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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Context-dependent protein folding of a virulence peptide in the bacterial and host environments: structure of an SycH–YopH chaperone–effector complex

The structure of a SycH–YopH chaperone–effector complex from Yersinia reveals the bacterial state of a protein that adopts different folds in the host and pathogen environments. Yersinia pestis injects numerous bacterial proteins into host cells through an organic nanomachine called the type 3 secretion system. One such substrate is the tyrosine phosphatase YopH, which requires an interaction with a cognate chaperone in order to be effectively injected. Here, the first crystal structure of a SycH–YopH complex is reported, determined to 1.9 Å resolution. The structure reveals the presence of (i) a nonglobular polypeptide in YopH, (ii) a so-called β-motif in YopH and (iii) a conserved hydrophobic patch in SycH that recognizes the β-motif. Biochemical studies establish that the β-motif is critical to the stability of this complex. Finally, since previous work has shown that the N-terminal portion of YopH adopts a globular fold that is functional in the host cell, aspects of how this polypeptide adopts radically different folds in the host and in the bacterial environments are analysed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides

Selenium-derivatized oligonucleotides may facilitate phase determination and high-resolution structure determination for protein–nucleic acid crystallography. The Se atom-specific mutagenesis (SAM) strategy may also enhance the study of nuclease catalysis. The crystal structures of protein–nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein–nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H–RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

ANS complex of St John’s wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning

Hyp-1, a pathogenesis-related class 10 (PR-10) protein from H. perforatum, was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The asymmetric unit of the tetartohedrally twinned crystal contains 28 copies of the protein arranged in columns with noncrystallographic sevenfold translational symmetry and with additional pseudotetragonal rotational NCS. Hyp-1, a pathogenesis-related class 10 (PR-10) protein from St John’s wort (Hypericum perforatum), was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The highly pseudosymmetric crystal has 28 unique protein molecules arranged in columns with sevenfold translational noncrystallographic symmetry (tNCS) along c and modulated X-ray diffraction with intensity crests at l = 7n and l = 7n ± 3. The translational NCS is combined with pseudotetragonal rotational NCS. The crystal was a perfect tetartohedral twin, although detection of twinning was severely hindered by the pseudosymmetry. The structure determined at 2.4 Å resolution reveals that the Hyp-1 molecules (packed as β-sheet dimers) have three novel ligand-binding sites (two internal and one in a surface pocket), which was confirmed by solution studies. In addition to 60 Hyp-1-docked ligands, there are 29 interstitial ANS molecules distributed in a pattern that violates the arrangement of the protein molecules and is likely to be the generator of the structural modulation. In particular, whenever the stacked Hyp-1 molecules are found closer together there is an ANS molecule bridging them.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target

In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structures of neurexophilin–neurexin complexes reveal a regulatory mechanism of alternative splicing

Neurexins are presynaptic, cell-adhesion molecules that specify the functional properties of synapses via interactions with trans-synaptic ligands. Neurexins are extensively alternatively spliced at six canonical sites that regulate multifarious ligand interactions, but the structural mechanisms underlying alternative splicing-dependent neurexin regulation are largely unknown. Here, we determined high-resolution structures of the complex of neurexophilin-1 and the second laminin/neurexin/sex-hormone-binding globulin domain (LNS2) of neurexin-1 and examined how alternative splicing at splice site #2 (SS2) regulates the complex. Our data reveal a unique, extensive, neurexophilin–neurexin binding interface that extends the jelly-roll β-sandwich of LNS2 of neurexin-1 into neurexophilin-1. The SS2A insert of LNS2 augments this interface, increasing the binding affinity of LNS2 for neurexophilin-1. Taken together, our data reveal an unexpected architecture of neurexophilin–neurexin complexes that accounts for the modulation of binding by alternative splicing, which in turn regulates the competition of neurexophilin for neurexin binding with other ligands.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Complexity and Simplicity: Putting Complexity Science in Perspective

As technical systems and social problems in modern society become ever more complex, many organizations are turning to what is commonly termed complexity science to find solutions. The problem many organizations face is that they frequently have no clear idea what they are trying to accomplish, no in-depth understanding of the nature, size and dimension of their problem, and only a limited understanding of what theoretical approaches and off-the-shelf analysis tools exist or are applicable to their particular problem. This paper examines the larger topic of complexity science, providing insight, and helping to place its promises in perspective.

