Search NASA⌕ Search

SEARCH · Search NASA

Results for “RESIDUAL INTERACTIONS”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Structures of Receptor Complexes of a North American H7N2 Influenza Hemagglutinin with a Loop Deletion in the Receptor Binding Site

Human infections with subtype H7 avian influenza viruses have been reported as early as 1979. In 1996, a genetically stable 24-nucleotide deletion emerged in North American H7 influenza virus hemagglutinins, resulting in an eight amino acid deletion in the receptor-binding site. The continuous circulation of these viruses in live bird markets, as well as its documented ability to infect humans, raises the question of how these viruses achieve structural stability and functionality. Here we report a detailed molecular analysis of the receptor binding site of the North American lineage subtype H7N2 virus A/New York/107/2003 (NY107), including complexes with an avian receptor analog (3'-sialyl-N-acetyllactosamine, 3'SLN) and two human receptor analogs (6'-sialyl-N-acetyllactosamine, 6'SLN; sialyllacto-N-tetraose b, LSTb). Structural results suggest a novel mechanism by which residues Arg220 and Arg229 (H3 numbering) are used to compensate for the deletion of the 220-loop and form interactions with the receptor analogs. Glycan microarray results reveal that NY107 maintains an avian-type ({alpha}2-3) receptor binding profile, with only moderate binding to human-type ({alpha}2-6) receptor. Thus despite its dramatically altered receptor binding site, this HA maintains functionality and confirms a need for continued influenza virus surveillance of avian and other animal reservoirs to define their zoonotic potential.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Structural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis

For the last decade, worldwide efforts for the treatment of anthrax infection have focused on developing effective vaccines. Patients that are already infected are still treated traditionally using different types of standard antimicrobial agents. The most popular are antibiotics such as tetracyclines and fluoroquinolones. While aminoglycosides appear to be less effective antimicrobial agents than other antibiotics, synthetic aminoglycosides have been shown to act as potent inhibitors of anthrax lethal factor and may have potential application as antitoxins. Here, we present a structural analysis of the BA2930 protein, a putative aminoglycoside acetyltransferase, which may be a component of the bacterium's aminoglycoside resistance mechanism. The determined structures revealed details of a fold characteristic only for one other protein structure in the Protein Data Bank, namely, YokD from Bacillus subtilis. Both BA2930 and YokD are members of the Antibiotic-NAT superfamily (PF02522). Sequential and structural analyses showed that residues conserved throughout the Antibiotic-NAT superfamily are responsible for the binding of the cofactor acetyl coenzyme A. The interaction of BA2930 with cofactors was characterized by both crystallographic and binding studies.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1990

Stratosphere chemistry in a 2-D model with residual circulation

The objective of this research was to examine the effects of chemical perturbations on the stratosphere using models which can incorporate fully interactive radiative, chemical, and dynamical responses, in the context of a zonally averaged model. Model runs for the unperturbed, chlorine-perturbed and simultaneously chlorine-and CO2-perturbed cases were completed using the JPL-87 chemical kinetics data. The base case was analyzed and submitted for publication. The perturbed cases show substantial sensitivity of the predicted column ozone depletion to the perturbations affecting lower stratosphere temperature, but less to far dynamical perturbations. The column ozone distribution changed substantially when the kinetics data was changed. This implies a greater-than-expected uncertainty in predicted latitude distributions of ozone depletion, due to uncertainty about the accuracy and completeness of the chemical kinetics data set.

Guthrie, Paul D.↗
DOE OSTI2017

Dark matter properties implied by gamma ray interstellar emission models

We infer dark matter properties from gamma ray residuals extracted using eight different interstellar emission scenarios proposed by the Fermi-LAT Collaboration to explain the Galactic Center gamma ray excess. Adopting the most plausible simplified ansatz, we assume that the dark matter particle is a Majorana fermion interacting with standard fermions via a scalar mediator. To trivially respect flavor constraints, we only couple the mediator to third generation fermions. Using this theoretical hypothesis, and the Fermi residuals, we calculate Bayesian evidences, including Fermi-LAT exclusion limits from 15 dwarf spheroidal galaxies as well. Our evidence ratios single out one of the Fermi scenarios as most compatible with the simplified dark matter model. In this scenario the dark matter (mediator) mass is in the 25-200 (1-1000) GeV range and its annihilation is dominated by bottom quark final state. Our conclusion is that the properties of dark matter extracted from gamma ray data are highly sensitive to the modeling of the interstellar emission.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Wnt5a promotes Frizzled-4 signalosome assembly by stabilizing cysteine-rich domain dimerization

