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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
NASA NTRS2002

A Self-Replicating Ligase Ribozyme

A self-replicating molecule directs the covalent assembly of component molecules to form a product that is of identical composition to the parent. When the newly formed product also is able to direct the assembly of product molecules, the self-replicating system can be termed autocatalytic. A self-replicating system was developed based on a ribozyme that catalyzes the assembly of additional copies of Itself through an RNA-catalyzed RNA ligation reaction. The R3C ligase ribozyme was redesigned so that it would ligate two substrates to generate an exact copy of itself, which then would behave in a similar manner. This self-replicating system depends on the catalytic nature of the RNA for the generation of copies. A linear dependence was observed between the initial rate of formation of new copies and the starting concentration of ribozyme, consistent with exponential growth. The autocatalytic rate constant was 0.011 per min, whereas the initial rate of reaction in the absence of pre-existing ribozyme was only 3.3 x 10(exp -11) M per min. Exponential growth was limited, however, because newly formed ribozyme molecules had greater difficulty forming a productive complex with the two substrates. Further optimization of the system may lead to the sustained exponential growth of ribozymes that undergo self-replication.

Paul, Natasha↗
NASA NTRS1999

Nucleic acid duplexes incorporating a dissociable covalent base pair

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

Non-NASA Center↗
NASA NTRS2013

Modeling Non-homologous End Joining

Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several NHEJ proteins such as Ku, DNA-PKcs, XRCC4, Ligase IV and so on. Once DSBs are generated, Ku is first recruited to the DNA end, followed by other NHEJ proteins for DNA end processing and ligation. Because of the direct ligation of break ends without the need for a homologous template, NHEJ turns out to be an error-prone but efficient repair pathway. Some mechanisms have been proposed of how the efficiency of NHEJ repair is affected. The type of DNA damage is an important factor of NHEJ repair. For instance, the length of DNA fragment may determine the recruitment efficiency of NHEJ protein such as Ku [1], or the complexity of the DNA breaks [2] is accounted for the choice of NHEJ proteins and subpathway of NHEJ repair. On the other hand, the chromatin structure also plays a role of the accessibility of NHEJ protein to the DNA damage site. In this talk, some mathematical models of NHEJ, that consist of series of biochemical reactions complying with the laws of chemical reaction (e.g. mass action, etc.), will be introduced. By mathematical and numerical analysis and parameter estimation, the models are able to capture the qualitative biological features and show good agreement with experimental data. As conclusions, from the viewpoint of modeling, how the NHEJ proteins are recruited will be first discussed for connection between the classical sequential model [4] and recently proposed two-phase model [5]. Then how the NHEJ repair pathway is affected, by the length of DNA fragment [6], the complexity of DNA damage [7] and the chromatin structure [8], will be addressed

Li, Yongfeng↗
DOE OSTI2023

Reagent to label proteins via lysine isopeptide bonds

Covalently cross-linked pilus polymers displayed on the cell surface of Gram-positive bacteria are assembled by class C sortase enzymes. These pilus-specific transpeptidases located on the bacterial membrane catalyze a two-step protein ligation reaction—first, cleaving the LPXTG motif of one pilin protomer to form an acyl-enzyme intermediate, and second, joining the terminal threonine to the nucleophilic lysine residue residing within the pilin motif of another pilin protomer. Informed by the high-resolution crystal structures of corynebacterial pilus-specific sortase (SrtA) and by developing structural variants of the sortase enzyme whose catalytic pocket has been unmasked by activating mutations, we have developed new reagents capable of forming isopeptide bonds in vitro. The reagents disclosed herein can catalyze ligation of isolated SpaA domains in vitro provide a facile and versatile new platform for protein engineering and bio-conjugation that has major implications for biotechnology.

