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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL

Overexpression of BCL-xL and BCL-2 play key roles in tumorigenesis and cancer drug resistance. Advances in PROTAC technology facilitated recent development of the first BCL-xL/BCL-2 dual degrader, 753b, a VHL-based degrader with improved potency and reduced toxicity compared to previous small molecule inhibitors. Here, we determine crystal structures of VHL/753b/BCL-xL and VHL/753b/BCL-2 ternary complexes. The two ternary complexes exhibit markedly different architectures that are accompanied by distinct networks of interactions at the VHL/753b-linker/target interfaces. The importance of these interfacial contacts is validated via functional analysis and informed subsequent rational and structure-guided design focused on the 753b linker and BCL-2/BCL-xL warhead. This results in the design of a degrader, WH244, with enhanced potency to degrade BCL-xL/BCL-2 in cells. Using biophysical assays followed by in cell activities, we are able to explain the enhanced target degradation of BCL-xL/BCL-2 in cells. Most PROTACs are empirically designed and lack structural studies, making it challenging to understand their modes of action and specificity. Our work presents a streamlined approach that combines rational design and structure-based insights backed with cell-based studies to develop effective PROTAC-based cancer therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Surfactant-like peptide gels are based on cross-β amyloid fibrils

Surfactant-like peptides, in which hydrophilic and hydrophobic residues are encoded within different domains in the peptide sequence, undergo facile self-assembly in aqueous solution to form supramolecular hydrogels. These peptides have been explored extensively as substrates for the creation of functional materials since a wide variety of amphipathic sequences can be prepared from commonly available amino acid precursors. The self-assembly behavior of surfactant-like peptides has been compared to that observed for small molecule amphiphiles in which nanoscale phase separation of the hydrophobic domains drives the self-assembly of supramolecular structures. Here, we investigate the relationship between sequence and supramolecular structure for a pair of bola-amphiphilic peptides, Ac-KLIIIK-NH 2 (L2) and Ac-KIIILK-NH 2 (L5). Despite similar length, composition, and polar sequence pattern, L2 and L5 form morphologically distinct assemblies, nanosheets and nanotubes, respectively. Cryo-EM helical reconstruction was employed to determine the structure of the L5 nanotube at near-atomic resolution. Rather than displaying self-assembly behavior analogous to conventional amphiphiles, the packing arrangement of peptides in the L5 nanotube displayed steric zipper interfaces that resembled those observed in the structures of β-amyloid fibrils. Like amyloids, the supramolecular structures of the L2 and L5 assemblies were sensitive to conservative amino acid substitutions within an otherwise identical amphipathic sequence pattern. This study highlights the need to better understand the relationship between sequence and supramolecular structure to facilitate the development of functional peptide-based materials for biomaterials applications.

Das, Abhinaba [Emory University, Atlanta, GA (Unit↗
DOE OSTI2026

Cs X Si 15 P 21 ( X = Sn or Pb): Polar Noncentrosymmetric Si–P Frameworks Stabilized by Covalent X –P Bonding

Metal silicon phosphides composed of earth-abundant Si and P tend to exhibit semiconducting properties and adopt diverse crystal structures with relatively small additions of structure-directing elements. The potential of silicon phosphide materials in nonlinear optical applications has been hindered by the inability to systematically produce noncentrosymmetric structures with such a flexible framework. Here, in this work, two isostructural compounds with a novel noncentrosymmetric structure were made possible by the inclusion of elements with stereochemically active lone pairs (Sn 2+ and Pb 2+ ). The structures were determined through single-crystal and synchrotron powder X-ray diffraction. Analysis of chemical bonding in real space through the electron localization function revealed stereochemically active Pb 2+ and Sn 2+ species in a trigonal pyramidal coordination with {Pb/Sn}–P bonds. Such covalent bonding between Pb and P is quite uncommon in extended solids and has been reported in a few rare instances. Band structure calculations and linear optical measurements confirm the semiconducting nature of Cs X Si 15 P 21 ( X = Sn or Pb). The synthesis was optimized to yield high-purity polycrystalline samples. The nonlinear optical properties show promising second-harmonic generation (SHG) coefficients from the Kurtz–Perry method. First-principles calculations of the nonlinear optical properties support the experimentally determined SHG values and provide moderate values of birefringence, suggesting Cs X Si 15 P 21 could be phase-matchable and practical nonlinear optical materials in the mid-IR region.

crystal structure↗
DOE OSTI2025

Structural Investigation of Six Quinary Sulfides Synthesized via the Flux-Assisted Boron-Chalcogen Mixture (BCM) Method: Eu 2+ Containing Members of the RE 3 MTQ 7 (M and T = Transition or Main Group Metals, Q = Chalcogens) Family

