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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 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
NASA NTRS1980

A current access, self-structured, multilayered bubble domain memory

Preliminary experimental results are reported on a self-structured, multilayer bubble memory with buried data layer. Stripe domains are used to move carrier bubbles by magnetostatic coupling. An expression is derived for that coupling as a function of thickness of the GGG separation layer. Experimental values of coupling are given as a function of bias field. An expression for stripe curvature as a function of bias field is derived. The performance of seven different current access stripe propagation circuits is reported.

Stermer, R. L., Jr.↗
DOE OSTI2018

The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s

Highlights: • The crystal structure of CYP116B45 (P450-TT) from T. thermophilus has been solved. • P450-TT crystal structure is the first example of a class VII P450 structure. • P450-TT adopts the typical P450-fold. • Structural deviation of regions involved in substrate recognition is observed. • Analysis of 96 class VII sequences revealed conservation of active site residues. The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes. A structure similarity search demonstrated that the P450-TT structure is similar to enzymes capable of oxy-functionalization of fatty acids, terpenes, macrolides, steroids and statins. The insight gained from solving this structure will provide a guideline for future engineering and modelling studies on this catalytically promiscuous class of enzymes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Crystal structure of an ENT domain from Trypanosoma brucei

Highlights: • This is the first structure of ENT domain from T. brucei. • The structural similarity between T. brucei and H. sapiens suggest a conserved conformation shared by ENT family. • The orientation of α5 helix of TbENT is significantly different from that of HsENT. • The conserved binding motif is absent in ENT domain containing proteins Q385P5. Trypanosoma brucei (T. brucei) is a parasitic protozoan causing human sleeping sickness and related animal diseases. ENT (EMSY N-terminal) domain was first found in EMSY protein which has been proved to be involved in multiple biological processes such as DNA repair, tumorigenesis, and transcriptional regulation. So far, little is known about the function and structure of ENT domains from protozoan. Q385P5 from T. brucei, containing an ENT domain at its N-terminus, is a conserved protein in related kinetoplastid parasites. In this work, the crystal structure of ENT domain of Q385P5 (TbENT) was solved at a resolution of 2.3 Å. TbENT adopts a club-like shape consisting of five helixes, which is similar to the structure of human EMSY ENT domain (HsENT). Interestingly, TbENT shows significantly different orientation on the fifth α-helix compared with HsENT. Meanwhile, human HP1 interacts with a conserved motif adjacent to EMSY ENT domain. However, this conserved binding motif is absent in Q385P5. These differences may imply the different protein interactions and roles of Q385P5 and its ENT domain in T. brucei.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Probing the impact of nairovirus genomic diversity on viral ovarian tumor domain protease (vOTU) structure and deubiquitinase activity

Post-translational modification of host and viral proteins by ubiquitin (Ub) and Ub-like proteins, such as interferon stimulated gene product 15 (ISG15), plays a key role in response to infection. Viruses have been increasingly identified that contain proteases possessing deubiquitinase (DUB) and/or deISGylase functions. This includes viruses in the Nairoviridae family that encode a viral homologue of the ovarian tumor protease (vOTU). vOTU activity was recently demonstrated to be critical for replication of the often-fatal Crimean-Congo hemorrhagic fever virus, with DUB activity suppressing the type I interferon responses and deISGylase activity broadly removing ISG15 conjugated proteins. There are currently about 40 known nairoviruses classified into fourteen species. Recent genomic characterization has revealed a high degree of diversity, with vOTUs showing less than 25% amino acids identities within the family. Previous investigations have been limited to only a few closely related nairoviruses, leaving it unclear what impact this diversity has on vOTU function. To probe the effects of vOTU diversity on enzyme activity and specificity, we assessed representative vOTUs spanning the Nairoviridae family towards Ub and ISG15 fluorogenic substrates. This revealed great variation in enzymatic activity and specific substrate preferences. A subset of the vOTUs were further assayed against eight biologically relevant di-Ub substrates, uncovering both common trends and distinct preferences of poly-Ub linkages by vOTUs. Four novel X-ray crystal structures were obtained that provide a biochemical rationale for vOTU substrate preferences and elucidate structural features that distinguish the vOTUs, including a motif in the Hughes orthonairovirus species that has not been previously observed in OTU domains. Additionally, structure-informed mutagenesis provided the first direct evidence of a second site involved in di-Ub binding for vOTUs. These results provide new insight into nairovirus evolution and pathogenesis, and further enhances the development of tools for therapeutic purposes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein

The structure of the SPRY domain of the human RNA helicase DDX1 was determined at 2.0 Å resolution. The SPRY domain provides a putative protein–protein interaction platform within DDX1 that differs from other SPRY domains in its structure and conserved regions. The human RNA helicase DDX1 in the DEAD-box family plays an important role in RNA processing and has been associated with HIV-1 replication and tumour progression. Whereas previously described DEAD-box proteins have a structurally conserved core, DDX1 shows a unique structural feature: a large SPRY-domain insertion in its RecA-like consensus fold. SPRY domains are known to function as protein–protein interaction platforms. Here, the crystal structure of the SPRY domain of human DDX1 (hDSPRY) is reported at 2.0 Å resolution. The structure reveals two layers of concave, antiparallel β-sheets that stack onto each other and a third β-sheet beneath the β-sandwich. A comparison with SPRY-domain structures from other eukaryotic proteins showed that the general β-sandwich fold is conserved; however, differences were detected in the loop regions, which were identified in other SPRY domains to be essential for interaction with cognate partners. In contrast, in hDSPRY these loop regions are not strictly conserved across species. Interestingly, though, a conserved patch of positive surface charge is found that may replace the connecting loops as a protein–protein interaction surface. The data presented here comprise the first structural information on DDX1 and provide insights into the unique domain architecture of this DEAD-box protein. By providing the structure of a putative interaction domain of DDX1, this work will serve as a basis for further studies of the interaction network within the hetero-oligomeric complexes of DDX1 and of its recruitment to the HIV-1 Rev protein as a viral replication factor.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Arabidopsis myosin XI sub-domains homologous to the yeast myo2p organelle inheritance sub-domain target subcellular structures in plant cells

Myosin XI motor proteins transport plant organelles on the actin cytoskeleton. The Arabidopsis gene family that encodes myosin XI has 13 members, 12 of which have sub-domains within the tail region that are homologous to well-characterized cargo-binding domains in the yeast myosin V myo2p. Little is presently known about the cargo-binding domains of plant myosin XIs. Prior experiments in which most or all of the tail regions of myosin XIs have been fused to yellow fluorescent protein (YFP) and transiently expressed have often not resulted in fluorescent labeling of plant organelles. We identified 42 amino-acid regions within 12 Arabidopsis myosin XIs that are homologous to the yeast myo2p tail region known to be essential for vacuole and mitochondrial inheritance. A YFP fusion of the yeast region expressed in plants did not label tonoplasts or mitochondria. We investigated whether the homologous Arabidopsis regions, termed by us the “PAL” sub-domain, could associate with subcellular structures following transient expression of fusions with YFP in Nicotiana benthamiana. Seven YFP::PAL sub-domain fusions decorated Golgi and six were localized to mitochondria. In general, the myosin XI PAL sub-domains labeled organelles whose motility had previously been observed to be affected by mutagenesis or dominant negative assays with the respective myosins. Simultaneous transient expression of the PAL sub-domains of myosin XI-H, XI-I, and XI-K resulted in inhibition of movement of mitochondria and Golgi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

The Streptococcus pyogenes Shr protein captures human hemoglobin using two structurally unique binding domains

In order to proliferate and mount an infection, many bacterial pathogens need to acquire iron from their host. The most abundant iron source in the body is the oxygen transporter hemoglobin (Hb). Streptococcus pyogenes , a potentially lethal human pathogen, uses the Shr protein to capture Hb on the cell surface. Shr is an important virulence factor, yet the mechanism by which it captures Hb and acquires its heme is not well-understood. In this work, we show using NMR and biochemical methods that Shr binds Hb using two related modules that were previously defined as domains of unknown function (DUF1533). These hemoglobin-interacting domains (HIDs), called HID1 and HID2, are autonomously folded and independently bind Hb. The 1.5 Å resolution crystal structure of HID2 revealed that it is a structurally unique Hb-binding domain. Mutagenesis studies revealed a conserved tyrosine in both HIDs that is essential for Hb binding. Our biochemical studies indicate that HID2 binds Hb with higher affinity than HID1 and that the Hb tetramer is engaged by two Shr receptors. NMR studies reveal the presence of a third autonomously folded domain between HID2 and a heme-binding NEAT1 domain, suggesting that this linker domain may position NEAT1 near Hb for heme capture.

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

Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove

This study characterizes the interaction between the carboxy-terminal (ERLI) motif of the essential polarity protein Crb and the Pals1/Stardust PDZ-domain protein. Structures of human Pals1 PDZ with and without a Crb peptide are described, explaining the highly conserved nature of the ERLI motif and revealing a sterically blocked peptide-binding groove in the absence of ligand. Many components of epithelial polarity protein complexes possess PDZ domains that are required for protein interaction and recruitment to the apical plasma membrane. Apical localization of the Crumbs (Crb) transmembrane protein requires a PDZ-mediated interaction with Pals1 (protein-associated with Lin7, Stardust, MPP5), a member of the p55 family of membrane-associated guanylate kinases (MAGUKs). This study describes the molecular interaction between the Crb carboxy-terminal motif (ERLI), which is required for Drosophila cell polarity, and the Pals1 PDZ domain using crystallography and fluorescence polarization. Only the last four Crb residues contribute to Pals1 PDZ-domain binding affinity, with specificity contributed by conserved charged interactions. Comparison of the Crb-bound Pals1 PDZ structure with an apo Pals1 structure reveals a key Phe side chain that gates access to the PDZ peptide-binding groove. Removal of this side chain enhances the binding affinity by more than fivefold, suggesting that access of Crb to Pals1 may be regulated by intradomain contacts or by protein–protein interaction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

