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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 1,459 records · Page 81
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

C-terminal region of DNA ligase IV drives XRCC4/DNA ligase IV complex to chromatin

Highlights: •Chromatin binding of XRCC4 is dependent on the presence of DNA ligase IV. •C-terminal region of DNA ligase IV alone can recruit itself and XRCC4 to chromatin. •Two BRCT domains of DNA ligase IV are essential for the chromatin binding of XRCC4. -- Abstract: DNA ligase IV (LIG4) and XRCC4 form a complex to ligate two DNA ends at the final step of DNA double-strand break (DSB) repair through non-homologous end-joining (NHEJ). It is not fully understood how these proteins are recruited to DSBs. We recently demonstrated radiation-induced chromatin binding of XRCC4 by biochemical fractionation using detergent Nonidet P-40. In the present study, we examined the role of LIG4 in the recruitment of XRCC4/LIG4 complex to chromatin. The chromatin binding of XRCC4 was dependent on the presence of LIG4. The mutations in two BRCT domains (W725R and W893R, respectively) of LIG4 reduced the chromatin binding of LIG4 and XRCC4. The C-terminal fragment of LIG4 (LIG4-CT) without N-terminal catalytic domains could bind to chromatin with XRCC4. LIG4-CT with W725R or W893R mutation could bind to chromatin but could not support the chromatin binding of XRCC4. The ability of C-terminal region of LIG4 to interact with chromatin might provide us with an insight into the mechanisms of DSB repair through NHEJ.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

A close look onto structural models and primary ligands of metallo-β-lactamases

β-Lactamases are hydrolytic enzymes capable of opening the β-lactam ring of antibiotics such as penicillin, thus endowing the bacteria that produce them with antibiotic resistance. Of particular medical concern are metallo-β-lactamases (MBLs), with an active site built around coordinated Zn cations. MBLs are pan-reactive enzymes that can break down almost all classes of β-lactams, including such last-resort antibiotics as carbapenems. They are not only broad-spectrum-reactive but are often plasmid-borne (e.g., the New Delhi enzyme, NDM), and can spread horizontally even among unrelated bacteria. Acquired MBLs are encoded by mobile genetic elements, which often include other resistance genes, making the microbiological situation particularly alarming. There is an urgent need to develop MBL inhibitors in order to rescue our antibiotic armory. A number of such efforts have been undertaken, most notably using the 3D structures of various MBLs as drug-design targets. Structure-guided drug discovery depends on the quality of the structures that are collected in the Protein Data Bank (PDB) and on the consistency of the information in dedicated β-lactamase databases. Here, we conducted a careful review of the crystal structures of class B β-lactamases, concluding that the quality of these structures varies widely, especially in the regions where small molecules interact with the macromolecules. In a number of examples the interpretation of the bound ligands (e.g., inhibitors, substrate/product analogs) is doubtful or even incorrect, and it appears that in some cases the modeling of ligands was not supported by electron density. For ten MBL structures, alternative interpretations of the original diffraction data could be proposed and the new models have been deposited in the PDB. In four cases, these models, prepared jointly with the authors of the original depositions, superseded the previous deposits. This review emphasizes the importance of critical assessment of structural models describing key drug design targets at the level of the raw experimental data. Since the structures reviewed here are the basis for ongoing design of new MBL inhibitors, it is important to identify and correct the problems with ambiguous crystallographic interpretations, thus enhancing reproducibility in this highly medically relevant area.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Density estimation techniques for multiscale coupling of kinetic models of the plasma material interface

In this work we analyze two classes of Density-Estimation techniques which can be used to consistently couple different kinetic models of the plasma-material interface, intended as the region of plasma immediately interacting with the first surface layers of a material wall. In particular, we handle the general problem of interfacing a continuum multi-species Vlasov-Poisson-BGK plasma model to discrete surface erosion models. The continuum model solves for the energy-angle distributions of the particles striking the surface, which are then driving the surface response. A modification to the classical Binary-Collision Approximation (BCA) method is here utilized as a prototype discrete model of the surface, to provide boundary conditions and impurity distributions representative of the material behavior during plasma irradiation. The numerical tests revealed the superior convergence properties of Gaussian Mixture Models over Kernel Density Estimation methods, with Gaussian Mixtures and Epanechnikov-KDEs both being up to two orders of magnitude faster than Gaussian-KDEs. The methodology here presented allows a self-consistent treatment of the plasma-material interface in magnetic fusion devices, including both the near-surface plasma (plasma sheath and presheath) in magnetized conditions, and surface effects such as sputtering, back-scattering, and ion implantation. The same coupling techniques can also be utilized for other discrete material models such as Molecular Dynamics.

