape–selectivity at high temperature, and for controlling SWCNT synthesis.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Dioscin-6’-O-acetate impairs migration of lung cancer cells through attenuations of MMP-2 and MMP-9 via NF-κB suppression

More than 90% of the cancer-associated mortality is attributed to its metastasis. Numerous studies demonstrated that natural steroidal saponins from plants had the capacity to inhibit lung cancer metastasis. Dioscin-6’-O-acetate (DA) was a novel steroidal saponin first obtained from the rhizomes of Dioscorea althaeoides R. Knuth. Our previous study indicated that it suppressed lung cancer cell proliferation via inducing cell-cycle arrest and enhancing caspase-dependent apoptosis. Until now, there were still no reports on its anti-migration activity. In the present study, we further verified the anti-proliferation and apoptosis-inducing effects and investigated the anti-migration effects of DA on human NSCLC (NCI-H460, NCI-H1299, NCI-H520) and SCLC (NCI-H446) cells for the first time. To clarify the possible mechanisms, western blot and/or RT-PCR analysis were used. The results revealed that DA treatment increased the levels of caspase 3, 8, 9, and Bax and markedly decreased the expression of bcl-2, PCNA, MMP-2, MMP-9, and NF-κB. Docking study indicated that DA presented strong affinity with the key metastasis-related proteins, such as MMP-2, MMP-9, and NF-κB. We proposed that DA might suppress lung cancer proliferation by downregulating PCNA, induce lung cancer apoptosis via activation of caspase-dependent apoptosis pathways, and inhibit lung cancer migration possibly by targeting MMP-2/9 through NF-κB signaling suppression. The findings would provide the foundation for the clinical use of DA in future.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Comparative α-glucosidase and α-amylase inhibition studies of rhodanine–pyrazole conjugates and their simple rhodanine analogues

Novel rhodanine–pyrazole conjugates (6a–i) and their simple rhodanine analogues (8a–e) were prepared and comparatively screened for their antidiabetic activities against enzymatic targets, α-glucosidase and α-amylase. As expected, the molecular hybrids exhibited significantly greater inhibitory activity against α-glucosidase (IC{sub 50} = 2.259 × 10{sup −6}–1.160 × 10{sup −4} mol/L), relative to their simple rhodanine counterparts (IC{sub 50} = 3.056 × 10{sup −4}–9.494 × 10{sup −4} mol/L). Amongst the screened derivatives compounds 6a and 6f displayed a 3-fold and 42-fold greater potency against α-glucosidase (IC{sub 50} = 2.854 × 10{sup −5} and 2.259 × 10{sup −6}mol/L, respectively) compared to the standard drug, acarbose. The designed molecular conjugates displayed an improved binding affinity toward α-glucosidase than α-amylase. Compound 6d was identified as the most potent inhibitor of α-amylase (IC{sub 50} = 6.377 × 10{sup −5} mol/L) with a 1.5-fold greater inhibitory activity than acarbose. Structural assessment of the molecules revealed that electron withdrawing (Cl) and electron donating (OCH{sub 3}) groups at the ortho-position played a significant role in the inhibitory activity. Molecular docking studies of the molecular conjugates and simple rhodanine analogues in the active site of α-glucosidase were performed to describe and highlight the putative binding interactions attributing to the selective inhibition. The identification of these novel rhodanine–pyrazole molecular hybrids forms part of a potential treatment in the management of diabetes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Design, synthesis and anticancer activities of halogenated Phenstatin analogs as microtubule destabilizing agent

A series of halogenated Phenstatin analogs were designed as microtubule destabilizing agent by docking study. It was synthesized within three steps starting from 2-chloro-5-iodobenzoic acid and substituted benzene. All the products were characterized by {sup 1}H NMR and {sup 13}C NMR spectral analysis, and the stereochemical structure was also confirmed by a single crystal X-ray diffraction crystallographic analysis. The microtubule destabilizing activities were evaluated in vitro with human liver cancer Huh-7 cell line and human lung cancer A549 cell line. Some of the HPAs were achieved IC{sub 50} about 5.0 μM against human liver cancer Huh-7 cells. .