Wnt/β-catenin signaling is activated when extracellular Wnt ligands bind Frizzled (FZD) receptors at the cell membrane. Wnts bind FZD cysteine-rich domains (CRDs) with high affinity through a palmitoylated N-terminal “thumb” and a disulfide-stabilized C-terminal “index finger,” yet how these binding events trigger receptor activation and intracellular signaling remains unclear. In this work, we report the crystal structure of the Frizzled-4 (FZD 4 ) CRD in complex with palmitoleic acid, which reveals a CRD tetramer consisting of two cross-braced CRD dimers. Each dimer is stabilized by interactions of one hydrophobic palmitoleic acid tail with two CRD palmitoleoyl-binding grooves oriented end to end, suggesting that the Wnt palmitoleoyl group stimulates CRD–CRD interaction. Using bioluminescence resonance energy transfer (BRET) in live cells, we show that WNT5A stimulates dimerization of membrane-anchored FZD 4 CRDs and oligomerization of full-length FZD 4 , which requires the integrity of CRD palmitoleoyl-binding residues. These results suggest that FZD receptors may form signalosomes in response to Wnt binding through the CRDs and that the Wnt palmitoleoyl group is important in promoting these interactions. These results complement our understanding of lipoprotein receptor-related proteins 5 and 6 (LRP5/6), Dishevelled, and Axin signalosome assembly and provide a more complete model for Wnt signalosome assembly both intracellularly and at the membrane.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1985

Review of research on wave mean flow interactions using FGGE data

Comparison is made between the conventional Eulerian diagnostics of wave mean flow interactions in the atmosphere and the diagnostics introduced by Andrews and McIntyre (1976). In the latter, the meridional circulation is represented by a residual circulation, and the eddy torque in the zonal momentum equation by the Eliassen-Palm (1960) flux divergence (or equivalently, by the poleward eddy flux of geostrophic potential vorticity). It is found that, while the new diagnostics are useful in studying stratospheric warmings and transports of conservative quantities, the conventional diagnostics are more useful in studying global energetics and wave mean flow interactions in the troposphere and lower stratosphere. Case studies diagnosed with FGGE IIIb data are presented to illustrate this point. Kung and Tanaka's (1983) comparisons of the atmospheric energy cycle for SOP-1 and SOP-2, estimated with the use of the ECMWF and GFDL FGGE IIIb data bases, are used to assess the uncertainty in calculations of energetics based on the use of FGGE IIIb data. These results demonstrate the high degree of model dependence in the FGGE IIb data sets.

Pfeffer, R. L.↗
DOE OSTI2011

NUMERICAL SIMULATION FOR MECHANICAL BEHAVIOR OF U10MO MONOLITHIC MINIPLATES FOR RESEARCH AND TEST REACTORS

This article presents assessment of the mechanical behavior of U-10wt% Mo (U10Mo) alloy based monolithic fuel plates subject to irradiation. Monolithic, plate-type fuel is a new fuel form being developed for research and test reactors to achieve higher uranium densities within the reactor core to allow the use of low-enriched uranium fuel in high-performance reactors. Identification of the stress/strain characteristics is important for understanding the in-reactor performance of these plate-type fuels. For this work, three distinct cases were considered: (1) fabrication induced residual stresses (2) thermal cycling of fabricated plates; and finally (3) transient mechanical behavior under actual operating conditions. Because the temperatures approach the melting temperature of the cladding during the fabrication and thermal cycling, high temperature material properties were incorporated to improve the accuracy. Once residual stress fields due to fabrication process were identified, solution was used as initial state for the subsequent simulations. For thermal cycling simulation, elasto-plastic material model with thermal creep was constructed and residual stresses caused by the fabrication process were included. For in-service simulation, coupled fluid-thermal-structural interaction was considered. First, temperature field on the plates was calculated and this field was used to compute the thermal stresses. For time dependent mechanical behavior, thermal creep of cladding, volumetric swelling and fission induced creep of the fuel foil were considered. The analysis showed that the stresses evolve very rapidly in the reactor. While swelling of the foil increases the stress of the foil, irradiation induced creep causes stress relaxation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2012

The E3 Ubiquitin Ligase- and Protein Phosphatase 2A (PP2A)-binding Domains of the Alpha4 Protein Are Both Required for Alpha4 to Inhibit PP2A Degradation