42 ENGINEERING↗
DOE OSTI2016

Crystallographic Structure of Truncated CCL21 and the Putative Sulfotyrosine-Binding Site

CCL21 chemokine binds the G protein-coupled receptor CCR7, aiding not only in immune response but also in cancer metastasis. Compared with other chemokines, CCL21 has a unique extended unstructured C-terminus that is truncated in some naturally occurring variants. We have determined the X-ray crystallographic structure of a truncated CCL21 (residues 1–79) lacking the extended C-terminus and identified, via two-dimensional nuclear magnetic resonance (NMR), a putative sulfotyrosine-binding site that may recognize such post-translationally modified tyrosine residues on the receptor. Compared to the previously determined NMR structure of full-length CCL21, the crystal structure presents new druggable binding hot spots resulting from an alternative N-loop conformation. In addition, whereas the previous NMR structure did not provide any structural information after residue 70, the C-terminus of the truncated CCL21, ordered up to Ala77 in our crystal structure, is placed near the N-loop and sulfotyrosine-binding site, indicating that the extended C-terminus of full-length CCL21 can interact with this important region for receptor binding. These observations suggest a potential origin for the autoinhibition of CCL21 activity that was recently described. In conclusion, the new crystal structure and binding hot spot analysis have important implications for the function of the CCL21 C-terminus and drug discovery.

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

Conjugation of Amphiphilic Proteins to Hydrophobic Ligands in Organic Solvent

Protein–ligand conjugations are usually carried out in aqueous media in order to mimic the environment within which the conjugates will be used. Here, we focus on the conjugation of amphiphilic variants of elastin-like polypeptide (ELP), short elastin (sEL), to poorly water-soluble compounds like OPPVs (p-phenylenevinylene oligomers), triarylamines, and polypyridine-metal complexes. These conjugations are problematic when carried out in aqueous phase because hydrophobic ligands tend to avoid exposure to water, which in turn causes the ligand to self-aggregate and/or interact noncovalently with hydrophobic regions of the amphiphile. Ultimately, this behavior leads to low conjugation efficiency and contamination with strong noncovalent “conjugates”. After exploring the solubility of sEL in various organic solvents, we have established an efficient conjugation methodology for obtaining covalent conjugates virtually free of contaminating noncovalent complexes. When conjugating carboxylated ligands to the amphiphile amines, we demonstrate that even when only one amine (the N-terminus) is present, its derivatization is 98% efficient. When conjugating amine moieties to the amphiphile carboxyls (a problematic configuration), protein multimerization is avoided, 98–100% of the protein is conjugated, and the unreacted ligand is recovered in pure form. Our syntheses occur in “one pot”, and our purification procedure is a simple workup utilizing a combination of water and organic solvent extractions. This conjugation methodology might provide a solution to problems arising from solubility mismatch of protein and ligand, and it is likely to be widely applied for modification of recombinant amphiphiles used for drug delivery (PEG-antibodies, polymer-enzymes, food proteins), cell adhesion (collagen, hydrophobins), synthesis of nanostructures (peptides), and engineering of biocompatible optoelectronics (biological polymers), to cite a few.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Binding Mechanisms of Electron Transport Proteins with Cyanobacterial Photosystem I: An Integrated Computational and Experimental Model

The stromal domain (PsaC, D, and E) of photosystem I (PSI) in cyanobacteria accepts electrons from PsaA and PsaB of photosystem I (PSI). These electrons are then used in the reduction of transiently bound ferredoxin (Fd) or flavodoxin. Experimental X-ray and NMR structures are known for all of these protein partners separately, yet to date, there is no known experimental structure of the PSI/Fd complexes in the published literature. Computational models of Fd docked with the stromal domain of cyanobacterial PSI were assembled here starting from X-ray and NMR structures of PSI and Fd. Predicted models of specific regions of protein–protein interactions were built on the basis of energetic frustration, residue conservation and evolutionary importance, as well as from experimental site-directed mutagenesis and cross-linking studies. Lastly, microsecond time-scale molecular dynamics simulations of the PSI/Fd complexes suggest, rather than a single complex structure, the possible existence of multiple transient complexes of Fd bound to PSI.