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Synthesis and in vitro biological evaluation of 1,3-bis-(1,2,3-triazol-1-yl)-propan-2-ol derivatives as antifungal compounds fluconazole analogues

A novel series of 1,3-bis-(1,2,3-triazol-1-yl)-propan-2-ol derivatives was synthesized from 1-aryl-1,3-diazidopropan-2-ol derivatives and diverse alkynes using copper catalyzed azide-alkyne cycloaddition in the key step. Most of synthesized compounds showed high activity against Candida spp. strains at a 0.04–0.5 μg/mL concentration range compared to Itraconazole and Fluconazole (MIC 2.56 and 1.28 μg/mL, respectively), which were used as reference compounds. A 1,3-bis-(1,2,3-triazol-1-yl)-propan-2-ol derivative (R{sup 1} = F and R{sup 2} = cyclopropyl) displayed an outstanding selectivity against Candida albicans and Candida krusei (MIC = 0.0075 µg/mL). Moreover, Artemia salina bioassay on 1,3-bis-(1,2,3-triazol-1-yl)-propan-2-ol derivatives revealed low toxicity in this kind of compounds. In addition, molecular docking studies suggest good binding affinity of halogen atoms in some 1-aryl-1,3-diazidopropan-2-ol derivatives to HEME group present in 14-alpha demethylase (CYP51), which might explain the high antifungal activity found in these compounds.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Xenicanes attenuate pro-inflammatory 5-lipoxygenase: Prospective natural anti-inflammatory leads from intertidal brown seaweed Padina tetrastromatica

Two previously unreported xenicane class of novaxenicin-type xenicin diterpenoids (1–2) bearing cyclonona[d]furo [2,3-b]pyrandiol and three xeniolide-type diterpenoids with unprecedented octahydrocyclonona[c]pyran-3(1H)-one backbones (3–5) were separated from the organic extract of the intertidal seaweed Padina tetrastomatica (family Dictyotaceae), collected from southern India. The compounds were deduced to bear a xenicane moiety with a 2-oxabicyclo[7.4.0]tridecane cyclic system. The structures of these specialized metabolites were attributed based on the extensive nuclear magnetic resonance spectral analyses, and comparison of related compounds. Xeniolide-type diterpenes (3–5) registered significantly greater attenuation potential against pro-inflammatory 5-lipoxygenase (IC{sub 50} ~ 2.04 mM) than that exhibited by non-steroidal anti-inflammatory drug ibuprofen (IC{sub 50} 4.50 mM, P< 0.05). The xeniolide derivative octahydro-1,7-dihydroxy-4-(4{sup 1}-hydroxy-4{sup 2}-methylpropyl)-6-(6{sup 1}-hydroxy-6{sup 2}-propenyl)-10-methyl-cyclonona[c]pyran-3(1H)-one (5) exhibited comparable antioxidant activity (DPPH IC{sub 50} 1.73 mM) along with standard antioxidative agent α-tocopherol (IC{sub 50} < 2 mM). In silico molecular modelling studies were performed to designate the 5-lipoxygenase inhibitory mechanism of the xenicanes, and the comparison of docking parameters suggested that the xeniolide derivative 5 exhibited least binding energy of −11.56 kcal mol{sup −1}, and that was corroborated with its greater inhibition potential against the pro-inflammatory enzyme. These results demonstrated that the xeniolide-type diterpenoids with previously unreported δ-lactone cyclononane framework might constitute promising anti-inflammatory leads with pro-inflammatory 5-lipoxygenase enzyme inhibitory activities.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Furanchalcone–biphenyl hybrids: synthesis, in silico studies, antitrypanosomal and cytotoxic activities

The synthesis, antitrypanosomal, and cytotoxic activities of 17 furanchalcone derivatives are described herein. The structure of the synthesized products was elucidated by a combination of spectrometric analyses. The synthesized compounds were evaluated against Trypanosoma cruzi, which is the pathogenic species to humans. Cytotoxicity was evaluated against human U-937 macrophages. Eleven compounds were active against amastigotes of T. cruzi with EC{sub 50} values lower than 40 µM. Hybrids 7b–7d and 8a–8g showed better activity than benznidazole. Structure activity relationship (SAR) showed that the presence of electron withdrawing groups, such as nitro or fluorine, increased the activity and that the degree of oxygenation is essential for activity. In addition, molecular docking was used to identify a possible protein target for the designed compounds. A spearman correlation of 0.608 between the predicted scores and the experimental data profile the enzyme cruzipain as a potential candidate. Finally, in silico ADMET studies of the arylfuranchalcones showed that these novel compounds have suitable drug-like properties, making them potentially promising agents for antichagasic therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

