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At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The structural basis for regulation of the glutathione transporter Ycf1 by regulatory domain phosphorylation

Yeast Cadmium Factor 1 (Ycf1) sequesters heavy metals and glutathione into the vacuole to counter cell stress. Ycf1 belongs to the ATP binding cassette C-subfamily (ABCC) of transporters, many of which are regulated by phosphorylation on intrinsically-disordered domains. The regulatory mechanism of phosphorylation is still poorly understood. Here, we report two cryo-EM structures of Ycf1 at 3.4 Å and 4.0 Å resolution in inward-facing open conformations that capture previously unobserved ordered states of the intrinsically disordered regulatory domain (R-domain). R-domain phosphorylation is clearly evident and induces a topology promoting electrostatic and hydrophobic interactions with Nucleotide Binding Domain 1 (NBD1) and the Lasso motif. These interactions stay constant between the structures and are related by rigid body movements of the NBD1/R-domain complex. Biochemical data further show R-domain phosphorylation reorganizes the Ycf1 architecture and is required for maximal ATPase activity. Together, we provide insights into how R-domains control ABCC transporter activity.

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

Serodominant SARS-CoV-2 Nucleocapsid Peptides Map to Unstructured Protein Regions

The SARS-CoV-2 nucleocapsid (N) protein is highly immunogenic, and anti-N antibodies are commonly used as markers for prior infection. While several studies have examined or predicted the antigenic regions of N, these have lacked consensus and structural context. Using COVID-19 patient sera to probe an overlapping peptide array, we identified six public and four private epitope regions across N, some of which are unique to this study. We further report the first deposited X-ray structure of the stable dimerization domain at 2.05 Å as similar to all other reported structures. Structural mapping revealed that most epitopes are derived from surface-exposed loops on the stable domains or from the unstructured linker regions. An antibody response to an epitope in the stable RNA binding domain was found more frequently in sera from patients requiring intensive care. Since emerging amino acid variations in N map to immunogenic peptides, N protein variation could impact detection of seroconversion for variants of concern.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Local control of perpendicular magnetic anisotropy of Pd/Co multilayers via ion bombardment

In this work, we have controlled locally the magnetic anisotropy of PdCo multilayers using ion beam modification. First, we have used techniques with different probing depths to confirm that cobalt is partially oxidized in the Pd/Co multilayers exhibiting PMA fabricated by sputtering, presumably due to the diffusion of atmospheric oxygen migrated through the Pd capping layer. Then, low energy ion bombardment has been employed to induce a structural disorder in the upper layers of the multilayer, gradually reducing the PMA at local scale with increasing ion doses. Medium ion doses lead to a marked decline in PMA, resulting in equivalent magnetic anisotropy directions and the loss of characteristic labyrinthine magnetic domain morphology. High ion doses completely suppress PMA, yielding a typical in-plane shape anisotropy. Furthermore, by combining controlled PMA reduction via lithographic techniques, we create elongated structures displaying distinct magnetic responses; bombarded regions exhibit reduced PMA, whereas adjacent regions maintain their PMA. Notably, regions with reduced PMA do not disrupt the distribution of perpendicular magnetic domains in neighboring PMA regions, even at widths as narrow as 500 nm, demonstrating the robustness of the PMA domain structure.

Sebastiani-Tofano, Eugenia [Universidad Complutens↗
DOE OSTI2025

A quantitative comparison of the fingerprint of twinned microstructures through surface and three-dimensional techniques

Assessing the fingerprint of a material’s microstructure is key for supporting materials design. With the emergence of a wide range of 3D characterization techniques, it is critical to understand the main differences in fingerprints reconstructed from 2D and 3D datasets. To this end, we introduce a graph-based microstructure reconstruction framework that enables structural comparisons of twin domain networks in high purity Ti using 3D and 2D electron backscatter diffraction. Insights into the structure of the twin networks are facilitated by combining statistical analysis of twin crystallography with visual and graphical analysis of the novel graph abstractions of the twins. We demonstrate that compared to 3D reconstructions, conventional 2D views of twinning miss key aspects of the microstructure including the high interconnectivity of domains into networks that span the full reconstruction volume. The reduced cross-grain and in-grain twin connectivity typically observed in 2D has notable implications on our understanding of how twinning mediates the plastic response of microstructures and how twin networks evolve. It is thus clear that 3D characterization is critical for accurately inferring both twin network morphologies as well as the key unit processes facilitating network formation.