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

Lithium Spatial Distribution and Split-Off Electronic Bands at Nanoscale V 2 O 5 /LiPON Interfaces

A combination of depth-resolved cathodoluminescence spectroscopy (DRCLS) and X-ray photoemission depth profiling (XPS) measured the pronounced changes in both the electronic density of states and lithium composition near the nanoscale LixV2O5/LiPON interface. DRCLS studies of electrochemically lithiated bare V2O5 and the sputterdeposited V2O5 plus LiPON overlayer electrochemically lithiated in stages both showed that in the bulk the luminescence intensity of the “split-off” hybridized bonding density of states was anticorrelated with XPSmeasured Li content, decreasing as the Li content increased. However, the LiPON overlayer was found to modify the band structure of the underlying LixV2O5 (LVO) to a depth of at least 30 nm beneath the V2O5 interface. DRCLS spectra near the electrochemically lithiated LiPON/ LVO interface showed a significant intensity of the split-off band, implying a low Li content. However, XPS depth profiling revealed a pronounced negative gradient of Li extending from a maximum Li content at the intimate LiPON boundary to its lowest content of ∼30 nm into the V2O5 in the same region, indicating a strong interaction between band structure and Li electrochemical potential near this heterojunction. These results provide evidence for substantial effects on the local band structure near an electrolyte/cathode interface and insights into the electrochemical interface behavior of solid-state batteries in general.

25 ENERGY STORAGE↗
DOE OSTI2024

Hydrogen–Deuterium Exchange Mass Spectrometry Identifies Local and Long-Distance Interactions within the Multicomponent Radical SAM Enzyme, PqqE

Interactions among proteins and peptides are essential for many biological activities including the tailoring of peptide substrates to produce natural products. The first step in the production of the bacterial redox cofactor pyrroloquinoline quinone (PQQ) from its peptide precursor is catalyzed by a radical SAM (rSAM) enzyme, PqqE. We describe the use of hydrogen–deuterium exchange mass spectrometry (HDX-MS) to characterize the structure and conformational dynamics in the protein–protein and protein–peptide complexes necessary for PqqE function. HDX-MS-identified hotspots can be discerned in binary and ternary complex structures composed of the peptide PqqA, the peptide-binding chaperone PqqD, and PqqE. Structural conclusions are supported by size-exclusion chromatography coupled to small-angle X-ray scattering (SEC-SAXS). HDX-MS further identifies reciprocal changes upon the binding of substrate peptide and S-adenosylmethionine (SAM) to the PqqE/PqqD complex: long-range conformational alterations have been detected upon the formation of a quaternary complex composed of PqqA/PqqD/PqqE and SAM, spanning nearly 40 Å, from the PqqA binding site in PqqD to the PqqE active site Fe 4 S 4 . Interactions among the various regions are concluded to arise from both direct contact and distal communication. The described experimental approach can be readily applied to the investigation of protein conformational communication among a large family of peptide-modifying rSAM enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

The Effect of Temperature, Cations, and Number of Acyl Chains on the Lamellar to Non-Lamellar Transition in Lipid-A Membranes: A Microscopic View

Lipopolysaccharides (LPS) are the main constituent of the outer bacterial membrane of Gram-negative bacteria. Lipid-A is the structural region of LPS that interacts with the innate immune system and induces inflammatory responses. It is formed by a phosphorylated β-d-glucosaminyl-(1→6)-α-N-glucosamine disaccharide backbone containing ester-linked and amide-linked long-chain fatty acids, which may vary in length and number depending on the bacterial strains and the environment. Phenotypical variation (i.e., number of acyl chains), cation type, and temperature influence the phase transition, aggregate structure, and endotoxic activity of Lipid-A. We have applied an extension of the GROMOS force field 45a4 carbohydrate parameter set to investigate the behavior of hexa- and pentaacylated Lipid-A of Pseudomonas aeruginosa at two temperatures (300 and 328 K) and in the presence of mono- and divalent cations (represented by Ca2+ and Na+, respectively) through molecular dynamics simulations. The distinct phase of Lipid-A aggregates was characterized by structural properties, deuterium order parameters, the molecular shape of the lipid units (conical versus cylindrical), and molecular packing. Our results show that Na+ ions induce a transition from the lamellar to nonlamellar phase. In contrast, the bilayer integrity is maintained in the presence of Ca2+ ions. Through these findings, we present microscopic insights on the influence of different cations on the molecular behavior of Lipid-A associated with the lamellar to nonlamellar transition.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2022

The Climatic Impact‐Driver Framework for Assessment of Risk‐Relevant Climate Information