99 GENERAL AND MISCELLANEOUS↗
NASA NTRS1980

Giant molecular complexes and OB associations. I - The Rosette molecular complex

CO observations of the Rosette molecular complex associated with Mon OB2 are presented. The complex is extended along the galactic plane, has a maximum extent of about 100 pc, and shows a striking interaction with the Rosette Nebula. The molecular gas appears to be embedded in a H I cloud with a mass comparable to the molecular mass. The molecular mass is estimated to be 130,000 solar masses, and the inferred volume density is about 30 per cu cm. The complex has an overall velocity gradient of 0.20 km/s pc. At high resolution the CO appears to be very clumpy.

Blitz, L.↗
NASA NTRS1990

Reactivity of pi-complexes of Ti, V, and Nb towards dithioacetic acid: Synthesis and structure of novel metal sulfur-containing complexes

In order to use sulfur-containing resources economically and with minimal environmental damage, it is important to understand the desulfurization processes. Hydrodesulfurization, for example, is carried out on the surface of a heterogeneous metal sulfide catalyst. Studies of simple, soluble inorganic systems provide information regarding the structure and reactivity of sulfur-containing compounds with metal complexes. Further, consistent with recent trends in materials chemistry, many model compounds warrant further study as catalyst precursors. The reactivity of low-valent organometallic sandwich pi-complexes toward dithiocarboxylic acids is described. For example, treatment of bisbenzene vanadium with CH3CSSH affords a divanadium tetrakis(dithioacetate) complex. The crystallographically determined V-V bond distance, 2.800(2), is nearly the same as the V-V bond distance in a V(mu-nu squared-S2)2V' unit in the mineral patonite (VS4)n. The stability of the V2S4 core in the dimer is demonstrated by evidence of V2S4(+) in the mass spectrum (70 eV, solid probe) of the vanadium dimer. Several other systems relevant to HDS catalysis are also discussed.

Duraj, Stan A.↗
NASA NTRS1994

The development and application of composite complexity models and a relative complexity metric in a software maintenance environment

A great deal of effort is now being devoted to the study, analysis, prediction, and minimization of software maintenance expected cost, long before software is delivered to users or customers. It has been estimated that, on the average, the effort spent on software maintenance is as costly as the effort spent on all other software costs. Software design methods should be the starting point to aid in alleviating the problems of software maintenance complexity and high costs. Two aspects of maintenance deserve attention: (1) protocols for locating and rectifying defects, and for ensuring that noe new defects are introduced in the development phase of the software process; and (2) protocols for modification, enhancement, and upgrading. This article focuses primarily on the second aspect, the development of protocols to help increase the quality and reduce the costs associated with modifications, enhancements, and upgrades of existing software. This study developed parsimonious models and a relative complexity metric for complexity measurement of software that were used to rank the modules in the system relative to one another. Some success was achieved in using the models and the relative metric to identify maintenance-prone modules.

Hops, J. M.↗
NASA NTRS2009

Trajectory-Oriented Approach to Managing Traffic Complexity: Trajectory Flexibility Metrics and Algorithms and Preliminary Complexity Impact Assessment

This document describes exploratory research on a distributed, trajectory oriented approach for traffic complexity management. The approach is to manage traffic complexity based on preserving trajectory flexibility and minimizing constraints. In particular, the document presents metrics for trajectory flexibility; a method for estimating these metrics based on discrete time and degree of freedom assumptions; a planning algorithm using these metrics to preserve flexibility; and preliminary experiments testing the impact of preserving trajectory flexibility on traffic complexity. The document also describes an early demonstration capability of the trajectory flexibility preservation function in the NASA Autonomous Operations Planner (AOP) platform.

