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Results for “helical junction”

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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25 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Electrostatic Design and Characterization of a 200 keV Photogun and Wien Spin Rotator

High-energy nuclear physics experiments at the Jefferson Lab Continuous Electron Beam Accelerator Facility (CEBAF) require high spin-polarization electron beams produced from strained super-lattice GaAs photocathodes activated to negative electron affinity in a high voltage photogun operating at 130 kV dc. A pair of Wien filter spin rotators in the injector provides precise control of the electron beam polarization at the end station target. An upgrade of the CEBAF injector to better support the upcoming Moller experiment requires increasing the electron beam energy to 200 keV, resulting in better transmission through injector apertures and improved photocathode lifetime. In addition, the energy increase is expected to reduce unwanted helicity correlated intensity and position systematics. These requirements led to the design of a shielding electrode described in this work, which minimizes the electric field at the triple-point junction and linearizes the potential along the insulator, thus reducing the risk of field emission induced insulator arcing. The Wien spin rotator design was modified for increasing the electric field from 1.6 to 2.7 MV/m and the magnetic field from 9.1 to 13 mT. The upgrades required detailed modeling in Solidworks, electrostatic simulations using CST, beam dynamics using GPT, device implementation, and in situ high voltage characterization of the world?s first 200 keV polarized photoelectron gun and compatible Wien filter spin rotator.

Palacios-Serrano, Gabriel↗
DOE OSTI2021

Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation

Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. Here, we have determined a 1.9-Å resolution crystal structure of the ligand-free THF riboswitch aptamer. The pseudoknot binding site ‘unwinds’ in the absence of ligand, whereby the adjacent helical domains (P1, P2, and P3) become disjointed, resulting in rotation and misalignment of the gene-regulatory P1 helix with respect to P3. In contrast, the second binding site at the three-way junction, which is the first to fold, is structurally conserved between apo and holo forms. This suggests a kinetic role for this site, in which binding of the first ligand molecule to the stably folded three-way junction promotes formation of the regulatory pseudoknot site and subsequent binding of the second molecule. As such, these findings provide a molecular basis for both conformational switching and kinetic control.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

De novo design of obligate ABC-type heterotrimeric proteins

The de novo design of three protein chains that associate to form a heterotrimer (but not any of the possible two-chain heterodimers) and that can drive the assembly of higher-order branching structures is an important challenge for protein design. We designed helical heterotrimers with specificity conferred by buried hydrogen bond networks and large aromatic residues to enhance shape complementary packing. We obtained ten designs for which all three chains cooperatively assembled into heterotrimers with few or no other species present. Crystal structures of a helical bundle heterotrimer and extended versions, with helical repeat proteins fused to individual subunits, showed all three chains assembling in the designed orientation. We used these heterotrimers as building blocks to construct larger cyclic oligomers, which were structurally validated by electron microscopy. Our three-way junction designs provide new routes to complex protein nanostructures and enable the scaffolding of three distinct ligands for modulation of cell signaling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

RKKY Exchange Bias Mediated Ultrafast All-Optical Switching of a Ferromagnet

The discovery of ultrafast helicity-independent all-optical switching (HI-AOS), as well as picosecond all-electrical switching of a ferrimagnet, has inspired the ultrafast spintronics community to explore ultrafast switching of a ferromagnet to achieve practical ultrafast storage and memory devices. Two explored mechanisms of HI-AOS of a ferromagnet in ferromagnet-ferrimagnet heterostructure are: a) exploiting the indirect exchange coupling with and b) injection of non-local spin current originated from a switching ferrimagnet. Here, in this manuscript, exchange mediated HI-AOS of a Ruderman–Kittel–Kasuya–Yosida (RKKY) exchange coupled “[Co/Pt]-multilayers/Pt spacer/CoGd” heterostructure is demonstrated. The authors have measured layer-resolved static magnetic properties, single-shot HI-AOS, and magnetization dynamics of the ferromagnetic Co/Pt multilayers (MLs), that are ferromagnetically or antiferromagnetically coupled with ferrimagnetic CoGd layers. Time-resolved magnetization dynamics reveal a 3.5 ps switching time of the Co/Pt MLs, which is the fastest switching of a ferromagnet reported to date. Employing an extended microscopic three-temperature model, the temporal dynamics of the exchange coupled ferromagnet–ferrimagnet heterostructure are simulated, qualitatively and quantitatively explaining the experimental switching phenomena. This work experimentally as well as theoretically establishes the mechanism of exchange mediated all-optical switching of ferromagnet-ferrimagnet heterostructures, which can be integrated with a magnetic tunnel junction for efficient reading after ultrafast energy-efficient switching.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state