N{sup 2}-Methylaurantiamide acetate: a new dipeptide from Mimusops elengi L. flowers

Mimusops elengi L. belonging to the Sapotaceae family is used in various folk systems of medicine in South and Southeast Asia. This study aims to identify the potential constituents responsible for anticancer activity of M. elengi flowers. The EtOAc fraction of M. elengi flowers methanolic extract possessed cytotoxicity and gave an intensive apoptotic response on human leukemia HL-60 cells. A new dipeptide N{sup 2}-methylaurantiamide acetate was isolated from the fraction along with two peptide derivatives and four phenolic compounds. Among the peptide constituents, N{sup 2}-methylaurantiamide acetate showed significant inhibition of cell proliferation and possible induction of apoptotic cell death. Molecular docking analysis demonstrated that N{sup 2}-methylaurantiamide acetate could fit tightly into the BH3-binding groove of anti-apoptotic protein Bcl-2. Our results provide further compelling evidence and enhance the ethnopharmacological value of M. elengi.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Design, synthesis and biological evaluation of novel indone derivatives as selective ERβ modulators

To reduce the endometrial toxicity and improve the efficacy of current selective estrogen receptor modulators used in breast cancer treatment by enhancing ERβ selectivity, inspired by active resveratrol oligomer, a series of analogs (5a–f, 6a–b, 7a–d, 8a–d) were designed, synthesized and biologically evaluated. Among them, the chiral indone analog (2R,3R)-8a exhibited best antiproliferative activity against both breast cancer cell lines (MDA-MB-231 and MCF-7) and better safety profile on uterus than tamoxifen. Analog (2R,3R)-8a demonstrated good binding affinity and selectivity toward ERβ, which was further proved by both molecular docking and radiometric competitive binding assay. Other studies for (2R,3R)-8a also have been explored including cell cycle and apoptosis evaluation and in vitro metabolic stability studies. These results demonstrated that (2R,3R)-8a could be a promising lead compound for future exploration of selective ERβ anti-breast cancer agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Functional relaxant effect of 6,7-dipropoxy-2H-chromen-2-one is mainly by calcium channel blockade in ex vivo assay of tracheal rings

Asthma is a prevalent disease characterized by airway chronic inflammation, airway hyperresponsiveness, edema and excess of mucus production. Molecules with coumarin scaffold have shown multiple biological effects, including anti-asthmatic. This study describes relaxant effect and mechanism of action of novel semisynthetic 6,7-dipropoxy-2H-chromen-2-one (6,7-DPC) on smooth muscle airways and in silico approaches. 6,7-DPC induced significant relaxant effect on tracheal rings pre-contracted with carbachol (E{sub max} = 100%; EC{sub 50} = 89 µM). Concentration-response curve of 6,7-DPC showed a significant shift to the left with respect to theophylline (positive control). Moreover, pre-treatment with 6,7-DPC inhibited the carbachol-induced contraction in a concentration-dependent manner with suppression of the maximum response. Also, KCl [80 mM]-induced contraction was partially abolished by 6,7-DPC compared with nifedipine; however, CaCl{sub 2} contraction curve only reached 30% of maximal response in the tissues pre-incubated with the test sample. 6,7-DPC was docked on an outer cavity located on the intracellular side of the human L-type calcium channel model and interacts in the following chains and residues: IIIS5.M26, IIIP.T45, IIIP.F49, IIIP.G51, IIIP.P53, IVP.C46, IVP.G49, IVP.E50, IVP.A51, IVP.W52, IVP.Q53, IVP.D54, IVS6.I4, IVS6.F7, IVS6.I8, IVS6.F10, and IVS6.F11. Also, nifedipine made unique interactions with IIIP.E50, IIIP.W52, IIIP.L55. Meanwhile, 6,7-DPC interacted with IIIS5.A22, IIIS2.Q27, and IVS6.C14, exclusively. In conclusion, 6,7-DPC showed a relaxant effect due to combined mechanism of action on rat tracheal rings, through non-competitive muscarinic receptor functional antagonism and preventing the calcium influx. This provides pharmacological basis for the use of 6,7-DPC in airways disorders, such as asthma or chronic obstructive pulmonary disease (COPD).

60 APPLIED LIFE SCIENCES↗