Idris, Husni↗
DOE OSTI2015

Influence of weak vibrational-electronic couplings on 2D electronic spectra and inter-site coherence in weakly coupled photosynthetic complexes

Coherence oscillations measured in two-dimensional (2D) electronic spectra of pigment-protein complexes may have electronic, vibrational, or mixed-character vibronic origins, which depend on the degree of electronic-vibrational mixing. Oscillations from intrapigment vibrations can obscure the inter-site coherence lifetime of interest in elucidating the mechanisms of energy transfer in photosynthetic light-harvesting. Huang-Rhys factors (S) for low-frequency vibrations in Chlorophyll and Bacteriochlorophyll are quite small (S ≤ 0.05), so it is often assumed that these vibrations influence neither 2D spectra nor inter-site coherence dynamics. In this work, we explore the influence of S within this range on the oscillatory signatures in simulated 2D spectra of a pigment heterodimer. To visualize the inter-site coherence dynamics underlying the 2D spectra, we introduce a formalism which we call the “site-probe response.” By comparing the calculated 2D spectra with the site-probe response, we show that an on-resonance vibration with Huang-Rhys factor as small as S = 0.005 and the most strongly coupled off-resonance vibrations (S = 0.05) give rise to long-lived, purely vibrational coherences at 77 K. We moreover calculate the correlation between optical pump interactions and subsequent entanglement between sites, as measured by the concurrence. At 77 K, greater long-lived inter-site coherence and entanglement appear with increasing S. This dependence all but vanishes at physiological temperature, as environmentally induced fluctuations destroy the vibronic mixing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

CSI1, PATROL1, and exocyst complex cooperate in delivery of cellulose synthase complexes to the plasma membrane

Significance Cellulose is synthesized at the plasma membrane by cellulose synthase complexes (CSCs). The ability to deliver CSCs to discrete sites at the cell surface is critical for cellulose synthesis. We discovered that the de novo secretion of CSCs is mediated by cooperation among a recently identified cellulose synthase interacting protein, exocyst complex, and a plant-specific protein PATROL1 in Arabidopsis thaliana . We present a timeline of events for exocytosis of CSCs. CSCs represent unique cargo proteins that are not conserved in the mammalian or yeast system. Plants offer unique opportunities to characterize the function and regulation of exocytosis that may provide insight into the evolution of exocytosis in eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

(Pentamethylcyclopentadienato)rhodium complexes for delivery of the curcumin anticancer drug [Rhodium pentamethylcyclopentadienato complexes for delivery of the curcumin anti-cancer drug]

[RhIII(*Cp)Cl(X,Y)] n+ complexes {X, Y = Cl, PTA, n = 0 (2); X, Y = en, n = 1 (3, Cl– salt; 4, PF 6 – salt); X, Y = acac, n = 0 (5); X, Y = cur, n = 0 (6), where *Cp = pentamethylcyclopentadienato, curH = curcumin; PTA = 1,3,5-triaza-7-phosphatricyclo[3.3.1.1]decane; en = 1,2-ethanediamine; acac = acetylacetonato = 2,4-pentanedionato(1–)} were synthesized from [Rh(*Cp)(µ-Cl)Cl] 2 (1). While 2–5 were inactive against human epithelial A549 lung-cancer cells in assays of cytotoxicity, and antimetastatic and proapoptotic behaviors, 6 had a cytotoxic activity similar to that of curH over 72 h, but at 24 h in real-time cell migration assays, it was less active, showing slow release of curH. All complexes underwent ligand-exchange reactions with biomolecules and cells within the timeframes of the assays (X-ray absorption spectroscopy). Intracellular elemental distributions (X-ray fluorescence microscopy) showed that 6 effectively delivered curH to cells, where it was released. Other elemental distributions and caspase activities were consistent with preapoptotic activities. As such, 6 is a promising delivery agent for bioactive ligands, such as curH. However, pure curcumin itself showed a previously unrecognized ability to promote migration of A549 cells at subtoxic concentrations in the presence of endothelial growth factor, which may be a concern for its widespread use as a nutritional supplement and as a potential drug. As a result, this aspect warrants further research.