For this work, a series of six quinary rare-earth sulfides Ce 4+ 1.85 Eu 2+ 1.15 Na 0.30 SiS 7 , Ce 4+ 1.91 Eu 2+ 1.09 K 0.18 SiS 7 , Ce 4+ 1.96 Eu 2+ 1.04 Rb 0.08 SiS 7 , Ce 4+ 1.98 Eu 2+ 1.02 Cs 0.05 SiS 7 , Ce 4+ 1.97 Eu 2+ 1.03 Ag 0.06 SiS 7 , and Ce 4+ 1.50 Eu 2+ 1.50 CuSiS 7 were obtained in an alkali iodide flux using the boron-chalcogen mixture (BCM) method. Single crystal X-ray diffraction was used to determine the structures of the high quality single crystals that were grown; their elemental compositions were confirmed by energy-dispersive spectroscopy (EDS). The compounds crystallize in the hexagonal crystal system in the noncentrosymmetric space group P63. The crystal structure consists of a three-dimensional network composed of mixed cerium and europium bicapped trigonal prisms, isolated SiS4 tetrahedra, and monovalent metals (Na, K, Rb, Cs, Ag, and Cu) located in cavities created by linked Ce/EuS 8 polyhedra. The structures are charge-balanced when Ce and Eu are in their +4 and +2 oxidation states, respectively. The effective magnetic moment of Ce 1.50 4+ Eu 1.50 2+ CuSiS 7 determined from the temperature dependence of the magnetic susceptibility data is consistent with the presence of Ce 4+ and Eu 2+ . Clear correlations between the alkali ion site occupancy, the ionic radius of the alkali cations, and the average bond length of Ce 4+ /Eu 2+ –S, were established. UV–vis diffuse reflectance data were collected for Ce 1.50 4+ Eu 1.50 2+ CuSiS 7 and a band gap of 1.9(1) eV was established.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Structural insights into transcriptional regulation by the helicase RECQL5

Abstract Transcription poses a major challenge for genome stability. The RECQL5 helicase helps safeguard genome integrity and is the only member of the human RecQ helicase family that directly binds to RNA polymerase II (Pol II) and affects its progression. While RECQL5 mitigates transcription stress in cells, the molecular mechanism underlying this phenomenon is unclear. Here, we use cryo-electron microscopy to determine the structures of stalled human Pol II elongation complexes (ECs) bound to RECQL5. Our structures reveal the molecular interactions stabilizing RECQL5 binding to the Pol II EC and highlight its role as a transcriptional roadblock. Additionally, we find that, in its nucleotide-free state, RECQL5 twists the downstream DNA in the EC and, upon nucleotide binding, undergoes a conformational change that allosterically induces Pol II toward a post-translocation state. We propose that this mechanism may help restart Pol II elongation and, therefore, contribute to reducing transcription stress.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Iridate Li8IrO 6 : An Antiferromagnetic Insulator

In this work, a polycrystalline iridate Li 8 IrO 6 material was prepared via heating Li 2 O and IrO 2 starting materials in a sealed quartz tube at 650 °C for 48 h. The structure was determined from Rietveld refinement of room-temperature powder neutron diffraction data. Li 8 IrO 6 adopts the nonpolar space group $R\bar{3}$ with Li atoms occupying the tetrahedral and octahedral sites, which is supported by the electron diffraction and solid-state 7Li NMR. This results in a crystal structure consisting of LiO 4 tetrahedral layers alternating with mixed IrO 6 and LiO 6 octahedral layers along the crystallographic c -axis. The +4 oxidation state of Ir 4+ was confirmed by near-edge X-ray absorption spectroscopy. An in situ synchrotron X-ray diffraction study of Li 8 IrO 6 indicates that the sample is stable up to 1000 °C and exhibits no structural transitions. Magnetic measurements suggest long-range antiferromagnetic ordering with a Néel temperature (TN) of 4 K, which is corroborated by heat capacity measurements. The localized effective moment $μ_{\text{eff}}$ (Ir) = 1.73 $μ_{\text{B}}$ and insulating character indicate that Li 8 IrO 6 is a correlated insulator. First-principles calculations support the nonpolar crystal structure and reveal the insulating behavior both in paramagnetic and antiferromagnetic states.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Importance of nuclear quantum effects on the hydration of chloride ion

