Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “structured”

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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids

Abstract Poleroviruses, enamoviruses, and luteoviruses are icosahedral, positive sense RNA viruses that cause economically important diseases in food and fiber crops. They are transmitted by phloem-feeding aphids in a circulative manner that involves the movement across and within insect tissues. The N-terminal portion of the viral readthrough domain ( N RTD) has been implicated as a key determinant of aphid transmission in each of these genera. Here, we report crystal structures of the N RTDs from the poleroviruses turnip yellow virus (TuYV) and potato leafroll virus (PLRV) at 1.53-Å and 2.22-Å resolution, respectively. These adopt a two-domain arrangement with a unique interdigitated topology and form highly conserved dimers that are stabilized by a C-terminal peptide that is critical for proper folding. We demonstrate that the PLRV N RTD can act as an inhibitor of virus transmission and identify N RTD mutant variants that are lethal to aphids. Sequence conservation argues that enamovirus and luteovirus N RTDs will follow the same structural blueprint, which affords a biological approach to block the spread of these agricultural pathogens in a generalizable manner.

Schiltz, Carl J. (ORCID:0000000332030784)↗
DOE OSTI2022

Design of protein-binding proteins from the target structure alone

The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge. Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder–target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein–protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT

Abstract Organisms have a myriad of strategies for sensing, responding to, and combating reactive oxygen species, which are unavoidable consequences of aerobic life. In the heterocystous cyanobacterium Nostoc sp. PCC 7120, one such strategy is the use of an ArsR-SmtB transcriptional regulator RexT that senses H 2 O 2 and upregulates expression of thioredoxin to maintain cellular redox homeostasis. Different from many other members of the ArsR-SmtB family which bind metal ions, RexT has been proposed to use disulfide bond formation as a trigger to bind and release DNA. Here, we present high-resolution crystal structures of RexT in the reduced and H 2 O 2 -treated states. These structures reveal that RexT showcases the ArsR-SmtB winged-helix-turn-helix fold and forms a vicinal disulfide bond to orchestrate a response to H 2 O 2 . The importance of the disulfide-forming Cys residues was corroborated using site-directed mutagenesis, mass spectrometry, and H 2 O 2 -consumption assays. Furthermore, an entrance channel for H 2 O 2 was identified and key residues implicated in H 2 O 2 activation were pinpointed. Finally, bioinformatics analysis of the ArsR-SmtB family indicates that the vicinal disulfide “redox switch” is a unique feature of cyanobacteria in the Nostocales order, presenting an interesting case where an ArsR-SmtB protein scaffold has been evolved to showcase peroxidatic activity and facilitate redox-based regulation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Unraveling the structural stability and the electronic structure of ThO 2 clusters

Unraveling the correlations between the geometry, the relative energy and the electronic structure of metal oxide nanostructures is crucial for a better control of their size, shape and properties. Here, we investigated these correlations for stoichiometric thorium dioxide clusters ranging from ThO 2 to Th 8 O 16 using a chemically-driven geometry search algorithm in combination with state-of-the-art first principles calculations. This strategy allows us to homogeneously screen the potential energy surface of actinide oxide clusters for the first time. It is found that the presence of peroxo and superoxo groups tends to increase the total energy of the system by at least 3.5 eV and 7 eV, respectively. For the larger clusters, the presence of terminal oxygen atoms increases the energy by about 0.5 eV. Regarding the electronic structure, it is found that the HOMO–LUMO gap is larger in systems containing only bridging oxygen atoms (~2–3.5 eV) than for systems containing oxo groups (~1–3 eV), peroxo groups (~0–2 eV), and superoxo groups (~0–1 eV). Furthermore, while the LUMO is always dominated by thorium orbitals, the composition of the HOMO changes in the presence or the absence of oxo, peroxo and/or superoxo groups: in the presence of peroxo groups, it is dominated by thorium orbitals, in all other cases, it is dominated by oxygen orbitals, and is rather localized in the presence of terminal oxo or superoxo groups. These correlations are of great interest for synthesizing clusters with tailored properties, especially for applications in the field of nuclear energy and heterogeneous catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Evaluating the effects of structural disorder on the magnetic properties of Nd 2 Zr 2 O 7

Motivated by the variation in reported lattice parameters of floating-zone-grown Nd 2 Zr 2 O 7 crystals, we have performed a detailed study of the relationship between synthesis environment, structural disorder, and magnetic properties. Using a combination of polycrystalline standards, electron-probe microanalysis, and scattering techniques, we show that crystals grown under atmospheric conditions have a reduced lattice parameter relative to pristine polycrystalline powders due to occupation of the Nd site by excess Zr (i.e., negative stuffing). In contrast, crystals grown under high-pressure Ar are nearly stoichiometric with an average lattice parameter approaching the polycrystalline value. While minimal disorder of the oxygen sublattices is observed on the scale of the average structure, neutron pair-distribution function analysis indicates a highly local disorder of the oxygen coordination, which is only weakly dependent on growth environment. Most importantly, our magnetization, heat capacity, and single-crystal neutron scattering data show that the magnetic properties of crystals grown under high-pressure Ar match closely with those of stoichiometric powders. Neutron scattering measurements reveal that the signature of magnetic moment fragmentation—the coexistence of all-in-all-out (AIAO) magnetic Bragg peaks and diffuse pinch-point scattering due to spin-ice correlations–persists in these nearly stoichiometric crystals. However, in addition to an increased AIAO transition temperature, the diffuse signal is seemingly stabilized and remains nearly unchanged upon warming to 800 mK. This behavior indicates that both the AIAO magnetic order and spin-ice correlations are sensitive to deviations of the Nd stoichiometry.

36 MATERIALS SCIENCE↗