36 MATERIALS SCIENCE↗
DOE OSTI2024

The Role of Interfacial Interactions and Oxygen Vacancies in Tuning Magnetic Anisotropy in LaCrO 3 /LaMnO 3 Heterostructures

The interplay of lattice, electronic, and spin degrees of freedom at epitaxial complex oxide interfaces provides a route to tune their magnetic ground states. Unraveling the competing contributions is critical for tuning their functional properties. The relationship between magnetic ordering and magnetic anisotropy and the lattice symmetry, oxygen content, and film thickness in compressively strained LaMnO 3 (LMO)/LaCrO 3 (LCO) superlattices is investigated. Mn–O–Cr antiferromagnetic superexchange interactions across the heterointerface result in a net ferrimagnetic magnetic structure. Bulk magnetometry measurements reveal isotropic in-plane magnetism for as-grown oxygen-deficient thin samples due to equal fractions of orthorhombic a+a-c-, and a-a+c- twin domains. As the superlattice thickness is increased, in-plane magnetic anisotropy emerges as the fraction of the a+a-c- domain increases. On annealing in oxygen, the suppression of oxygen vacancies results in a contraction of the lattice volume, and an orthorhombic to rhombohedral transition leads to isotropic magnetism independent of the film thickness. The complex interactions are investigated using high-resolution synchrotron diffraction and X-ray absorption spectroscopy. These results highlight the role of the evolution of structural domains with film thickness, interfacial spin interactions, and oxygen-vacancy-induced structural phase transitions in tuning the magnetic properties of complex oxide heterostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Kainate receptor channel opening and gating mechanism

Kainate receptors, a subclass of ionotropic glutamate receptors, are tetrameric ligand-gated ion channels that mediate excitatory neurotransmission. Kainate receptors modulate neuronal circuits and synaptic plasticity during the development and function of the central nervous system and are implicated in various neurological and psychiatric diseases, including epilepsy, depression, schizophrenia, anxiety and autism. Although structures of kainate receptor domains and subunit assemblies are available, the mechanism of kainate receptor gating remains poorly understood. Here we present cryo-electron microscopy structures of the kainate receptor GluK2 in the presence of the agonist glutamate and the positive allosteric modulators lectin concanavalin A and BPAM344. Concanavalin A and BPAM344 inhibit kainate receptor desensitization and prolong activation by acting as a spacer between the amino-terminal and ligand-binding domains and a stabilizer of the ligand-binding domain dimer interface, respectively. Channel opening involves the kinking of all four pore-forming M3 helices. Our structures reveal the molecular basis of kainate receptor gating, which could guide the development of drugs for treatment of neurological disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The N‐terminal intrinsically disordered region of Ncb5or docks with the cytochrome b 5 core to form a helical motif that is of ancient origin