Clubb, Robert T.↗
DOE OSTI2023

Open and Close-Packed, Shape-Engineered Polygonal Nanoparticle Metamolecules with Tailorable Fano Resonances

In this study, a top-down lithographic patterning and deposition process is reported for producing nanoparticles (NPs) with well-defined sizes, shapes, and compositions that are often not accessible by wet-chemical synthetic methods. These NPs are ligated and harvested from the substrate surface to prepare colloidal NP dispersions. Using a template-assisted assembly technique, fabricated NPs are driven by capillary forces to assemble into size- and shape-engineered templates and organize into open or close-packed multi-NP structures or NP metamolecules. The sizes and shapes of the NPs and of the templates control the NP number, coordination, interparticle gap size, disorder, and location of defects such as voids in the NP metamolecules. The plasmonic resonances of polygonal-shaped Au NPs are exploited to correlate the structure and optical properties of assembled NP metamolecules. Comparing open and close-packed architectures highlights that introduction of a center NP to form close-packed assemblies supports collective interactions, altering magnetic optical modes and multipolar interactions in Fano resonances. Decreasing the distance between NPs strengthens the plasmonic coupling, and the structural symmetries of the NP metamolecules determine the orientation-dependent scattering response.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Deliberate Construction of Polyoxoniobates Exploiting the Carbonate Ligand

Abstract Polyoxometalates (POMs, metals=V V , Nb V , Ta V , Mo VI , W VI ) are molecular metal oxides that can be isolated without capping ligands. The high negative charge of polyoxoniobates (PONb) provides strong interactions with heterocations, advantageous for electrostatic assembly of modular materials. In four single‐crystal X‐ray structures, we demonstrate that carbonate combined with the very reactive decaniobate [Nb 10 O 28 ] 6− reassembles into a new decaniobate, [Nb 10 O 25 (CO 3 ) 6 ] 12− , featuring three carbonate‐ligated Nb‐polyhedra. These Nb‐sites can be replaced by heterometals (lanthanides), and the tridentate carbonate can serve as an anchor point to build niobate‐frameworks. Small‐angle X‐ray scattering and two additional X‐ray structures reveal that the reaction pathway proceeds through a Nb 24 ‐PONb intermediate, and the obtained PONb (with or without carbonate) is counterion, temperature, and solvent‐dependent (water or mixed water‐methanol). This provides an uncommon level of control for PONb chemistry.

Amiri, Mehran↗
DOE OSTI2024

A Stable Site‐Isolated Mono(phosphine)‐Rhodium Catalyst on a Metal‐Organic Layer for Highly Efficient Hydrogenation Reactions

Abstract Phosphine‐ligated transition metal complexes play a pivotal role in modern catalysis, but our understanding of the impact of ligand counts on the catalysis performance of the metal center is limited. Here we report the synthesis of a low‐coordinate mono(phosphine)‐Rh catalyst on a metal‐organic layer (MOL), P‐MOL • Rh, and its applications in the hydrogenation of mono‐, di‐, and tri‐substituted alkenes as well as aryl nitriles with turnover numbers (TONs) of up to 390000. Mechanistic investigations and density functional theory calculations revealed the lowering of reaction energy barriers by the low steric hindrance of site‐isolated mono(phosphine)‐Rh sites on the MOL to provide superior catalytic activity over homogeneous Rh catalysts. The MOL also prevents catalyst deactivation to enable recycle and reuse of P‐MOL • Rh in catalytic hydrogenation reactions.

Chemistry↗
DOE OSTI2023

Chemo-Enzymatic Synthesis of Long-Chain Oligosaccharides for Studying Xylan-Modifying Enzymes

Plant research is hampered in several aspects by a lack of pure oligosaccharide samples that closely represent structural features of cell wall glycans. An alternative to purely chemical synthesis to access these oligosaccharides is chemo-enzymatic synthesis using glycosynthases. These enzymes enable the ligation of oligosaccharide donors, when activated for example as α-glycosyl fluorides, with suitable acceptor oligosaccharides. Herein, the synthesis of xylan oligosaccharides up to dodecasaccharides is reported, with glycosynthase-mediated coupling reactions as key steps. The xylo-oligosaccharide donors were protected at the non-reducing end with a 4-O-tetrahydropyranyl (THP) group to prevent polymerization. Installation of an unnatural 3-O-methylether substituent at the reducing end xylose of the oligosaccharides ensured good water solubility. Biochemical assays demonstrated enzymatic activity for the xylan acetyltransferase XOAT1 from Arabidopsis thaliana, xylan arabinofuranosyl-transferase XAT3 enzymes from rice and switchgrass, and the xylan glucuronosyltransferase GUX3 from Arabidopsis thaliana. In case of the glucuronosyltransferase GUX3, MALDI-MS/MS analysis of the reaction product suggested that a single glucuronosyl substituent was installed primarily at the central xylose residues of the dodecasaccharide acceptor, demonstrating the value of long-chain acceptors for assaying biosynthetic glycosyltransferases.