Protein phosphatase 2A (PP2A) is regulated through a variety of mechanisms, including post-translational modifications and association with regulatory proteins. Alpha4 is one such regulatory protein that binds the PP2A catalytic subunit (PP2Ac) and protects it from polyubiquitination and degradation. Alpha4 is a multidomain protein with a C-terminal domain that binds Mid1, a putative E3 ubiquitin ligase, and an N-terminal domain containing the PP2Ac-binding site. In this work, we present the structure of the N-terminal domain of mammalian Alpha4 determined by x-ray crystallography and use double electron-electron resonance spectroscopy to show that it is a flexible tetratricopeptide repeat-like protein. Structurally, Alpha4 differs from its yeast homolog, Tap42, in two important ways: (1) the position of the helix containing the PP2Ac-binding residues is in a more open conformation, showing flexibility in this region; and (2) Alpha4 contains a ubiquitin-interacting motif. The effects of wild-type and mutant Alpha4 on PP2Ac ubiquitination and stability were examined in mammalian cells by performing tandem ubiquitin-binding entity precipitations and cycloheximide chase experiments. Our results reveal that both the C-terminal Mid1-binding domain and the PP2Ac-binding determinants are required for Alpha4-mediated protection of PP2Ac from polyubiquitination and degradation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Mechanism of pathogen recognition by human dectin-2

Dectin-2, a C-type lectin on macrophages and other cells of the innate immune system, functions in response to pathogens, particularly fungi. The carbohydrate-recognition domain (CRD) in dectin-2 is linked to a transmembrane sequence that interacts with the common Fc receptor subunit to initiate immune signaling. The molecular mechanism by which dectin-2 selectively binds to pathogens has been investigated by characterizing the CRD expressed in a bacterial system. Competition binding studies indicated that the CRD binds to monosaccharides with modest affinity and that affinity was greatly enhanced for mannose-linked1-2 or1-4 to a second mannose residue. Glycan array analysis confirmed selective binding of the CRD to glycans that contain Man1-2Man epitopes. Crystals of the CRD in complex with a mammalian-type high-mannose Man9GlcNAc2 oligosaccharide exhibited interaction with Man1–2Man on two different termini of the glycan, with the reducing-end mannose residue ligated to Ca2 in a primary binding site and the nonreducing terminal mannose residue occupying an adjacent secondary site. Comparison of the binding sites in DC-SIGN and langerin, two other pathogen-binding receptors of the innate immune system, revealed why these two binding sites accommodate only terminal Man1-2Man structures, whereas dectin-2 can bind Man1–2Man in internal positions in mannans and other polysaccharides. The specificity and geometry of the dectin-2-binding site provide the molecular mechanism for binding of dectin-2 to fungal mannans and also to bacterial lipopolysaccharides, capsular polysaccharides, and lipoarabinomannans that contain the Man1-2Man disaccharide unit.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ending the Chase for a Perfect Binder: Role of Surface Chemistry Variation and its Influence on Silicon Anodes

In this work we examine the influence of the type of silicon source material (two milled and two plasma enhanced chemical vapor deposition) on the electrochemical performance of silicon-based anodes for Li-ion batteries. The four representative Si sources were previously identified in literature but have never been compared side by side, which is critical to understanding the wide variation in performance reported for silicon-based electrodes. These particles display unique surface features associated with surface oxides and residual precursor species (Si-N, Si-C, Si-H) which impact processability by changing interactions within the electrode slurry and the resulting electrochemical performance. These properties should be taken into consideration when utilizing “off-the-shelf” Si powders for investigations and would be good variables to explore to understand why certain chemistries display suitable performance, while others “don't work.”

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Structural characterization of the novel aminoglycoside phosphotransferase AphVIII from Streptomyces rimosus with enzymatic activity modulated by phosphorylation

Aminoglycoside phosphotransferases represent a broad class of enzymes that promote bacterial resistance to aminoglycoside antibiotics via the phosphorylation of hydroxyl groups in the latter. Here we report the spatial structure of the 3′-aminoglycoside phosphotransferase of novel VIII class (AphVIII) solved by X-ray diffraction method with a resolution of 2.15 Å. Deep analysis of APHVIII structure and its comparison with known structures of aminoglycoside phosphotransferases of various types reveals that AphVIII has a typical two-domain fold and, however, possesses some unique characteristics that distinguish the enzyme from its known homologues. The most important difference is the presence of the activation loop with unique Ser146 residue. We demonstrate that in the apo-state of the enzyme the activation loop does not interact with other parts of the enzyme and seems to adopt catalytically competent state only after substrate binding. - Highlights: • 3D structure of the novel aminoglycoside phosphotransferase AphVIII was obtained. • AphVIII activation loop is clearly identified in the electron density. • AphVIII has some unique structural features in its substrate C-ring binding pocket.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