Path-integral ab initio molecular dynamics (PI-AIMD) calculations have been employed to probe the nature of chloride ion solvation in aqueous solution. Nuclear quantum effects (NQEs) are shown to weaken hydrogen bonding between the chloride anion and the solvation shell of water molecules. As a consequence, the disruptive effect of the anion on the solvent water structure is significantly reduced compared to what is found in the absence of NQEs. Additionally, the chloride hydration structure obtained from PI-AIMD agrees well with information extracted from neutron scattering data. In particular, the observed satellite peak in the hydrogen-chloride-hydrogen triple angular distribution serves as a clear signature of NQEs. The present results suggest that NQEs are likely to play a crucial role in determining the structure of saline solutions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Systems, methods and patches for monitoring a structural health of a connector in overhead transmission lines

Systems, methods and piezoelectric patches are provided for monitoring the structural health of connectors in overhead transmission lines. A plurality of piezoelectric patches is mounted to different locations on the connector. At least one of the patches is actuated using an AC voltage and certain electrical properties either from the same patch or of a different patch are evaluated over time to determine the structural health of the connectors.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Short-range magnetic order and planar anisotropy in the topological ferrimagnet Mn 3 ⁢Si 2 ⁢Te 6

Mn 3 ⁢Si 2 ⁢Te 6 is a ferrimagnetic topological nodal-line semiconductor that exhibits unconventional colossal magnetoresistance behavior, with short-range spin fluctuations being potentially intimately linked to the emergent properties. Here we determine the short-range magnetic order and anisotropy through total neutron scattering and polarized neutron powder diffraction measurements on polycrystalline Mn 3 ⁢Si 2⁢ Te 6 . Strong in-plane anisotropy is quantified on the Mn ions through extraction of the local site susceptibility tensor. Here, the real-space local spin structure is determined through the application of magnetic pair distribution function analysis covering a wide temperature range. Short-range order over a locally frustrated trimer of three nearest neighbors is found to exist well above the long-range ferrimagnetic transition.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging

One of the outstanding analytical problems in X-ray single-particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and the fact that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. Proposed here are two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA), provides a rough classification which is essentially parameter free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs), can generate 3D structures of the objects at any point in the structural landscape. Both these methods are implemented in combination with the noise-tolerant expand–maximize–compress (EMC) algorithm and its utility is demonstrated by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern. Both discrete structural classes and continuous deformations are recovered. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility of moving beyond the study of homogeneous sample sets to addressing open questions on topics such as nanocrystal growth and dynamics, as well as phase transitions which have not been externally triggered.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine

Abstract The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic‐level three‐dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB‐101 was launched to support teachers, students, and the general public in PDB archive exploration ( pdb101.rcsb.org ). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB‐101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB‐101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year‐on‐year. In addition, PDB‐101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB‐101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.

Zardecki, Christine↗
DOE OSTI2020

Structural signatures in EPR3 define a unique class of plant carbohydrate receptors

Abstract Receptor-mediated perception of surface-exposed carbohydrates like lipo- and exo-polysaccharides (EPS) is important for non-self recognition and responses to microbial associated molecular patterns in mammals and plants. In legumes, EPS are monitored and can either block or promote symbiosis with rhizobia depending on their molecular composition. To establish a deeper understanding of receptors involved in EPS recognition, we determined the structure of the Lotus japonicus ( Lotus ) exopolysaccharide receptor 3 (EPR3) ectodomain. EPR3 forms a compact structure built of three putative carbohydrate-binding modules (M1, M2 and LysM3). M1 and M2 have unique βαββ and βαβ folds that have not previously been observed in carbohydrate binding proteins, while LysM3 has a canonical βααβ fold. We demonstrate that this configuration is a structural signature for a ubiquitous class of receptors in the plant kingdom. We show that EPR3 is promiscuous, suggesting that plants can monitor complex microbial communities though this class of receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Investigation of porous polydimethylsiloxane structures with tunable properties induced by the phase separation technique

This article reports the fabrication and characterization of porous polydimethylsiloxane (PDMS) structures developed by the solvent evaporationinduced phase separation technique. Here, ternary systems containing water/ tetrahydrofuran (THF)/PDMS with various concentrations are produced to form a stable solution. The porous PDMS structures are formed by removing the solvent (THF) and nonsolvent (water) phases during the stepping heat treatment procedure. The analytical ternary phase diagram is constructed based on the thermodynamic equilibrium state in the polymer solution to explain the stable/unstable formulations and the possible composition change path. The results show that the isolated pores with the adjustable pore size ranging from 330 to 1900 μm are obtained by tuning the water to the THF ratio. The mechanical properties of the porous PDMS structures are determined by conducting the tensile tests on the prepared dog bone-shaped specimens. A wide range of elastic modulus ranging between 0.49 and 1.05 MPa was achieved without affecting the density of the porous sample by adjusting the solvent and non-solvent content in the solution. It is shown that the flexibility of the porous structures can be improved by reducing the ratio of water to THF and decreasing the PDMS content. The porosity measurements reveal that the PDMS concentration is the major phase controlling the porosity of the structure, while the effect of water/THF is negligible.

