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All sources NASA NTRS DOE OSTI

DOE OSTI2023

Modular adjuvant-free pan-HLA-DR-immunotargeting subunit vaccine against SARS-CoV-2 elicits broad sarbecovirus-neutralizing antibody responses

Subunit vaccines typically require co-administration with an adjuvant to elicit protective immunity, adding development hurdles that can impede rapid pandemic responses. To circumvent the need for adjuvant in a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) subunit vaccine, we engineer a thermostable immunotargeting vaccine (ITV) that leverages the pan-HLA-DR monoclonal antibody 44H10 to deliver the viral spike protein receptor-binding domain (RBD) to antigen-presenting cells. X-ray crystallography shows that 44H10 binds to a conserved epitope on HLA-DR, providing the basis for its broad HLA-DR reactivity. Adjuvant-free ITV immunization in rabbits and ferrets induces robust anti-RBD antibody responses that neutralize SARS-CoV-2 variants of concern and protect recipients from SARS-CoV-2 challenge. We demonstrate that the modular nature of the ITV scaffold with respect to helper T cell epitopes and diverse RBD antigens facilitates broad sarbecovirus neutralization. Our findings support anti-HLA-DR immunotargeting as an effective means to induce strong antibody responses to subunit antigens without requiring an adjuvant.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Colloidal immobilized protein based on stable colloid of TiO 2 nanoparticles at neutral pH for protein microarray

A stable colloid of titanium dioxide nanoparticles was specially prepared at neutral pH so that horse radish peroxidase as a model protein can interact and be immobilized with colloidal titanium dioxide nanoparticles, while usually titanium dioxide colloid is only stable at acidic condition. Colloidal immobilized peroxidase based on titanium dioxide nanoparticles at neutral pH were highly active and stably dispersible in aqueous solution. The resulting colloidal immobilized peroxidase can be readily printed using a standard microarray printer for facile fabrication of protein microarrays. After printing, the colloidal immobilized protein formed uniform membrane of proteinated nanoparticles with 3-dimensional nanoconfiguration. Finally, the protein microarray sensitivity based on peroxidase-titanium dioxide nanoparticles was nearly 20 times as high as that using conventional technology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity

Most antibodies isolated from individuals with coronavirus disease 2019 (COVID-19) are specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, COVA1-16 is a relatively rare antibody that also cross-neutralizes SARS-CoV. Here, we determined a crystal structure of the COVA1-16 antibody fragment (Fab) with the SARS-CoV-2 receptor-binding domain (RBD) and negative-stain electron microscopy reconstructions with the spike glycoprotein trimer to elucidate the structural basis of its cross-reactivity. COVA1-16 binds a highly conserved epitope on the SARS-CoV-2 RBD, mainly through a long complementarity-determining region (CDR) H3, and competes with the angiotensin-converting enzyme 2 (ACE2) receptor because of steric hindrance rather than epitope overlap. COVA1-16 binds to a flexible up conformation of the RBD on the spike and relies on antibody avidity for neutralization. These findings, along with the structural and functional rationale for epitope conservation, provide insights for development of more universal SARS-like coronavirus vaccines and therapies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Epstein-Barr virus gH/gL has multiple sites of vulnerability for virus neutralization and fusion inhibition

Epstein-Barr virus (EBV) is nearly ubiquitous in adults. EBV causes infectious mononucleosis and is associated with B cell lymphomas, epithelial cell malignancies, and multiple sclerosis. The EBV gH/gL glycoprotein complex facilitates fusion of virus membrane with host cells and is a target of neutralizing antibodies. Here, in this study, we examined the sites of vulnerability for virus neutralization and fusion inhibition within EBV gH/gL. We developed a panel of human monoclonal antibodies (mAbs) that targeted five distinct antigenic sites on EBV gH/gL and prevented infection of epithelial and B cells. Structural analyses using X-ray crystallography and electron microscopy revealed multiple sites of vulnerability and defined the antigenic landscape of EBV gH/gL. One mAb provided near-complete protection against viremia and lymphoma in a humanized mouse EBV challenge model. Our findings provide structural and antigenic knowledge of the viral fusion machinery, yield a potential therapeutic antibody to prevent EBV disease, and emphasize gH/gL as a target for herpesvirus vaccines and therapeutics.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Carbon neutral manufacturing via on-site CO 2 recycling