Structural Insights into the Functional Role of the Hcn Sub-domain of the Receptor-Binding Domain of the Botulinum Neurotoxin Mosaic Serotype C/D

Botulinum neurotoxin (BoNT), the causative agent of the deadly neuroparalytic disease botulism, is the most poisonous protein known for humans. Produced by different strains of the anaerobic bacterium Clostridium botulinum, BoNT effects cellular intoxication via a multistep mechanism executed by the three modules of the activated protein. Endocytosis, the first step of cellular intoxication, is triggered by the ~50 kDa, heavy-chain receptor-binding module (HCR) that is specific for a ganglioside and a protein receptor on neuronal cell surfaces. This dual receptor recognition mechanism between BoNT and the host cell’s membrane is well documented and occurs via specific intermolecular interactions with the C-terminal sub-domain, Hcc, of BoNT-HCR. The N-terminal sub-domain of BoNT-HCR, Hcn, comprises ~50% of BoNT-HCR and adopts a B-sheet jelly roll fold. While suspected in assisting cell surface recognition, no unambiguous function for the Hcn sub-domain in BoNT has been indentified. To obtain insights into the potential function of the Hcn sub-domain in BoNT, the first crystal structure of a BoNT with an organic ligand bound to the Hcn sub-domain has been obtained. Here, we describe the crystal structure of BoNT/CD-HCR determined at 1.70 Å resolution with a tetraethylene glycol (PG4) molecule bound in an hydrophobic cleft between B-strands in the B-sheet jelly fold roll of the Hcn sub-domain. The molecule is completely engulfed in the cleft, making numerous hydrophobic (Y932, S959, W966, and D1042) and hydrophilic (S935, W977, L979, N1013, and I1066) contacts with the protein’s side chain and backbone that may mimic in vivo interactions with the phospholipid membranes on neuronal cell surfaces. A sulfate ion was also observed bound to residues T1176, D1177, K1196, and R1243 in the Hcc sub-domain of BoNT/CD-HCR. In the crystal structure of a similar protein, BoNT/D-HCR, a sialic acid

botulinum neurotoxin↗
DOE OSTI2018

A Copper Relay System Involving Two Periplasmic Chaperones Drives cbb 3 -Type Cytochrome c Oxidase Biogenesis in Rhodobacter capsulatus

PccA and SenC are periplasmic copper chaperones required for the biogenesis of cbb 3 -type cytochrome c oxidase (cbb 3 -Cox) in Rhodobacter capsulatus at physiological Cu concentrations. However, both proteins are dispensable for cbb 3 -Cox assembly when the external Cu concentration is high. PccA and SenC bind Cu using Met and His residues and Cys and His residues as ligands, respectively, and both proteins form a complex during cbb 3 -Cox biogenesis. SenC also interacts directly with cbb 3 -Cox, as shown by chemical cross-linking. Here we determined the periplasmic concentrations of both proteins in vivo and analyzed their Cu binding stoichiometries and their Cu(I) and Cu(II) binding affinity constants (KD) in vitro. Our data show that both proteins bind a single Cu atom with high affinity. In vitro Cu transfer assays demonstrate Cu transfer both from PccA to SenC and from SenC to PccA at similar levels. We conclude that PccA and SenC constitute a Cu relay system that facilitates Cu delivery to cbb 3 -Cox.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mechanism of glycoform specificity and in vivo protection by an anti-afucosylated IgG nanobody

Abstract Immunoglobulin G (IgG) antibodies contain a complex N -glycan embedded in the hydrophobic pocket between its heavy chain protomers. This glycan contributes to the structural organization of the Fc domain and determines its specificity for Fcγ receptors, thereby dictating distinct cellular responses. The variable construction of this glycan structure leads to highly-related, but non-equivalent glycoproteins known as glycoforms. We previously reported synthetic nanobodies that distinguish IgG glycoforms. Here, we present the structure of one such nanobody, X0, in complex with the Fc fragment of afucosylated IgG1. Upon binding, the elongated CDR3 loop of X0 undergoes a conformational shift to access the buried N -glycan and acts as a ‘glycan sensor’, forming hydrogen bonds with the afucosylated IgG N -glycan that would otherwise be sterically hindered by the presence of a core fucose residue. Based on this structure, we designed X0 fusion constructs that disrupt pathogenic afucosylated IgG1-FcγRIIIa interactions and rescue mice in a model of dengue virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Nuclear localization of the DNA repair scaffold XRCC1: Uncovering the functional role of a bipartite NLS