X-ray investigation of lateral hetero-structures of inversion domains in LiNbO{sub 3}, KTiOPO{sub 4} and KTiOAsO{sub 4}

Periodically-poled ferroelectric crystals are studied by observing their superlattice (grating) diffraction profiles with high-resolution X-ray diffraction. In order to successfully model the data, the effects of strain, and sample and beam coherence, must be taken into account. In this paper periodically domain-inverted (PDI) ferroelectric crystals are studied using high-resolution X-ray diffraction. Rocking curves and reciprocal-space maps of the principal symmetric Bragg reflections in LiNbO{sub 3} (LN) (Λ = 5 µm), KTiOPO{sub 4} (KTP) (Λ = 9 µm) and KTiOAsO{sub 4} (KTA) (Λ = 39 µm) are presented. For all the samples strong satellite reflections were observed as a consequence of the PDI structure. Analysis of the satellites showed that they were caused by a combination of coherent and incoherent scattering between the adjacent domains. Whilst the satellites contained phase information regarding the structure of the domain wall, this information could not be rigorously extracted without a priori knowledge of the twinning mechanism. Analysis of the profiles reveals strain distributions of Δd/d = 1.6 × 10{sup −4} and 2.0 × 10{sup −4} perpendicular to domain walls in KTP and LN samples, respectively, and lateral correlation lengths of 63 µm (KTP), 194 µm (KTA) and 10 µm (LN). The decay of crystal truncation rods in LN and KTP was found to support the occurrence of surface corrugations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Role of κ→λ light-chain constant-domain switch in the structure and functionality of A17 reactibody

Catalytic antibody variants with κ and λ light-chain constant domains show differences in their crystal structures which lead to subtle changes in catalytic efficiency and thermodynamic parameters as well as in their affinity for peptide substrates. The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophosphate-metabolizing reactibody A17 has been re-engineered by replacing its constant κ light chain by the λ chain (A17λ), and the X-ray structure of A17λ has been determined at 1.95 Å resolution. It was found that compared with A17κ the active centre of A17λ is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the V{sub L} and V{sub H} domains. These V{sub L}/V{sub H} domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126° compared with 138° in A17κ. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17κ and A17λ variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Structural Interconversion between Agglomerated Palladium Domains and Mononuclear Pd(II) Cations in Chabazite Zeolites

Palladium-exchanged zeolites are candidate materials for passive NO x adsorption in automotive exhaust aftertreatment, where mononuclear Pd cations behave as precursors to the purported NO x adsorption sites. Yet, the structures of zeolite lattice binding sites capable of stabilizing mononuclear Pd 2+ ions, and the mechanisms that interconvert agglomerated PdO and Pd domains into mononuclear Pd 2+ ions during Pd redispersion treatments, remain incompletely understood. In this work, we use a suite of spectroscopic methods and quantitative site titration techniques to characterize mononuclear and agglomerated Pd species on zeolites with varying material properties and treatment history. Aqueous-phase methods to introduce Pd onto NH 4 -form zeolites initially form mononuclear [Pd(NH 3 ) 4 ] 2+ complexes, but subsequent thermal treatments (573–723 K; air) lead to in situ formation of H 2 that first reduces Pd 2+ to metallic Pd domains, which are then oxidized by air to PdO domains. Progressive treatment of Pd-zeolites in air to higher temperatures (723–1023 K) converts larger fractions of agglomerated PdO to mononuclear Pd 2+ , as quantified by H 2 temperature programmed reduction, because higher temperature treatments facilitate Pd redispersion toward deeper locations within chabazite (CHA) crystallites, which is corroborated by complementary titrimetric and spectroscopic data. Pd-CHA zeolites synthesized with similar bulk Pd and framework Al content, but varying framework Al arrangement, provide evidence that six-membered rings (6-MR) hosting paired Al sites (Al–O–(Si–O) x –Al, x = 1, 2) stabilize Pd 2+ ions and that otherwise isolated Al sites can stabilize [PdOH] + species, identifiable by an IR OH stretch at 3660 cm –1 . These findings clarify the underlying chemical processes and gas environments that cause Pd agglomeration in zeolites and their subsequent redispersion to mononuclear Pd 2+ ions, which prefer binding at 6-MR paired Al sites in CHA, and indicate that higher temperature air treatments lead to more uniform Pd spatial distributions throughout zeolite crystallites.

36 MATERIALS SCIENCE↗