The chemical industry needs to significantly decrease carbon dioxide (CO 2 ) emissions in order to meet the 2050 carbon neutrality goal. Utilization of CO 2 as a chemical feedstock for bulk products is a promising way to mitigate industrial emissions; however, CO 2 -based manufacturing is currently not competitive with the established petrochemical methods and its deployment requires creation of a new value chain. Here, we show that an alternative approach, using CO 2 conversion as an add-on to existing manufactures, can disrupt the global carbon cycle while minimally perturbing the operation of chemical plants. Proposed closed-loop on-site CO 2 recycling processes are economically viable in the current market and have the potential for rapid introduction in the industries. Retrofit-based CO 2 recycling can reduce annually between 4 and 10 Gt CO 2 by 2050 and contribute to achieving up to 50% of the industrial carbon neutrality goal.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2022

Neutral-current neutrino cross section and expected supernova signals for 40 Ar from a three-fold increase in the magnetic dipole strength

In view of the great interest in liquid argon neutrino detectors, the 40 Ar(γ,γ') 40 Ar reaction was revisited to guide a calculation of the neutral current neutrino cross section at supernova energies. Using the nuclear resonance fluorescence technique with a monoenergetic, 99% linearly polarized photon beam, in this work we report a three-fold increase in magnetic dipole strength at around 10 MeV in 40 Ar. Based on shell-model calculations, and using the experimentally identified transitions, the neutral current neutrino cross sections for low-energy reactions on 40 Ar are calculated.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Search for a new heavy resonance decaying to a top quark and a neutral scalar boson in proton-proton collisions at $\sqrt{s}$ = 13 TeV

A first search at the LHC for a new heavy resonance decaying to a top quark and a neutral scalar boson ϕ in the fully hadronic final state is presented, where the ϕ boson is identified by its decay into a bottom quark-antiquark pair. The search is focused on final states in which the decay products of the highly Lorentz boosted top quark and ϕ boson are each reconstructed as a single, large-radius jet with distinct substructure. The analysis is performed using proton-proton collision data at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 138 fb −1 , recorded with the CMS detector at the LHC in 2016–2018. The single production of a vector-like top quark, T′, is used as a benchmark model for the signal process. The results of this search are combined with those of a previous CMS search in which semileptonic decays of the top quark were used. No significant excess of data is observed with respect to the background prediction. For the case where the neutral scalar is a standard model Higgs boson and the T′ quark width is 5% of its mass, T′ quark masses between 0.85 and 1.3 TeV are excluded at 95% confidence level and the most stringent limits to date are set for masses above 2 TeV . For other ϕ boson masses, upper limits as low as 0.1 fb are set on the product of the T′ quark production cross section and branching fraction for its decay to a top quark and a ϕ boson.

Boosted↗

DOE OSTI2023

Binding of Li + to Negatively Charged and Neutral Ligands in Polymer Electrolytes

Conceptually, single-ion polymer electrolytes (SIPE) with the anion bound to the polymer could solve major issues in Li-ion batteries, but their conductivity is too low. Experimentally, weakly interacting anionic groups have the best conductivity. To provide a theoretical basis for this result, density functional theory calculations of the optimized geometries and energies are performed for charged ligands used in SIPE. Comparison is made to neutral ligands found in dual-ion conductors, which demonstrate higher conductivity. Further, the free energy differences between adding and subtracting a ligand are small enough for the neutral ligands to have the conductivity seen experimentally. However, charged ligands have large barriers, implying that lithium transport will coincide with the slow polymer diffusion, as observed in experiments. Overall, SIPE will require additional solvent to achieve a sufficiently high conductivity. Additionally, the binding of mono- and bidentate geometries varies, providing a simple and clear reason that polarizable force fields are required for detailed interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Oxide-Encapsulated Ruthenium Oxide Catalysts for Selective Oxygen Evolution in Unbuffered pH-Neutral Seawater