The thiamine pyrophosphate (TPP)-sensing riboswitch is one of the earliest discovered and most widespread riboswitches. Numerous structural studies have been reported for this riboswitch bound with various ligands. However, the ligand-free (apo) structure remains unknown. Here, we report a 3.1 Å resolution crystal structure of Escherichia coli TPP riboswitch in the apo state, which exhibits an extended, Y-shaped conformation further supported by small-angle X-ray scattering data and driven molecular dynamics simulations. The loss of ligand interactions results in helical uncoiling of P5 and disruption of the key tertiary interaction between the sensory domains. Opening of the aptamer propagates to the gene-regulatory P1 helix and generates the key conformational flexibility needed for the switching behavior. Much of the ligand-binding site at the three-way junction is unaltered, thereby maintaining a partially preformed pocket. Together, these results paint a dynamic picture of the ligand-induced conformational changes in TPP riboswitches that confer conditional gene regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Amino Acid Sequence Controls Enhanced Electron Transport in Heme-Binding Peptide Monolayers

Metal-binding proteins have the exceptional ability to facilitate long-range electron transport in nature. Despite recent progress, the sequence-structure–function relationships governing electron transport in heme-binding peptides and protein assemblies are not yet fully understood. In this work, the electronic properties of a series of heme-binding peptides inspired by cytochrome bc1 are studied using a combination of molecular electronics experiments, molecular modeling, and simulation. Self-assembled monolayers (SAMs) are prepared using sequence-defined heme-binding peptides capable of forming helical secondary structures. Following monolayer formation, the structural properties and chemical composition of assembled peptides are determined using atomic force microscopy and X-ray photoelectron spectroscopy, and the electronic properties (current density–voltage response) are characterized using a soft contact liquid metal electrode method based on eutectic gallium–indium alloys (EGaIn). Our results show a substantial 1000-fold increase in current density across SAM junctions upon addition of heme compared to identical peptide sequences in the absence of heme, while maintaining a constant junction thickness. These findings show that amino acid composition and sequence directly control enhancements in electron transport in heme-binding peptides. Overall, this study demonstrates the potential of using sequence-defined synthetic peptides inspired by nature as functional bioelectronic materials.

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

Structure of pre-miR-31 reveals an active role in Dicer–TRBP complex processing

As an essential posttranscriptional regulator of gene expression, microRNA (miRNA) levels must be strictly maintained. The biogenesis of many miRNAs is mediated by trans-acting protein partners through a variety of mechanisms, including remodeling of the RNA structure. miR-31 functions as an oncogene in numerous cancers, and interestingly, its biogenesis is not known to be regulated by protein-binding partners. Therefore, the intrinsic structural properties of the precursor element of miR-31 (pre-miR-31) can provide a mechanism by which its biogenesis is regulated. We determined the solution structure of pre-miR-31 to investigate the role of distinct structural elements in regulating processing by the Dicer–TRBP complex. We found that the presence or absence of mismatches within the helical stem does not strongly influence Dicer–TRBP processing of the pre-miRNAs. However, both the apical loop size and structure at the Dicing site are key elements for discrimination by the Dicer–TRBP complex. Interestingly, our NMR-derived structure reveals the presence of a triplet of base pairs that link the Dicer cleavage site and the apical loop. Mutational analysis in this region suggests that the stability of the junction region strongly influences processing by the Dicer–TRBP complex. Our results enrich our understanding of the active role that RNA structure plays in regulating miRNA biogenesis, which has direct implications for the control of gene expression.

59 BASIC BIOLOGICAL SCIENCES↗