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

Organo‐Functionalized Lacunary Double Cubane‐Type Oxometallates: Synthesis, Structure, and Properties of [(M II Cl) 2 (V IV O) 2 {((HOCH 2 CH 2 )(H)N(CH 2 CH 2 O))(HN(CH 2 CH 2 O) 2 )} 2 ] (M=Co, Zn)

Abstract Organofunctionalized tetranuclear clusters [(M II Cl) 2 (V IV O) 2 {((HOCH 2 CH 2 )(H)N(CH 2 CH 2 O))(HN(CH 2 CH 2 O) 2 )} 2 ] (1, M=Co,2: M=Zn) containing an unprecedented oxometallacyclic {M 2 V 2 Cl 2 N 4 O 8 } (M=Co, Zn) framework have been prepared by solvothermal reactions. The new oxo‐alkoxide compounds were fully characterized by spectroscopic methods, magnetic susceptibility measurement, DFT and ab initio computational methods, and complete single‐crystal X‐ray diffraction structure analysis. The isostructural clusters are formed of edge‐sharing octahedral {VO 5 N} and trigonal bipyramidal {MO 3 NCl} units. Diethanolamine ligates the bimetallic lacunary double cubane core of1and2in an unusual two‐mode fashion, unobserved previously. In the crystalline state, the clusters of1and2are joined by hydrogen bonds to form a three‐dimensional network structure. Magnetic susceptibility data indicate weakly antiferromagnetic interactions between the vanadium centers [J iso (V IV −V IV )=−5.4(1); −3.9(2) cm −1 ], and inequivalent antiferromagnetic interactions between the cobalt and vanadium centers [J iso (V IV −Co II )=−12.6 and −7.5 cm −1 ] contained in1.

Chemistry↗
DOE OSTI2025

Photophysical and Time‐resolved Infrared Properties of Long‐Lived Rhenium(I) 4,5‐Diazafluorene Tricarbonyl Chromophores

This report investigates the synthesis, structural characterization, fundamental molecular photophysics, electrochemistry, UV-Vis spectroelectrochemistry, and time-resolved infrared spectroscopic properties of eight [fac-Re(dafR)(CO) 3 L] 0/+ complexes, where R=ethyl [(dedaf); 1, 3, 5, 7] or H [(dafH); 2, 4, 6, 8] and L=Cl− (1, 2), imidazole [(Im); 3, 4], 4-ethylpyridine [(4-Etpy); 5, 6], or pyridine [(py); 7, 8]. Universally, 1–8 yield higher energy photoluminescence (PL) emission bands and higher PL quantum yields (up to 53 %) than the classic 2,2’-bipyridine (bpy) and 1,10-phenanthroline (phen) ligated Re(I) tricarbonyl complexes. The excited state lifetimes of 1–8 lie between those corresponding to the bpy and phen derivatives, ranging from 120 and 1300 ns at room temperature. Combinations of reductive UV-Vis spectroelectrochemistry, transient absorption spectroscopy, and time-resolved infrared spectroscopy consistently assigned the lowest excited states in 1–8 being of metal-to-ligand charge transfer (MLCT) character. These new ReI MLCT chromophores follow classic energy gap law behavior and possess the characteristics necessary for serving as valuable photosensitizers suitable to energize excited state electron and energy transfer photochemistry.