Abstract NADH cytochromeb 5 oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochromeb 5 (b 5 ) and cytochromeb 5 reductase (b 5 R) domains separated by a CHORD‐Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter‐domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full‐length human Ncb5or has proven resistant to crystallization, we have succeeded in obtaining high‐resolution atomic structures of theb 5 domain and a construct containing the CS andb 5 R domains (CS/b 5 R). Ncb5or also contains an N‐terminal intrinsically disordered region of 50 residues that has no homologs in other protein families in animals but features a distinctive, conserved L 34 MDWIRL 40 motif also present in reduced lateral root formation (RLF) protein in rice and increased recombination center 21 in baker's yeast, all attaching to ab 5 domain. After unsuccessful attempts at crystallizing a human Ncb5or construct comprising the N‐terminal region naturally fused to theb 5 domain, we were able to obtain a high‐resolution atomic structure of a recombinant rice RLF construct corresponding to residues 25–129 of human Ncb5or (52% sequence identity; 74% similarity). The structure reveals Trp 120 (corresponding to invariant Trp 37 in Ncb5or) to be part of an 11‐residue α‐helix (S 116 QMDWLKLTRT 126 ) packing against two of the four helices in theb 5 domain that surround heme (α2 and α5). The Trp 120 side chain forms a network of interactions with the side chains of four highly conserved residues corresponding to Tyr 85 and Tyr 88 (α2), Cys 124 (α5), and Leu 47 in Ncb5or. Circular dichroism measurements of human Ncb5or fragments further support a key role of Trp 37 in nucleating the formation of the N‐terminal helix, whose location in the N/b 5 module suggests a role in regulating the function of this multi‐domain redox enzyme. This study revealed for the first time an ancient origin of a helical motif in the N/b 5 module as reflected by its existence in a class of cytochromeb 5 proteins from three kingdoms among eukaryotes.

Biochemistry & Molecular Biology↗
NASA NTRS1983

Advances and trends in structural and solid mechanics; Proceedings of the Symposium, Washington, DC, October 4-7, 1982

The mechanics of materials and material characterization are considered, taking into account micromechanics, the behavior of steel structures at elevated temperatures, and an anisotropic plasticity model for inelastic multiaxial cyclic deformation. Other topics explored are related to advances and trends in finite element technology, classical analytical techniques and their computer implementation, interactive computing and computational strategies for nonlinear problems, advances and trends in numerical analysis, database management systems and CAD/CAM, space structures and vehicle crashworthiness, beams, plates and fibrous composite structures, design-oriented analysis, artificial intelligence and optimization, contact problems, random waves, and lifetime prediction. Earthquake-resistant structures and other advanced structural applications are also discussed, giving attention to cumulative damage in steel structures subjected to earthquake ground motions, and a mixed domain analysis of nuclear containment structures using impulse functions.

Noor, A. K.↗
DOE OSTI2026

Domain-Dependent Electronic Properties of 2D Copper Boride Synthesized from Reversible Subsurface Diffusion on Cu(111)

Emerging boron-based 2D materials hold properties with potential applications ranging from electronic devices to catalysis and energy storage. Using physical vapor deposition, 2D copper borides are formed on Cu(111) at elevated temperatures. However, the as-prepared surfaces often contain boron clusters that compromise structural homogeneity, and the dynamics of their formation is not yet fully understood. Through in situ low-energy electron microscopy (LEEM), Auger electron spectroscopy (AES), and scanning tunneling microscopy/spectroscopy (STM/STS), we show that cluster-free 2D CuB x is synthesized via reversible subsurface diffusion of boron atoms. The resolved regular atomic structure aligns with the previously calculated Cu 8 B 14 model. In a rare case, possibly due to surface strain and a change of orientation, a second domain of CuB x was observed with a pronounced change in electronic properties, yet electronic states remain delocalized in both domains. In conclusion, these findings demonstrate the sensitivity of electronic properties to domain structure and highlight a potential opportunity to tune 2D CuB x for diverse applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

The first DEP domain of the RhoGEF P-Rex1 autoinhibits activity and contributes to membrane binding

