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At least 199 records · Page 11

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DOE OSTI2021

Cryo-EM structures of HIV-1 trimer bound to CD4-mimetics BNM-III-170 and M48U1 adopt a CD4-bound open conformation

Human immunodeficiency virus-1 (HIV-1), the causative agent of AIDS, impacts millions of people. Entry into target cells is mediated by the HIV-1 envelope (Env) glycoprotein interacting with host receptor CD4, which triggers conformational changes allowing binding to a coreceptor and subsequent membrane fusion. Small molecule or peptide CD4-mimetic drugs mimic CD4’s Phe43 interaction with Env by inserting into the conserved Phe43 pocket on Env subunit gp120. Here, we present single-particle cryo-EM structures of CD4-mimetics BNM-III-170 and M48U1 bound to a BG505 native-like Env trimer plus the CD4-induced antibody 17b at 3.7 Å and 3.9 Å resolution, respectively. CD4-mimetic-bound BG505 exhibits canonical CD4-induced conformational changes including trimer opening, formation of the 4-stranded gp120 bridging sheet, displacement of the V1V2 loop, and formation of a compact and elongated gp41 HR1C helical bundle. We conclude that CD4-induced structural changes on both gp120 and gp41 Env subunits are induced by binding to the gp120 Phe43 pocket.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage

Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In some individuals broadly neutralizing antibodies develop to recognize rapidly mutating pathogens with extensive sequence diversity. Vaccine design for pathogens such as HIV-1 and influenza has therefore focused on recapitulating the natural affinity maturation process. Here, we determine structures of antibodies in complex with HIV-1 Envelope for all observed members and ancestral states of the broadly neutralizing HIV-1 V3-glycan targeting DH270 antibody clonal B cell lineage. These structures track the development of neutralization breadth from the unmutated common ancestor and define affinity maturation at high spatial resolution. By elucidating contacts mediated by key mutations at different stages of antibody development we identified sites on the epitope-paratope interface that are the focus of affinity optimization. Thus, our results identify bottlenecks on the path to natural affinity maturation and reveal solutions for these that will inform immunogen design aimed at eliciting a broadly neutralizing immune response by vaccination.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Adaptative Survival of Aspergillus fumigatus to Echinocandins Arises from Cell Wall Remodeling Beyond β-1,3-glucan Synthesis Inhibition

Antifungal echinocandins inhibit the biosynthesis of β-1,3-glucan, a major and essential polysaccharide component of the fungal cell wall. However, the efficacy of echinocandins against the pathogen Aspergillus fumigatus is limited. Here, we use solid-state nuclear magnetic resonance (ssNMR) and other techniques to show that echinocandins induce dynamic changes in the assembly of mobile and rigid polymers within the A. fumigatus cell wall. The reduction of β-1,3- glucan induced by echinocandins is accompanied by a concurrent increase in levels of chitin, chitosan and highly polymorphic α-1,3-glucans, whose physical association with chitin maintains cell wall integrity and modulates water permeability. The rearrangement of the macromolecular network is dynamic and controls the permeability and circulation of the drug throughout the cell wall. Thus, our results indicate that echinocandin treatment triggers compensatory rearrangements in the cell wall that may help A. fumigatus to tolerate the drugs’ antifungal effects.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Dual blockade of IL-10 and PD-1 leads to control of SIV viral rebound following analytical treatment interruption

Human immunodeficiency virus (HIV) persistence during antiretroviral therapy (ART) is associated with heightened plasma interleukin-10 (IL-10) levels and PD-1 expression. We hypothesized that IL-10 and PD-1 blockade would lead to control of viral rebound following analytical treatment interruption (ATI). Twenty-eight ART-treated, simian immunodeficiency virus (SIV)mac 239 -infected rhesus macaques (RMs) were treated with anti-IL-10, anti-IL-10 plus anti-PD-1 (combo) or vehicle. ART was interrupted 12 weeks after introduction of immunotherapy. Durable control of viral rebound was observed in nine out of ten combo-treated RMs for >24 weeks post-ATI. Induction of inflammatory cytokines, proliferation of effector CD8 + T cells in lymph nodes and reduced expression of BCL-2 in CD4 + T cells pre-ATI predicted control of viral rebound. Twenty-four weeks post-ATI, lower viral load was associated with higher frequencies of memory T cells expressing TCF-1 and of SIV-specific CD4 + and CD8 + T cells in blood and lymph nodes of combo-treated RMs. These results map a path to achieve long-lasting control of HIV and/or SIV following discontinuation of ART.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS

Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish, E. coli and few other organisms. However, a spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotated H. salinarum NRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon. Data and spectral assay libraries are available via ProteomeXchange (PXD042770, PXD042774) and SWATHAtlas (SAL00312-SAL00319).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

A non-canonical fungal peroxisome PTS-1 signal, SYM, and its evolutionary aspects

Abstract Proteins localized to peroxisomes, particularly those expressed under specific conditions or in low abundance, are often undetected by routine proteomics methods due to detection sensitivity limits. In silico identification and experimental validation of peroxisomal targeting signals (PTSs) offer a reliable alternative. We demonstrate that SYM, a non-canonical plant PTS-1 signal, functions similarly inAspergillus nidulans, as GFP tagged with a SYM C-terminal tripeptide localizes to peroxisomes. One of two nativeA. nidulansproteins with C-terminal SYM tripeptide shows weak peroxisomal localization alongside cytoplasmic presence, indicating that only a subset of proteins with non-canonical signals access peroxisomes.In silicoanalysis of 1,010 fungal genomes identified diverse SYM-proteins with variable functions, suggesting that non-canonical PTS-1 signals may evolve spontaneously. Two-thirds of SYM-proteins are predicted to localize to specific intracellular compartments other than the peroxisome. We propose that despite their predicted localization, these proteins possessing SYM as a non-canonical peroxisomal signal might also have peroxisomal presence. Among SYM-proteins, pectinesterases, known plant pathogen virulence factors, were frequent. Notably, 25% of fungal pectinesterases harbor non-canonical PTS-1 signals, suggesting that partial peroxisomal localization of pectinesterases has evolved convergently. This suggests that partial peroxisomal localization may enhance protein functional flexibility, contributing to the organism’s adaptability.

Science & Technology - Other Topics↗

DOE OSTI2020

An analytic asymmetric-piston model for the impact of mode-1 shell asymmetry on ICF implosions

For many years, low mode asymmetry in inertially confined fusion (ICF) implosions has been recognized as a potential performance limiting factor, but analysis has been limited to using simulations and searching for data correlations. In this paper, an analytically solvable model based upon the simple picture of an asymmetric piston is presented. Asymmetry of the shell driving the implosion, as opposed to asymmetry in the hot-spot, is key to the model. The model provides a unifying framework for the action of mode-1 shell asymmetry and the resulting connections between various diagnostic signatures. A key variable in the model is the shell asymmetry fraction, f, which is related to the areal density variation of the shell surrounding the hot-spot. It is shown that f is simply related to the observed hot-spot mode-1 velocity and to the concept of residual energy in an implosion. The model presented in this paper yields explicit expressions for the hot-spot diameter, stagnation pressure, hot-spot energy, inertial confinement-time, Lawson parameter, hot-spot temperature, and fusion yield under the action of mode-1 asymmetry. Agreement is found between the theory scalings when compared to ICF implosion data from the National Ignition Facility and to large ensembles of detailed simulations, making the theory a useful tool for interpreting data. The theory provides a basis for setting tolerable limits on asymmetry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Precise equilibrium structures of 1 H - and 2 H -1,2,3-triazoles (C 2 H 3 N 3 ) by millimeter-wave spectroscopy