Charge transfer↗
DOE OSTI2023

Development of molecular cluster models to probe pyrite surface reactivity

Abstract The recent discovery that anaerobic methanogens can reductively dissolve pyrite and utilize dissolution products as a source of iron and sulfur to meet their biosynthetic demands for these elements prompted the development of atomic‐scale nanoparticle models, as maquettes of reactive surface sites, for describing the fundamental redox steps that take place at the mineral surface during reduction. The given report describes our computational approach for modeling n (FeS 2 ) nanoparticles originated from mineral bulk structure. These maquettes contain a comprehensive set of coordinatively unsaturated Fe (II) sites that are connected via a range of persulfide (S 2 2− ) ligation. In addition to the specific maquettes with n = 8, 18, and 32 FeS 2 units, we established guidelines for obtaining low‐energy structures by considering the pattern of ionic, covalent, and magnetic interactions among the metal and ligand sites. The developed models serve as computational nano‐reactors that can be used to describe the reductive dissolution mechanism of pyrite to better understand the reactive sites on the mineral, where microbial extracellular electron‐transfer reactions can occur.

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

Erratum to: Soft- and reactive landing of ions onto surfaces: concepts and applications

Soft- and reactive landing of mass-selected ions is gaining attention as a promising approach for the precisely-controlled preparation of materials on surfaces that are not amenable to deposition using conventional methods. A broad range of ionization sources and mass filters are available that make ion soft-landing a versatile tool for surface modification using beams of hyperthermal (<100?eV) ions. The ability to select the mass-to-charge ratio of the ion, its kinetic energy and charge state, along with precise control of the size, shape, and position of the ion beam on the deposition target distinguishes ion soft landing from other surface modification techniques. Soft- and reactive landing have been used to prepare interfaces for practical applications as well as precisely-defined model surfaces for fundamental investigations in chemistry, physics, and materials science. For instance, soft- and reactive landing have been applied to study the surface chemistry of ions isolated in the gas-phase, prepare arrays of proteins for high-throughput biological screening, produce novel carbon-based and polymer materials, enrich the secondary structure of peptides and the chirality of organic molecules, immobilize electrochemically-active proteins and organometallics on electrodes, create thin films of complex molecules, and immobilize catalytically active organometallics as well as ligated metal clusters. In addition, soft landing has enabled investigation of the size-dependent behavior of bare metal clusters in the critical subnanometer size regime where chemical and physical properties do not scale predictably with size. The morphology, aggregation, and immobilization of larger bare metal nanoparticles, which are directly relevant to the design of catalysts as well as improved memory and electronic devices, have also been studied using ion soft landing. This review article begins in section 1 with a brief introduction to the existing applications of ion soft- and reactive landing. Section 2 provides an overview of the ionization sources and mass filters that have been used to date for soft landing of mass-selected ions. A discussion of the competing processes that occur during ion deposition as well as the types of ions and surfaces that have been investigated follows in section 3. Section 4 discusses the physical phenomena that occur during and after ion soft landing, including retention and reduction of ionic charge along with factors that impact the efficiency of ion deposition. The influence of soft landing on the secondary structure and biological activity of complex ions is addressed in section 5. Lastly, an overview of the structure and mobility as well as the catalytic, optical, magnetic, and redox properties of bare ionic clusters and nanoparticles deposited onto surfaces is presented in section 6. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:439–479, 2016.

Johnson, Grant E.↗
DOE OSTI2020

Solution structure for an Encephalitozoon cuniculi adrenodoxin-like protein in the oxidized state

Encephalitozoon cuniculi is a unicellular, obligate intracellular eukaryotic parasite in the Microsporidia family and one of the agents responsible for microsporidosis infections in humans. Like most Microsporidia, the genome of E. cuniculi is markedly reduced and the organism contains mitochondria-like organelles called mitosomes instead of mitochondria. Here we report the solution NMR structure for a protein physically associated with mitosome-like organelles in E. cuniculi, the 128-residue, adrenodoxin-like protein Ec-Adx (UniProt ID Q8SV19) in the [2Fe-2S] ferredoxin superfamily. Oxidized Ec-Adx contains a mixed four-strand β-sheet, β2-β1-β4-β3 (↓↑↑↓), loosely encircled by three α-helices and two 310-helices. This fold is similar to the structure observed in other adrenodoxin and adrenodoxin-like proteins except for the absence of a fifth anti-parallel β-strand next to β3 and the position of α3. Cross peaks are missing or cannot be unambiguously assigned for 20 amide resonances in the 1 H- 15 N HSQC spectrum of Ec-Adx. These missing residues are clustered primarily in two regions, G48-V61 and L94-L98, containing the four cysteine residues predicted to ligate the paramagnetic [2Fe-2S] cluster. Missing amide resonances in 1 H- 15 N HSQC spectra are detrimental to NMR-based solution structure calculations because 1 H- 1 H NOE restraints are absent (glass half-empty) and this may account for the absent β-strand (β5) and the position of α3 in oxidized Ec-Adx. On the other hand, the missing amide resonances unambiguously identify the presence, and immediate environment, of the paramagnetic [2Fe-2S] cluster in oxidized Ec-Adx (glass half-full).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

