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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 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Multi-direction high-efficiency second harmonic generation in ellipse structure nonlinear photonic crystals

We have designed and fabricated a lithium niobate (LN) nonlinear photonic crystal (NPC) with a two-dimensional (2D) ellipse structure of inverse poling domains. The structure can offer continuously varying reciprocal lattice vectors in different directions to compensate the phase-mismatching during the second harmonic generation (SHG) for diverse pump wavelengths. We consider three propagation directions with large effective nonlinear susceptibility and measure the nonlinear conversion efficiency of SHG. The experimental data are in good agreement with the quantitative calculation results using the effective susceptibility model with pump depletion. With high-efficiency SHG in multiple propagation direction, the 2D ellipse structure of LN NPC has the potential to realize various broadband nonlinear frequency conversion processes in different propagation direction with a single crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA

The recently characterized mammalian writer (methyltransferase) and eraser (demethylase) of the DNA N6-methyladenine (N6mA) methyl mark act on single-stranded (ss) and transiently-unpaired DNA. As YTH domain-containing proteins bind N6mA-containing RNA in mammalian cells, we investigated whether mammalian YTH domains are also methyl mark readers of N6mA DNA. Here, we show that the YTH domain of YTHDC1 (known to localize in the nucleus) binds ssDNA containing N6mA, with a 10 nM dissociation constant. This binding is stronger by a factor of 5 than in an RNA context, tested under the same conditions. However, the YTH domains of YTHDF2 and YTHDF1 (predominantly cytoplasmic) exhibited the opposite effect with ~1.5–2× stronger binding to ssRNA containing N6mA than to the corresponding DNA. We determined two structures of the YTH domain of YTHDC1 in complex with N6mA-containing ssDNA, which illustrated that YTHDC1 binds the methylated adenine in a single-stranded region flanked by duplexed DNA. We discuss the hypothesis that the writer-reader-eraser of N6mA-containining ssDNA is associated with maintaining genome stability. Structural comparison of YTH and SRA domains (the latter a DNA 5-methylcytosine reader) revealed them to be diverse members of a larger family of DNA/RNA modification readers, apparently having originated from bacterial modification-dependent restriction enzymes.

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

Needle-Like Ferroelastic Domains in Individual Ferroelectric Nanoparticles

Superior structural, physical and electronic properties make ferroelectric nanocrystals essential in enabling a range of next-generation devices. Ferroelectric responses are determined by crystal structure and domain morphology. The ability to reversibly displace, create and annihilate elastic domains is critical to device applications. Whereas electric-field control has been demonstrated for ferroelectric 180° surface domain walls and vortices, similar control of ferroelastic domains and domain boundaries within individual nanocrystals remains challenging. Using controlled external compressive and tensile axial stress, deterministic and reversible control of highly mobile ferroelastic domains and axial polarization in three dimensions is demonstrated in this study. While many studies exist on ferroelastic domains in thin films and bulk, little is known about ferroelastic interactions at the single nanoparticle level, especially involving domain boundaries. Through combining Bragg coherent X-ray diffractive imaging and Landau theory, strain gradients in individual BaTiO3 nanocrystals are shown to stabilize needle-like ferroelastic twin domains. These domains are highly labile under applied axial stress, producing a locally enhanced electric polarization mediated by a ferroelectric phase transition. The efficacy of Bragg coherent X-ray diffractive imaging in studying in operando domains in three-dimensions is demonstrated, while synergy with theory provides a paradigm for domain boundary engineering and potential for nanoscale functional devices.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Visualizing domain wall and reverse domain superconductivity

In magnetically coupled, planar ferromagnet-superconductor (F/S) hybrid structures, magnetic domain walls can be used to spatially confine the superconductivity. In contrast to a superconductor in a uniform applied magnetic field, the nucleation of the superconducting order parameter in F/S structures is governed by the inhomogeneous magnetic field distribution. The interplay between the superconductivity localized at the domain walls and far from the walls leads to effects such as re-entrant superconductivity and reverse domain superconductivity with the critical temperature depending upon the location. Here we use scanning tunnelling spectroscopy to directly image the nucleation of superconductivity at the domain wall in F/S structures realized with Co-Pd multilayers and Pb thin films. Our results demonstrate that such F/S structures are attractive model systems that offer the possibility to control the strength and the location of the superconducting nucleus by applying an external magnetic field, potentially useful to guide vortices for computing application.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3, 4 domains of integrin α6β4