Phosphatidylinositol (3,4,5)-trisphosphate (PIP 3 )-dependent Rac exchanger 1 (P-Rex1) catalyzes the exchange of GDP for GTP on Rac GTPases, thereby triggering changes in the actin cytoskeleton and in transcription. Its overexpression is highly correlated with the metastasis of certain cancers. P-Rex1 recruitment to the plasma membrane and its activity are regulated via interactions with heterotrimeric Gβγ subunits, PIP 3 , and protein kinase A (PKA). Deletion analysis has further shown that domains C-terminal to its catalytic Dbl homology (DH) domain confer autoinhibition. Among these, the first dishevelled, Egl-10, and pleckstrin domain (DEP1) remains to be structurally characterized. DEP1 also harbors the primary PKA phosphorylation site, suggesting that an improved understanding of this region could substantially increase our knowledge of P-Rex1 signaling and open the door to new selective chemotherapeutics. Here we show that the DEP1 domain alone can autoinhibit activity in context of the DH/PH-DEP1 fragment of P-Rex1 and interacts with the DH/PH domains in solution. The 3.1 Å crystal structure of DEP1 features a domain swap, similar to that observed previously in the Dvl2 DEP domain, involving an exposed basic loop that contains the PKA site. Using purified proteins, we show that although DEP1 phosphorylation has no effect on the activity or solution conformation of the DH/PH-DEP1 fragment, it inhibits binding of the DEP1 domain to liposomes containing phosphatidic acid. Thus, we propose that PKA phosphorylation of the DEP1 domain hampers P-Rex1 binding to negatively charged membranes in cells, freeing the DEP1 domain to associate with and inhibit the DH/PH module.

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

Structure of metallochaperone in complex with the cobalamin-binding domain of its target mutase provides insight into cofactor delivery

G-protein metallochaperone MeaB in bacteria [methylmalonic aciduria type A (MMAA) in humans] is responsible for facilitating the delivery of adenosylcobalamin (AdoCbl) to methylmalonyl-CoA mutase (MCM), the only AdoCbl-dependent enzyme in humans. Genetic defects in the switch III region of MMAA lead to the genetic disorder methylmalonic aciduria in which the body is unable to process certain lipids. Here, we present a crystal structure of Methylobacterium extorquens MeaB bound to a nonhydrolyzable guanosine triphosphate (GTP) analog guanosine-5'-[(β,γ)-methyleno]triphosphate (GMPPCP) with the Cbl-binding domain of its target mutase enzyme (MeMCM cbl ). This structure provides an explanation for the stimulation of the GTP hydrolyase activity of MeaB afforded by target protein binding. We find that upon MCM cbl association, one protomer of the MeaB dimer rotates ~180°, such that the inactive state of MeaB is converted to an active state in which the nucleotide substrate is now surrounded by catalytic residues. Importantly, it is the switch III region that undergoes the largest change, rearranging to make direct contacts with the terminal phosphate of GMPPCP. These structural data additionally provide insights into the molecular basis by which this metallochaperone contributes to AdoCbl delivery without directly binding the cofactor. Our data suggest a model in which GTP-bound MeaB stabilizes a conformation of MCM that is open for AdoCbl insertion, and GTP hydrolysis, as signaled by switch III residues, allows MCM to close and trap its cofactor. Substitutions of switch III residues destabilize the active state of MeaB through loss of protein:nucleotide and protein:protein interactions at the dimer interface, thus uncoupling GTP hydrolysis from AdoCbl delivery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding

Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the cobalamin riboswitch with predicted structural features was identified in Bacillus subtilis over a decade ago, but its structure and mechanisms of cobalamin selectivity and translational control have remained unsolved. We present the crystal structure of the aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, including its expression platform domain. We demonstrate that this riboswitch binds to multiple cobalamin derivatives and correlate its promiscuous behavior to its structure and unique arrangement of peripheral elements. Comparative structural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promiscuous ligand binding is intrinsic structural adaptability encoded in the RNA structure. It suggests that cobalamin selectivity might ultimately be viewed as existing on a spectrum of affinity for each derivative rather than as belonging to distinct types based on ligand specificities. Our work provides an interesting and notable example of functional coupling of ligand-sensing and adaptive folding by a structured RNA molecule.

59 BASIC BIOLOGICAL SCIENCES↗