X‐ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double‐strand break repair impacting cell and cancer biology

Abstract Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIV BRCT –Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes

Abstract Sequence variation in related proteins is an important characteristic that modulates activity and selectivity. An example of a protein family with a large degree of sequence variation is that of bacterial sortases, which are cysteine transpeptidases on the surface of gram‐positive bacteria. Class A sortases are responsible for attachment of diverse proteins to the cell wall to facilitate environmental adaption and interaction. These enzymes are also used in protein engineering applications for sortase‐mediated ligations (SML) or sortagging of protein targets. We previously investigated SrtA from Streptococcus pneumoniae , identifying a number of putative β7–β8 loop‐mediated interactions that affected in vitro enzyme function. We identified residues that contributed to the ability of S. pneumoniae SrtA to recognize several amino acids at the P1′ position of the substrate motif, underlined in LPXT G , in contrast to the strict P1′ Gly recognition of SrtA from Staphylococcus aureus . However, motivated by the lack of a structural model for the active, monomeric form of S. pneumoniae SrtA, here, we expanded our studies to other Streptococcus SrtA proteins. We solved the first monomeric structure of S. agalactiae SrtA which includes the C‐terminus, and three others of β7–β8 loop chimeras from S. pyogenes and S. agalactiae SrtA. These structures and accompanying biochemical data support our previously identified β7–β8 loop‐mediated interactions and provide additional insight into their role in Class A sortase substrate selectivity. A greater understanding of individual SrtA sequence and structural determinants of target selectivity may also facilitate the design or discovery of improved sortagging tools.

Gao, Melody↗
DOE OSTI2025

Discovery of a Ferromagnetic Nickel Chalcogenide Nanocluster Ni 3 S 3 H(PEt 3 ) 5

Atomically precise ligated nanoclusters (NC) are promising cluster-based materials with novel molecular architectures and tunable magnetic properties. Herein, the synthesis and characterization of a nickel sulfide NC Ni 3 S 3 H(PEt 3 ) 5 (PEt 3 = triethylphosphine) with distinct magnetic properties are reported. Magnetization measurements reveal its magnetic moment of 1.5 µ B in the solid phase, consistent with the existence of one unpaired electron predicted by density functional theory (DFT) calculations. Additionally, experimental measurements indicate the presence of ferromagnetic ordering within each Ni 3 S 3 H(PEt 3 ) 5 NC and strong coercivity at temperatures below 20 K. Ion mobility-mass spectrometry is employed in conjunction with DFT calculations and collision cross-section simulations to investigate the structure of the isolated Ni 3 S 3 H(PEt 3 ) 5 . Theoretical studies show that [Ni 3 S 3 H(PEt 3 ) 5 ] + has a planar Ni 3 S 3 core where three Ni atoms are arranged in a triangle with three bridging S atoms residing in the same plane. This structure is preserved in both solution and solid phases, which is confirmed by spectroscopic studies of Ni 3 S 3 H(PEt 3 ) 5 . Additionally, DFT calculations indicate that all spins at the Ni sites are aligned parallel, confirming the presence of ferromagnetic coupling. Overall, this study provides key insights into the structure and magnetic properties of Ni 3 S 3 H(PEt 3 ) 5 , which will facilitate the design of new NC-based magnetic materials.

Nickel sulfide nanocluster↗