42 ENGINEERING↗
DOE OSTI2022

G4Boost: a machine learning-based tool for quadruplex identification and stability prediction

Background: G-quadruplexes (G4s), formed within guanine-rich nucleic acids, are secondary structures involved in important biological processes. Although every G4 motif has the potential to form a stable G4 structure, not every G4 motif would, and accurate energy-based methods are needed to assess their structural stability. Here, we present a decision tree-based prediction tool, G4Boost, to identify G4 motifs and predict their secondary structure folding probability and thermodynamic stability based on their sequences, nucleotide compositions, and estimated structural topologies. Results: G4Boost predicted the quadruplex folding state with an accuracy greater then 93% and an F1-score of 0.96, and the folding energy with an RMSE of 4.28 and R 2 of 0.95 only by the means of sequence intrinsic feature. G4Boost was successfully applied and validated to predict the stability of experimentally-determined G4 structures, including for plants and humans. Conclusion: G4Boost outperformed the three machine-learning based prediction tools, DeepG4, Quadron, and G4RNA Screener, in terms of both accuracy and F1-score, and can be highly useful for G4 prediction to understand gene regulation across species including plants and humans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural basis of LAIR1 targeting by polymorphic Plasmodium RIFINs

RIFIN, a large family of Plasmodium variant surface antigens, plays a crucial role in malaria pathogenesis by mediating immune suppression through activation of inhibitory receptors such as LAIR1, and antibodies with LAIR1 inserts have been identified that bind infected erythrocytes through RIFIN. However, details of RIFIN-mediated LAIR1 recognition and receptor activation have been unclear. Here, we use negative-stain EM to define the architecture of LAIR1-inserted antibodies and determine crystal structures of RIFIN-variable 2 (V2) domain in complex with a LAIR1 domain. These structures reveal the LAIR1-binding region of RIFIN to be hydrophobic and membrane-distal, to exhibit extensive structural diversity, and to interact with RIFIN-V2 in a one-to-one fashion. Through structural and sequence analysis of various LAIR1 constructs, we identify essential elements of RIFIN-binding on LAIR1. Furthermore, a structure-derived LAIR1-binding sequence signature ascertained >20 LAIR1-binding RIFINs, including some from P. falciparum field strains and Plasmodium species infecting gorillas and chimpanzees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

HVEM structures and mutants reveal distinct functions of binding to LIGHT and BTLA/CD160

HVEM is a TNF (tumor necrosis factor) receptor contributing to a broad range of immune functions involving diverse cell types. It interacts with a TNF ligand, LIGHT, and immunoglobulin (Ig) superfamily members BTLA and CD160. Assessing the functional impact of HVEM binding to specific ligands in different settings has been complicated by the multiple interactions of HVEM and HVEM binding partners. To dissect the molecular basis for multiple functions, we determined crystal structures that reveal the distinct HVEM surfaces that engage LIGHT or BTLA/CD160, including the human HVEM–LIGHT–CD160 ternary complex, with HVEM interacting simultaneously with both binding partners. Based on these structures, we generated mouse HVEM mutants that selectively recognized either the TNF or Ig ligands in vitro. Knockin mice expressing these muteins maintain expression of all the proteins in the HVEM network, yet they demonstrate selective functions for LIGHT in the clearance of bacteria in the intestine and for the Ig ligands in the amelioration of liver inflammation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Ammonothermal Synthesis, Crystal Structure, and Vibrational Properties of the Doubly Deprotonated Calcium Guanidinate, CaC(NH) 3

We report the synthesis of the doubly deprotonated calcium guanidinate, CaC(NH) 3 , from liquid ammonia and its crystal structure as determined from powder X‐ray and neutron diffraction, and confirmed using CNH elemental analysis and infrared (IR) spectroscopy data. CaC(NH) 3 crystallizes in the hexagonal system with space group P 6 3 / m (no. 176) with Z = 2 and a = 5.2666(13) Å, c = 6.5881(6) Å and V = 158.25(4) Å 3 . We also compare the structural similarities and differences of this phase with the isotypical strontium and ytterbium compounds.

Ogutu, George↗