The structure of the FnIII-3, 4 region of integrin β4 was solved using a hybrid approach that combines crystallographic structures, SAXS, DEER and molecular modelling. The structure helps in understanding how integrin β4 might bind to other hemidesmosomal proteins and mediate signalling. Integrin α6β4 is a major component of hemidesmosomes that mediate the stable anchorage of epithelial cells to the underlying basement membrane. Integrin α6β4 has also been implicated in cell proliferation and migration and in carcinoma progression. The third and fourth fibronectin type III domains (FnIII-3, 4) of integrin β4 mediate binding to the hemidesmosomal proteins BPAG1e and BPAG2, and participate in signalling. Here, it is demonstrated that X-ray crystallography, small-angle X-ray scattering and double electron–electron resonance (DEER) complement each other to solve the structure of the FnIII-3, 4 region. The crystal structures of the individual FnIII-3 and FnIII-4 domains were solved and the relative arrangement of the FnIII domains was elucidated by combining DEER with site-directed spin labelling. Multiple structures of the interdomain linker were modelled by Monte Carlo methods complying with DEER constraints, and the final structures were selected against experimental scattering data. FnIII-3, 4 has a compact and cambered flat structure with an evolutionary conserved surface that is likely to correspond to a protein-interaction site. Finally, this hybrid method is of general application for the study of other macromolecules and complexes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

DNA Recognition by a σ 54 Transcriptional Activator from Aquifex aeolicus

Transcription initiation by bacterial σ 54 -polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain. The structurally characterized DNA-binding domains from activators all belong to the Factor for Inversion Stimulation (Fis) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DNA-binding domain of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of σ 54 activators. Two NtrC4 binding sites were identified upstream (-145 and -85 base pairs) from the start of the lpxC gene, which is responsible for the first committed step in Lipid A biosynthesis. This is the first experimental evidence for σ 54 regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the -145 binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homologue, Fis. Ultimately, the greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base specific contacts contributing to affinity than for Fis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structure of the catalytic domain of the colistin resistance enzyme MCR-1

Due to the paucity of novel antibiotics, colistin has become a last resort antibiotic for treating multidrug resistant bacteria. Colistin acts by binding the lipid A component of lipopolysaccharides and subsequently disrupting the bacterial membrane. The recently identified plasmid-encoded MCR-1 enzyme is the first transmissible colistin resistance determinant and is a cause for concern for the spread of this resistance trait. MCR-1 is a phosphoethanolamine transferase that catalyzes the addition of phosphoethanolamine to lipid A to decrease colistin affinity. The structure of the catalytic domain of MCR-1 at 1.32 Å reveals the active site is similar to that of related phosphoethanolamine transferases. The putative nucleophile for catalysis, threonine 285, is phosphorylated in cMCR-1 and a zinc is present at a conserved site in addition to three zincs more peripherally located in the active site. As noted for catalytic domains of other phosphoethanolamine transferases, binding sites for the lipid A and phosphatidylethanolamine substrates are not apparent in the cMCR-1 structure, suggesting that they are present in the membrane domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Out-of-plane chiral domain wall spin-structures in ultrathin in-plane magnets

Chiral spin textures in ultrathin films, such as skyrmions or chiral domain walls, are believed to offer large performance advantages in the development of novel spintronics technologies. While in-plane magnetized films have been studied extensively as media for current- and field-driven domain wall dynamics with applications in memory or logic devices, the stabilization of chiral spin textures in in-plane magnetized films has remained rare. Here we report a phase of spin structures in an in-plane magnetized ultrathin film system where out-of-plane spin orientations within domain walls are stable. Moreover, while domain walls in in-plane films are generally expected to be non-chiral, we show that right-handed spin rotations are strongly favoured in this system, due to the presence of the interfacial Dzyaloshinskii-Moriya interaction. These results constitute a platform to explore unconventional spin dynamics and topological phenomena that may enable high-performance in-plane spin-orbitronics devices.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Crystal Structure and Biochemical Characterization of a Mycobacterium smegmatis AAA-Type Nucleoside Triphosphatase Phosphohydrolase (Msm0858)