The 1H- and 2H-1,2,3-triazoles are isomeric five-membered ring, aromatic heterocycles that may undergo chemical equilibration by virtue of intramolecular hydrogen migration (tautomerization). Using millimeter-wave spectroscopy in the 130–375 GHz frequency range, we measured the spectroscopic constants for thirteen 1H-1,2,3-triazole and sixteen 2H-1,2,3-triazole isotopologues. Herein, we provide highly accurate and highly precise semi-experimental equilibrium (r e SE ) structures for the two tautomers based on the spectroscopic constants of each set of isotopologues, together with vibration–rotation interaction and electron-mass distribution corrections calculated using coupled-cluster singles, doubles, and perturbative triples calculations [CCSD(T)/cc-pCVTZ]. The resultant structures are compared with a “best theoretical estimate” (BTE), which has recently been shown to be in exceptional agreement with the semi-experimental equilibrium structures of other aromatic molecules. Bond distances of the 1H tautomer are determined to <0.0008 Å and bond angles to <0.2°. For the 2H tautomer, bond angles are also determined to <0.2°, but bond distances are less precise (2σ ≤ 0.0015). Finally, agreement between BTE and r e SE values is discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

The MIST-1 and MIST-2 multicusp ion sources for high-current $H$$^{+}_{2}$ beams

We present two iterations of the Multicusp Ion Source Technology at MIT (MIST) sources, designed to fulfill the requirements of the HCHC-XX cyclotron design. The HCHC-XX is a novel compact cyclotron accelerating $H$$^{+}_{2}$. Beam is injected through a radio-frequency quadrupole buncher-accelerator (embedded in the cyclotron yoke) and utilizes so-called vortex motion during acceleration. If successful, it will deliver 10 mA of protons at 60 MeV in CW mode. This scheme requires a low-emittance, high-current initial beam with high $H$$^{+}_{2}$ purity. We briefly summarize the design and previous results of the MIST-1 ion source and, for the first time, the detailed design of the new and improved MIST-2, including the mechanical, electrical, and control system design. We further show experimental results of using the MIST-2 backplate on the MIST-1 body, present a study using different types of permanent magnets for confinement (including no magnets), and finally, we present first results of the MIST-2 in full operation. In this first commissioning run, we were able to increase the total extracted current from the MIST-2 to 7 mA—a factor of 2 over the MIST-1.

Winklehner, D. [Massachusetts Institute of Technol↗

DOE OSTI2020

A molecular dynamics simulation study of thermal conductivity anisotropy in β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (β-HMX)

Molecular dynamics (MD) simulations were used to predict the thermal conductivity of β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (β-HMX) along directions normal to the (011), (110), and (010) crystal planes. These directions were selected based on the measured morphological importance of the corresponding crystal surfaces. A reverse non-equilibrium MD approach was used wherein a constant heat flux is imposed along a prescribed direction and the resulting steady-state temperature gradient determined. The coefficient of thermal conductivity λ is the quotient of heat flux and temperature gradient (i.e. Fourier's law). Finite-size effects and sensitivity to imposed heat flux were investigated. The results reveal a modest dependence of the conductivity on crystal orientation, significant finite-size effects, and low sensitivity to imposed flux so long as the Fourier's law analysis is limited to the spatial interval in the simulation cell for which the temperature gradient is constant. Infinite-length thermal conductivities were estimated by linear regression of λ -1 (L) versus reciprocal cell length L -1 for each direction. The predicted values are systematically larger, but within a factor of two, than most published experimental determinations, the latter of which were obtained for pressed-powder or composite samples rather than oriented single crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Evidence for C and Mg variations in the GD-1 stellar stream

ABSTRACT Dynamically cold stellar streams are the relics left over from globular cluster dissolution. These relics offer a unique insight into a now fully disrupted population of ancient clusters in our Galaxy. Using a combination of Gaia eDR3 proper motions, optical and near-UV colours, we select a sample of likely Red Giant Branch stars from the GD-1 stream for medium-low resolution spectroscopic follow-up. Based on radial velocity and metallicity, we are able to find 14 new members of GD-1, 5 of which are associated with the spur and blob/cocoon off-stream features. We measured C-abundances to probe for abundance variations known to exist in globular clusters. These variations are expected to manifest in a subtle way in globular clusters with such low masses ($\sim 10^4\,{\rm ~\textrm {M}_\odot }$) and metallicities ([Fe/H] ∼ −2.1 dex). We find that the C-abundances of the stars in our sample display a small but significant (3σ level) spread. Furthermore, we find ∼3σ variation in Mg-abundances among the stars in our sample that have been observed by APOGEE. These abundance patterns match the ones found in Galactic globular clusters of similar metallicity. Our results suggest that GD-1 represents another fully disrupted low-mass globular cluster where light-element abundance spreads have been found.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Spin-1 Kitaev-Heisenberg model on a honeycomb lattice