Abstract The climate science and applications communities need a broad and demand‐driven concept to assess physical climate conditions that are relevant for impacts on human and natural systems. Here, we augment the description of the “climatic impact‐driver” (CID) approach adopted in the Working Group I (WGI) contribution to the Intergovernmental Panel on Climate Change (IPCC) Sixth Assessment Report. CIDs are broadly defined as “physical climate system conditions (e.g., means, events, and extremes) that affect an element of society or ecosystems. Depending on system tolerance, CIDs and their changes can be detrimental, beneficial, neutral, or a mixture of each across interacting system elements and regions.” We give background information on the IPCC Report process that led to the development of the 7 CID types (heat and cold, wet and dry, wind, snow and ice, coastal, open ocean, and other) and 33 distinct CID categories, each of which may be evaluated using a variety of CID indices. This inventory of CIDs was co‐developed with WGII to provide a useful collaboration point between physical climate scientists and impacts/risk experts to assess the specific climatic phenomena driving sectoral responses and identify relevant CID indices within each sector. The CID Framework ensures that a comprehensive set of climatic conditions informs adaptation planning and risk management and may also help prioritize improvements in modeling sectoral dynamics that depend on climatic conditions. CIDs contribute to climate services by increasing coherence and neutrality when identifying and communicating relevant findings from physical climate research to risk assessment and planning activities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Raman scattering enhanced by plasmonic clusters and its application to single-molecule imaging

The optical response of the linear Au{sub 8} cluster is investigated by the linear response theory based on the density functional theory. It is revealed that the observed many peaks in the visible region originate from the interaction of the ideal plasmonic excitation along the molecular axis with the background d-electron excitations, i.e., the Landau damping. In spite of the existence of the damping, the Raman scattering is shown to be enhanced remarkably by the incident light resonant to the visible excitations. The novel imaging experiment with the atomic resolution is proposed by utilizing a plasmonic cluster as the probing tip.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

An exact factorization perspective on quantum interferences in nonadiabatic dynamics

Nonadiabatic quantum interferences emerge whenever nuclear wavefunctions in different electronic states meet and interact in a nonadiabatic region. In this work, we analyze how nonadiabatic quantum interferences translate in the context of the exact factorization of the molecular wavefunction. In particular, we focus our attention on the shape of the time-dependent potential energy surface—the exact surface on which the nuclear dynamics takes place. We use a one-dimensional exactly solvable model to reproduce different conditions for quantum interferences, whose characteristic features already appear in one-dimension. The time-dependent potential energy surface develops complex features when strong interferences are present, in clear contrast to the observed behavior in simple nonadiabatic crossing cases. Nevertheless, independent classical trajectories propagated on the exact time-dependent potential energy surface reasonably conserve a distribution in configuration space that mimics one of the exact nuclear probability densities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex

Acetylation is correlated with chromatin decondensation and transcriptional activation, but its regulation by histone deacetylase (HDAC)-bearing corepressor complexes is poorly understood. Here, we describe the mechanism of assembly of the mammalian Sin3L/Rpd3L complex facilitated by Sds3, a conserved subunit deemed critical for proper assembly. Sds3 engages a globular, helical region of the HDAC interaction domain (HID) of the scaffolding protein Sin3A through a bipartite motif comprising a helix and an adjacent extended segment. Sds3 dimerizes through not only one of the predicted coiled-coil motifs but also, the segment preceding it, forming an ~150-Å-long antiparallel dimer. Contrary to previous findings in yeast, Sin3A rather than Sds3 functions in recruiting HDAC1 into the complex by engaging the latter through a highly conserved segment adjacent to the helical HID subdomain. In the resulting model for the ternary complex, the two copies of the HDACs are situated distally and dynamically because of a natively unstructured linker connecting the dimerization domain and the Sin3A interaction domain of Sds3; these features contrast with the static organization described previously for the NuRD (nucleosome remodeling and deacetylase) complex. Finally, the Sds3 linker features several conserved basic residues that could potentially maintain the complex on chromatin by nonspecific interactions with DNA after initial recruitment by sequence-specific DNA-binding repressors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

VARIATIONS OF SOLAR ELECTRON AND PROTON FLUX IN MAGNETIC CLOUD BOUNDARY LAYERS AND COMPARISONS WITH THOSE ACROSS THE SHOCKS AND IN THE RECONNECTION EXHAUSTS