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

A step forward from high-entropy ceramics to compositionally complex ceramics: a new perspective

High-entropy ceramics (HECs) have quickly gained attention since 2015. To date, nearly all work has focused on five-component, equimolar compositions. This perspective article briefly reviews different families of HECs and selected properties. Following a couple of our most recent studies, we propose a step forward to expand HECs to compositionally-complex ceramics (CCCs) to include medium-entropy and/or non-equimolar compositions. Here, using defective fluorite and ordered pyrochlore oxides as two primary examples, we further consider the complexities of aliovalent cations and anion vacancies as well as ordered structures with two cation sublattices. Better thermally-insulating yet stiff CCCs have been found in non-equimolar compositions with optimal amounts of oxygen vacancies and in ordered pyrochlores with large size disorder; it is demonstrated that medium-entropy ceramics (MECs) can prevail over their high-entropy counterparts. The diversifying classes of CCCs provide even more possibilities than HECs to tailor the composition, defects, disorder/order, and consequently various properties.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Gold core/ceria shell-based redox active nanozyme mimicking the biological multienzyme complex phenomenon

Catalytically active individual gold (Au) and cerium oxide (CeO2) nanoparticles are well known to exhibit specific enzyme-like activities, such as natural catalase, oxidase, superoxide dismutase, and peroxidase enzymes. These activities have been maneuvered to design several biological applications such as immunoassays, glucose detection, radiation and free radical protection and tissue engineering. A functional nanozyme depicting multienzyme like properties that functions as a synthetic super enzyme has eluded the researchers in the nanoscience community for past decade. In current report, we have designed a functional multienzyme in the form of Gold (core)-CeO2 (shell) nanoparticles (Au@CeO2 CSNPs) exhibiting excellent peroxidase, catalase and superoxide dismutase enzyme-like activities that are controlled simply by tuning the pH. The reaction kinetic parameters reveal that the peroxidase-like activity of this core shell nanozyme is comparable to natural HRP enzyme. Unlike peroxidase-like activity exhibited by other nanomaterials, Au@CeO2 CSNPs showed decrease in hydroxyl radical formation, suggesting that the bio catalytic reactions are performed by efficient electron transfers. A significant enzyme-like activity of this core shell nanoparticle was conserved at extreme pH (2 – 11) and temperatures (up to 90 °C), clearly suggesting the superiority over natural enzymes. Further, the utility of peroxidase-like activity of this core shell nanoparticles was extended for the detection of glucose, which showed a linear range of detection between (100 µM – 1 mM). It is hypothesized that the proximity of the redox potentials of Au+/Au and Ce (III)/Ce (IV) may result in a redox couple promoting the multienzyme activity of core shell nanoparticles. Au@CeO2 CSNPs may open new directions for development of single platform sensors in multiple biosensing applications.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2013

The impact of crystal symmetry on the electronic structure and functional properties of complex lanthanum chromium oxides

Complex oxides exhibit a wide range of crystal structures, chemical compositions and physical properties. The underlying drivers determining the complicated structure-composition-property phase diagrams are the relative positions and orbital overlaps between the metal cations and the oxygen anions. Here we report a combined experimental and theoretical investigation of the structure and bonding in a series of lanthanum chromium oxides prepared by reactive molecular beam epitaxy. Of particular interest is the charge state and local coordination of the Cr. We have stabilized LaCrO 3 , LaCrO 4 and La 2 CrO 6 films by controlling the three elemental fluxes during deposition, and have carried out x-ray diffraction, x-ray photoemission, and x-ray absorption spectroscopy, as well as first-principles calculations, to determine structure, charge state, chemical bonding, and electronic structure. Significant changes in bonding character and orbital interaction are revealed with decreasing ligand symmetry from octahedral to tetrahedral Cr coordination. Both LaCrO 4 and LaCrO 6 with tetrahedrally coordinated Cr show strong pre-edge features in the Cr K-edge near-edge structure whereas LaCrO 3 with octahedrally coordinated Cr exhibits very weak pre-edge features. The origin of these pre-edge features is discussed based on various selection rules and ligand symmetry. We also demonstrate an increase in cation-anion orbital hybridization and a decrease in long-range ligand coupling induced by this symmetry reduction. These in turn result in dramatic modifications of the macroscopic optical and magnetic properties.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