We study the Kitaev-Heisenberg model with spin-1 local degree of freedom on a honeycomb lattice numerically by the infinite density matrix renormalization group method on a cylinder geometry. By tuning the relative value of the Kitaev and Heisenberg exchange couplings, we obtain the phase diagram with two spin liquid phases and four symmetry-broken phases. Here, we identify that the spin liquid phases are gapless by calculating the central charge at the pure Kitaev points without the Heisenberg interactions. Comparing to its spin-1/2 counterpart, the position and number of gapless modes of the spin-1 case are quite different. Due to the approximate Z 2 local conservations, the expectation value of the Wilson loop operator measuring the flux of each plaquette stays near to 1, and the static spin-spin correlations remain short range in the entire spin liquid phases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Tunable Magnon Interactions in a Ferromagnetic Spin-1 Chain

NiNb 2 O 6 is an almost ideal realization of a 1D spin-1 ferromagnetic Heisenberg chain compound with weak unidirectional anisotropy. Using time-domain THz spectroscopy, we measure the low-energy electrodynamic response of NiNb 2 O 6 as a function of temperature and external magnetic field. At low temperatures, we find a magnonlike spin excitation, which corresponds to the lowest energy excitation at q ~ 0. At higher temperatures, we unexpectedly observe a temperature-dependent renormalization of the spin-excitation energy, which has a strong dependence on field direction. Using theoretical arguments, exact diagonalizations, and finite temperature dynamical Lanczos calculations, we construct a picture of magnon-magnon interactions that naturally explains the observed renormalization. In this work, we show how magnetic field strength and direction may be used to directly tune the sign of the magnon-magnon interaction. This unique scenario is a consequence of the spin-1 nature and has no analog in the more widely studied spin-1/2 systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Stereoinversion via Alcohol Dehydrogenases Enables Complete Catabolism of β-1-Type Lignin-Derived Aromatic Isomers

Sphingobium sp. strain SYK-6 is an efficient aromatic catabolic bacterium that can consume all four stereoisomers of 1,2-diguaiacylpropane-1,3-diol (DGPD), which is a ring-opened β-1-type dimer. Recently, LdpA-mediated catabolism of erythro-DGPD was reported in SYK-6, but the catabolic pathway for threo-DGPD was as yet unknown. Here, in this study, we elucidated the catabolism of threo-DGPD, which proceeds through conversion to erythro-DGPD. When threo-DGPD was incubated with SYK-6, the Cα hydroxy groups of threo-DGPD (DGPD I and II) were initially oxidized to produce the Cα carbonyl form (DGPD-keto I and II). This initial oxidation step is catalyzed by Cα-dehydrogenases, which belong to the short-chain dehydrogenase/reductase (SDR) family and are involved in the catabolism of β-O-4-type dimers. Analysis of seven candidate genes revealed that NAD + -dependent LigD and LigL are mainly involved in the conversion of DGPD I and II, respectively. Next, we found that DGPD-keto I and II were reduced to erythro-DGPD (DGPD III and IV) in the presence of NADPH. Genes involved in this reduction were sought from Cα-dehydrogenase and ldpA-neighboring SDR genes. The gene products of SLG_12690 (ldpC) and SLG_12640 (ldpB) catalyzed the NADPH-dependent conversion of DGPD-keto I to DGPD III and DGPD-keto II to DGPD IV, respectively. Mutational analysis further indicated that ldpC and ldpB are predominantly involved in the reduction of DGPD-keto. Together, these results demonstrate that SYK-6 harbors a comprehensive catabolic enzyme system to utilize all four β-1-type stereoisomers through successive oxidation and reduction reactions of the Cα hydroxy group of threo-DGPD with a net stereoinversion using multiple dehydrogenases.