The magnetic cloud boundary layer (BL) is a dynamic region formed by the interaction of the magnetic cloud (MC) and the ambient solar wind. In the present study, we comparatively investigate the proton and electron mean flux variations in the BL, in the interplanetary reconnection exhaust (RE), and across the MC-driven shock by using the Wind data from 1995 to 2006. In general, the proton flux has higher increments at lower energy bands compared with the ambient solar wind. Inside the BL, the core electron flux increases quasi-isotropically and the increments decrease monotonously with energy from {approx}30% (at 18 eV) to {approx}10% (at 70 eV); the suprathermal electron flux usually increases in either parallel or antiparallel direction; the correlation coefficient of electron flux variations in parallel and antiparallel directions changes sharply from {approx}0.8 below 70 eV to {approx}0 above 70 eV. Similar results are also found for RE. However, different phenomena are found across the shock where the electron flux variations first increase and then decrease with a peak increment (>200%) near 100 eV. The correlation coefficient of electron flux variations in parallel and antiparallel directions is always around 0.8. The similar behavior of flux variations in BL and RE suggests that reconnection may commonly occur in BL. Our work also implies that the strong energy dependence and direction selectivity of electron flux variations, which were previously thought to have not enough relevance to magnetic reconnection, could be considered as an important signature of solar wind reconnection in the statistical point of view.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

CO STRUCTURE OF THE 21 {mu}m SOURCE IRAS 22272+5435: A SIGN OF A JET LAUNCH?

We report the results of radio interferometric observations of the 21 {mu}m source IRAS 22272+5435 in the CO J = 2-1 line. 21 {mu}m sources are carbon-rich objects in the post-asymptotic-giant-branch phase of evolution, which show an unidentified emission feature at 21 {mu}m. Since 21 {mu}m sources usually also have circumstellar molecular envelopes, the mapping of CO emission from the envelope will be useful in tracing the nebular structure. From observations made with the Combined Array for Research in Millimeter-wave Astronomy, we find that a torus and spherical wind model can explain only part of the CO structure. An additional axisymmetric region created by the interaction between an invisible jet and ambient material is suggested.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

HADRON-QUARK CROSSOVER AND MASSIVE HYBRID STARS WITH STRANGENESS

Using the idea of smooth crossover from hadronic matter with hyperons to quark matter with strangeness, we show that the maximum mass (M {sub max}) of neutron stars with quark matter cores can be larger than those without quark matter cores. This is in contrast to the conventional softening of the equation of state due to exotic components at high density. The essential conditions for reaching our conclusion are that (1) the crossover takes place at relatively low densities, around three times the normal nuclear density and (2) the quark matter is strongly interacting in the crossover region. From these, the pressure of the system can be greater than that of purely hadronic matter at a given baryon density in the crossover density region and leads to M {sub max} greater than 2 solar mass. This conclusion is insensitive to the different choice of the hadronic equation of state with hyperons. We remark upon several implications of this result to the nuclear incompressibility, the hyperon mixing, and the neutrino cooling.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

On ultra-high energy cosmic ray acceleration at the termination shock of young pulsar winds

Pulsar wind nebulae (PWNe) are outstanding accelerators in Nature, in the sense that they accelerate electrons up to the radiation reaction limit. Motivated by this observation, this paper examines the possibility that young pulsar wind nebulae can accelerate ions to ultra-high energies at the termination shock of the pulsar wind. We consider here powerful PWNe, fed by pulsars born with ∼ millisecond periods. Assuming that such pulsars exist, at least during a few years after the birth of the neutron star, and that they inject ions into the wind, we find that protons could be accelerated up to energies of the order of the Greisen-Zatsepin-Kuzmin cut-off, for a fiducial rotation period P ∼ 1 msec and a pulsar magnetic field B{sub *} ∼ 10{sup 13} G, implying a fiducial wind luminosity L{sub p} ∼ 10{sup 45} erg/s and a spin-down time t{sub sd} ∼ 3× 10{sup 7} s. The main limiting factor is set by synchrotron losses in the nebula and by the size of the termination shock; ions with Z≥ 1 may therefore be accelerated to even higher energies. We derive an associated neutrino flux produced by interactions in the source region. For a proton-dominated composition, our maximum flux lies slightly below the 5-year sensitivity of IceCube-86 and above the 3-year sensitivity of the projected Askaryan Radio Array. It might thus become detectable in the next decade, depending on the exact level of contribution of these millisecond pulsar wind nebulae to the ultra-high energy cosmic ray flux.

79 ASTRONOMY AND ASTROPHYSICS↗