We have characterized the nuclear localization signal (NLS) of XRCC1 structurally using X-ray crystallography and functionally using fluorescence imaging. Crystallography and binding studies confirm the bipartite nature of the XRCC1 NLS interaction with Importin α (Impα) in which the major and minor binding motifs are separated by >20 residues, and resolve previous inconsistent determinations. Binding studies of peptides corresponding to the bipartite NLS, as well as its major and minor binding motifs, to both wild-type and mutated forms of Impα reveal pronounced cooperative binding behavior that is generated by the proximity effect of the tethered major and minor motifs of the NLS. The cooperativity stems from the increased local concentration of the second motif near its cognate binding site that is a consequence of the stepwise binding behavior of the bipartite NLS. We predict that the stepwise dissociation of the NLS from Impα facilitates unloading by providing a partially complexed intermediate that is available for competitive binding by Nup50 or the Importin β binding domain. This behavior gives a basis for meeting the intrinsically conflicting high affinity and high flux requirements of an efficient nuclear transport system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Dissecting the substrate recognition of 3-O-sulfotransferase for the biosynthesis of anticoagulant heparin

Heparin is a polysaccharide-based natural product that is used clinically as an anticoagulant drug. Heparan sulfate 3-O-sulfotransferase (3-OST) is an enzyme that transfers a sulfo group to the 3-OH position of a glucosamine unit. 3-OST is present in multiple isoforms, and the polysaccharides modified by these different isoforms perform distinct biological functions. 3-OST isoform 1 (3-OST-1) is the key enzyme for the biosynthesis of anticoagulant heparin. Here, we report the crystal structure of the ternary complex of 3-OST-1, 3'-phosphoadenosine 5'-phosphate, and a heptasaccharide substrate. Comparisons to previously determined structures of 3-OST-3 reveal unique binding modes used by the different isoforms of 3-OST for distinguishing the fine structures of saccharide substrates. Our data demonstrate that the saccharide substrates display distinct conformations when interacting with the different 3-OST isoforms. Site-directed mutagenesis data suggest that several key amino residues, including Lys259, Thr256, and Trp283 in 3-OST-3 and Arg268 in 3-OST-1, play important roles in substrate binding and specificity between isoforms. These results deepen our understanding of the biosynthetic mechanism of heparan sulfate and provide structural information for engineering enzymes for an enhanced biosynthetic approach to heparin production.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I

RNAs with 5'-triphosphate (ppp) are detected in the cytoplasm principally by the innate immune receptor Retinoic Acid Inducible Gene-I (RIG-I), whose activation triggers a Type I IFN response. It is thought that self RNAs like mRNAs are not recognized by RIG-I because 5'ppp is capped by the addition of a 7-methyl guanosine (m7G) (Cap-0) and a 2'-O-methyl (2'-OMe) group to the 5'-end nucleotide ribose (Cap-1). Here we provide structural and mechanistic basis for exact roles of capping and 2'-O-methylation in evading RIG-I recognition. Surprisingly, Cap-0 and 5'ppp double-stranded (ds) RNAs bind to RIG-I with nearly identical K d values and activate RIG-I’s ATPase and cellular signaling response to similar extents. On the other hand, Cap-0 and 5'ppp single-stranded RNAs did not bind RIG-I and are signaling inactive. Three crystal structures of RIG-I complexes with dsRNAs bearing 5'OH, 5'ppp, and Cap-0 show that RIG-I can accommodate the m7G cap in a cavity created through conformational changes in the helicase-motif IVa without perturbing the ppp interactions. In contrast, Cap-1 modifications abrogate RIG-I signaling through a mechanism involving the H830 residue, which we show is crucial for discriminating between Cap-0 and Cap-1 RNAs. Furthermore, m7G capping works synergistically with 2'-O-methylation to weaken RNA affinity by 200-fold and lower ATPase activity. Interestingly, a single H830A mutation restores both high-affinity binding and signaling activity with 2'-O-methylated dsRNAs. Our work provides new structural insights into the mechanisms of host and viral immune evasion from RIG-I, explaining the complexity of cap structures over evolution.

59 BASIC BIOLOGICAL SCIENCES↗