09 BIOMASS FUELS↗

DOE OSTI2022

A computational study of Al n - and Al n -1 1Pt - clusters: the effects of doping and a uniform tuning gauge for single-atom nanocatalysts

Results of density functional theory calculations on Al n - and Al n -1 1Pt - , n = 2-8, clusters are presented and analyzed. The analysis includes different structural forms of the clusters characterized in terms of binding energy, spin and symmetry, and a comparative evaluation of various properties of the two systems viewed as connected through a single-Pt substitutional doping and examined in terms of their respective most stable structures. Furthermore, the Al n -1 1Pt - clusters are then used as a paradigmatic (model) case of single-atom nanocatalysts, with Pt as the catalytic center and Al n-1 as its support, to implement a uniform descriptor for gauging the tuning effects of all the parameters ( "knobs ") of a nanocatalyst that include the identity of the active center and the material and size of its support.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Water4Energy Tier-1 Raw Observations for TVA Seasonal Prediction, Version 1

Tier-1 (Step-1) raw observation staging collection for the Water4Energy Genesis Task-1 project on weeks-to-years prediction of Tennessee Valley temperature and precipitation. This data-only deposit includes CPC/PSL teleconnection indices, NOAA OISST monthly and ERSST sea-surface temperature, ERA5-derived daily 1° fields (t2m, tp, msl for 1980–2024), CFSv2 NMME ensemble-mean seasonal baselines, and a TVA boundary mask. The product supports seasonal teleconnection diagnostics and construction of AI ready-to-train packs published separately. Multi-terabyte hourly archives are excluded from this version.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Demonstration of thermal fracture limits of gas-cooled Nd:APG-1 and Tm:YLF slabs

High-energy short-pulse laser systems demonstrated to date have been limited to low repetition rates due to significant thermal management challenges associated with scaling these systems to high average power, including the need to understand the thermal fracture limits of laser gain media. In this paper, we demonstrate the thermal fracture limits of two high-average-power gain media in a realistic diode-pumped amplifier geometry: a 5 mm thick Nd:APG-1 slab and a 2 mm thick Tm:YLF slab, both cooled by room-temperature helium gas. Finite element analysis revealed maximum tensile stress at fracture of 25 ± 3 MPa for Nd:APG-1 and 30 ± 3 MPa for Tm:YLF. These stress levels correspond to average volumetric heat loads of 13 ± 1 W/cm 3 in Nd:APG-1 and 247 ± 12 W/cm 3 in Tm:YLF. Additional simulations show geometric scaling: thinner slabs tolerate higher heat loads before fracture, while larger pump spots reach the fracture stress at lower heat loads.

Lasers↗

DOE OSTI2023

New structures of Class II Fructose-1,6-Bisphosphatase from Francisella tularensis provide a framework for a novel catalytic mechanism for the entire class

Class II Fructose-1,6-bisphosphatases (FBPaseII) (EC: 3.1.3.11) are highly conserved essential enzymes in the gluconeogenic pathway of microorganisms. Previous crystallographic studies of FBPasesII provided insights into various inactivated states of the enzyme in different species. Presented here is the first crystal structure of FBPaseII in an active state, solved for the enzyme from Francisella tularensis (FtFBPaseII), containing native metal cofactor Mn 2+ and complexed with catalytic product fructose-6-phosphate (F6P). Another crystal structure of the same enzyme complex is presented in the inactivated state due to the structural changes introduced by crystal packing. Analysis of the interatomic distances among the substrate, product, and divalent metal cations in the catalytic centers of the enzyme led to a revision of the catalytic mechanism suggested previously for class II FBPases. We propose that phosphate-1 is cleaved from the substrate fructose-1,6-bisphosphate (F1,6BP) by T89 in a proximal α-helix backbone (G88-T89-T90-I91-T92-S93-K94) in which the substrate transition state is stabilized by the positive dipole of the $\langle$-helix backbone. Once cleaved a water molecule found in the active site liberates the inorganic phosphate from T89 completing the catalytic mechanism. Additionally, a crystal structure of Mycobacterium tuberculosis FBPaseII (MtFBPaseII) containing a bound F1,6BP is presented to further support the substrate binding and novel catalytic mechanism suggested for this class of enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