AAA proteins (ATPases associated with various cellular activities) use the energy of ATP hydrolysis to drive conformational changes in diverse macromolecular targets. Here, we report the biochemical characterization and 2.5-Å crystal structure of a Mycobacterium smegmatis AAA protein Msm0858, the ortholog of Mycobacterium tuberculosis Rv0435c. Msm0858 is a magnesium-dependent ATPase and is active with all nucleoside triphosphates (NTPs) and deoxynucleoside triphosphates (dNTPs) as substrates. The Msm0858 structure comprises (i) an N-terminal domain (amino acids [aa] 17 to 201) composed of two β-barrel modules and (ii) two AAA domains, D1 (aa 212 to 473) and D2 (aa 476 to 744), each of which has ADP in the active site. Msm0858-ADP is a monomer in solution and in crystallized form. Msm0858 domains are structurally homologous to the corresponding modules of mammalian p97. However, the position of the N-domain modules relative to the AAA domains in the Msm0858-ADP tertiary structure is different and would impede the formation of a p97-like hexameric quaternary structure. Mutational analysis of the A-box and B-box motifs indicated that the D1 and D2 AAA domains are both capable of ATP hydrolysis. Simultaneous mutations of the D1 and D2 active-site motifs were required to abolish ATPase activity. ATPase activity was effaced by mutation of the putative D2 arginine finger, suggesting that Msm0858 might oligomerize during the ATPase reaction cycle. A truncated variant Msm0858 (aa 212 to 745) that lacks the N domain was characterized as a catalytically active homodimer. Recent studies have underscored the importance of AAA proteins (ATPases associated with various cellular activities) in the physiology of mycobacteria. This study reports the ATPase activity and crystal structure of a previously uncharacterized mycobacterial AAA protein, Msm0858. Msm0858 consists of an N-terminal β-barrel domain and two AAA domains, each with ADP bound in the active site. Msm0858 is a structural homolog of mammalian p97, with respect to the linear order and tertiary structures of their domains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO–POL enzyme

Mycobacterial Pol1 is a bifunctional enzyme composed of an N-terminal DNA flap endonuclease/5' exonuclease domain (FEN/EXO) and a C-terminal DNA polymerase domain (POL). Here we document additional functions of Pol1: FEN activity on the flap RNA strand of an RNA:DNA hybrid and reverse transcriptase activity on a DNA-primed RNA template. We report crystal structures of the POL domain, as apoenzyme and as ternary complex with 3'-dideoxy-terminated DNA primer-template and dNTP. The thumb, palm, and fingers subdomains of POL form an extensive interface with the primer-template and the triphosphate of the incoming dNTP. Progression from an open conformation of the apoenzyme to a nearly closed conformation of the ternary complex entails a disordered-to-ordered transition of several segments of the thumb and fingers modules and an inward motion of the fingers subdomain—especially the O helix—to engage the primer-template and dNTP triphosphate. Distinctive structural features of mycobacterial Pol1 POL include a manganese binding site in the vestigial 3' exonuclease subdomain and a non-catalytic water-bridged magnesium complex at the protein-DNA interface. We report a crystal structure of the bifunctional FEN/EXO–POL apoenzyme that reveals the positions of two active site metals in the FEN/EXO domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

The structure of the cyanobactin domain of unknown function from PatG in the patellamide gene cluster

The highly conserved domain of unknown function in the cyanobactin superfamily has a novel fold. The protein does not appear to bind the most plausible substrates, leaving questions as to its role. Patellamides are members of the cyanobactin family of ribosomally synthesized and post-translationally modified cyclic peptide natural products, many of which, including some patellamides, are biologically active. A detailed mechanistic understanding of the biosynthetic pathway would enable the construction of a biotechnological ‘toolkit’ to make novel analogues of patellamides that are not found in nature. All but two of the protein domains involved in patellamide biosynthesis have been characterized. The two domains of unknown function (DUFs) are homologous to each other and are found at the C-termini of the multi-domain proteins PatA and PatG. The domain sequence is found in all cyanobactin-biosynthetic pathways characterized to date, implying a functional role in cyanobactin biosynthesis. Here, the crystal structure of the PatG DUF domain is reported and its binding interactions with plausible substrates are investigated.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase

Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion using noncanonical amino acids, yet its structure and function are not completely understood. In this work, we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNAPyl. This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also highlights why tRNAPyl recognition by PylRS is anticodon independent: the anticodon does not contact the enzyme. Furthermore, using standard microbiological culture equipment, we established a new method for laboratory evolution—a noncontinuous counterpart of the previously developed phage-assisted continuous evolution. With this method, we evolved novel PylRS variants with enhanced activity and amino acid specificity. Finally, we employed an evolved PylRS variant to determine its N-terminal domain structure and show how its mutations improve PylRS activity in the genetic encoding of a noncanonical amino acid.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure of the glucosyltransferase domain of TcdA in complex with RhoA provides insights into substrate recognition

Clostridioides difficile is one of the most common causes of antibiotic-associated diarrhea in developed countries. As key virulence factors of C. difficile, toxin A (TcdA) and toxin B (TcdB) act by glucosylating and inactivating Rho and Ras family small GTPases in host cells, which leads to actin cytoskeleton disruption, cell rounding, and ultimately cell death. Here we present the co-crystal structure of the glucosyltransferase domain (GTD) of TcdA in complex with its substrate human RhoA at 2.60-angstrom resolution. This structure reveals that TcdA GTD grips RhoA mainly through its switch I and switch II regions, which is complemented by interactions involving RhoA’s pre-switch I region. Comprehensive structural comparisons between the TcdA GTD–RhoA complex and the structures of TcdB GTD in complex with Cdc42 and R-Ras reveal both the conserved and divergent features of these two toxins in terms of substrate recognition. Taken together, these findings establish the structural basis for TcdA recognition of small GTPases and advance our understanding of the substrates selectivity of large clostridial toxins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural basis for p50RhoGAP BCH domain–mediated regulation of Rho inactivation

Significance Small GTPases are binary proteins that rapidly switch between active and inactive states through the actions of GEF- and GTPase-activating proteins (GAPs), respectively. GAPs play significant roles in cellular signaling, and their dysregulation is linked to numerous cancers. Here, we show that the BNIP-2 and Cdc42GAP Homology (BCH) domain of p50RhoGAP, known to autoinhibit the adjacent GAP domain, adopts an intertwined, dimeric structure with unique RhoA interactions. The β5-strand of the BCH domain plays a crucial role in the autoinhibition of the GAP domain. A mutation in the β5-strand destabilizes this autoinhibition and leads to RhoGAP activation. Our studies on the dynamics of the RhoGAP BCH domain will clarify its potential role in cancer and other diseases.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Crystal Structure of the Catalytic Domain of a Serine Threonine Protein Phosphatase

Reversible phosphorylation of serine and threonine residues is a well-recognized mechanism in eukaryotic cells for the regulation of cell-cycle progression, cell growth and metabolism. Human serine/threonine phosphatases can be placed into two major families, PPP and PPM. To date the structure on one PPP family member (PPl) has been determined. Here we present the structure of a 323-residue catalytic domain of a second phosphatase belonging to the PPP family of enzyme. catalytic domain of the enzyme has been determined to 1.60Angstrom resolution and refined to R=17.5 and Rfree = 20.8%. The catalytic domain possesses a unique fold consisting of a largely monolithic structure, divisible into closely-associated helical and sheet regions. The catalytic site contains two manganese ions that are involved in substrate binding and catalysis. The enzyme crystallizes as a dimer that completely buries catalytic surfaces of both monomers, Also, the structure shows evidence of some flexibility around the active site cleft that may be related to substrate specificity of this enzyme.

Swinglel, Mark↗
DOE OSTI2020

Improving the picture of atomic structure in nonoriented polymer domains using the pair distribution function: A study of polyamide 6

Abstract Investigations of the atomic structures within polyamides started over 80 years ago and continue today. These weakly ordered materials diffract X‐rays poorly and typically require postprocessing to obtain idealized samples for structural studies. An important goal remains to develop techniques to study the local structure in its natural state, with atomic resolution, and with sensitivity to subtle changes due to synthesis conditions or other technologically relevant processing procedures. Here, we compare the structures of as‐produced, nonoriented polyamide 6 ([C 6 H 11 NO] n ) from both hydrolytic and anionic processes. A total scattering pair distribution function approach is used to elucidate information about the atomic bonding, molecular conformation, chain packing, crystallite size, and ratio of ordered to disordered domain content. The results are compared with those from standard analytical methods.

Terban, Maxwell W.↗