Direct seawater electrolysis is a promising approach to producing green hydrogen in water-scarce environments using renewable energy. However, the undesirable chlorine evolution reaction and hypochlorite evolution reaction compete with the desired oxygen evolution reaction (OER) at the anode electrocatalyst. This issue is most pronounced in unbuffered pH-neutral solutions due to local acidification resulting from the OER. To overcome this challenge, this study provides a comprehensive evaluation of the use of silicon oxide (SiO x ) and titanium oxide (TiO x ) nanoscale overlayers coated on metallic ruthenium (Ru) and ruthenium oxide (RuO x ) thin film electrodes and their ability to block chloride ions from reaching active sites during operation in an unbuffered 0.6 M NaCl electrolyte. Using a combination of (electro)analytical techniques, encapsulated RuO x anodes are shown to effectively suppress Cl - transport to buried catalyst active sites while allowing for the desired OER to occur, leading to increases in OER faradaic efficiency at moderate overpotentials. Evidence for the ability of SiO x overlayers to block Cl - ions from reaching the active buried interface was obtained by monitoring the ν(O-H) stretching mode of OH adsorbates using in situ Raman spectroscopy. Here, this study also reports trade-offs between the activity, selectivity, and stability of bare and encapsulated Ru and RuO x electrocatalysts, finding that the magnitude of these trade-offs strongly depends on the complex interplay between electrode architecture, material properties, and catalytic performance, especially in unbuffered pH-neutral seawater.

58 GEOSCIENCES↗

DOE OSTI2022

Neutral Loss Mass Spectral Data Enhances Molecular Similarity Analysis in $\mathrm{METLIN}$

We report Neutral loss (NL) spectral data presents a mirror of MS 2 data and is a valuable yet largely untapped resource for molecular discovery and similarity analysis. Tandem mass spectrometry (MS 2 ) data is effective for the identification of known molecules and the putative identification of novel, previously uncharacterized molecules (unknowns). Yet, MS 2 data alone is limited in characterizing structurally related molecules. To facilitate unknown identification and complement the METLIN-MS 2 fragment ion database for characterizing structurally related molecules, we have created a MS 2 to NL converter as a part of the METLIN platform. The converter has been used to transform METLIN’s MS 2 data into a neutral loss database (METLIN-NL) on over 860 000 individual molecular standards. The platform includes both the MS 2 to NL converter and a graphical user interface enabling comparative analyses between MS 2 and NL data. Examples of NL spectral data are shown with oxylipin analogues and two structurally related statin molecules to demonstrate NL spectra and their ability to help characterize structural similarity. Mirroring MS 2 data to generate NL spectral data offers a unique dimension for chemical and metabolite structure characterization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Carbon‐Neutral Pathways for the United States

Abstract The Intergovernmental Panel on Climate Change (IPCC) Special Report on Global Warming of 1.5°C points to the need for carbon neutrality by mid‐century. Achieving this in the United States in only 30 years will be challenging, and practical pathways detailing the technologies, infrastructure, costs, and tradeoffs involved are needed. Modeling the entire U.S. energy and industrial system with new analysis tools that capture synergies not represented in sector‐specific or integrated assessment models, we created multiple pathways to net zero and net negative CO 2 emissions by 2050. They met all forecast U.S. energy needs at a net cost of 0.2–1.2% of GDP in 2050, using only commercial or near‐commercial technologies, and requiring no early retirement of existing infrastructure. Pathways with constraints on consumer behavior, land use, biomass use, and technology choices (e.g., no nuclear) met the target but at higher cost. All pathways employed four basic strategies: energy efficiency, decarbonized electricity, electrification, and carbon capture. Least‐cost pathways were based on >80% wind and solar electricity plus thermal generation for reliability. A 100% renewable primary energy system was feasible but had higher cost and land use. We found multiple feasible options for supplying low‐carbon fuels for non‐electrifiable end uses in industry, freight, and aviation, which were not required in bulk until after 2035. In the next decade, the actions required in all pathways were similar: expand renewable capacity 3.5 fold, retire coal, maintain existing gas generating capacity, and increase electric vehicle and heat pump sales to >50% of market share. This study provides a playbook for carbon neutrality policy with concrete near‐term priorities.

Williams, James H.↗

DOE OSTI2020

Scalable neutral H 2 O 2 electrosynthesis by platinum diphosphide nanocrystals by regulating oxygen reduction reaction pathways

Despite progress in small scale electrocatalytic production of hydrogen peroxide (H 2 O 2 ) using a rotating ring-disk electrode, further work is needed to develop a non-toxic, selective, and stable O 2 -to-H 2 O 2 electrocatalyst for realizing continuous on-site production of neutral hydrogen peroxide. We report ultrasmall and monodisperse colloidal PtP 2 nanocrystals that achieve H 2 O 2 production at near zero-overpotential with near unity H 2 O 2 selectivity at 0.27 V vs. RHE. Density functional theory calculations indicate that P promotes hydrogenation of OOH* to H 2 O 2 by weakening the Pt-OOH* bond and suppressing the dissociative OOH* to O* pathway. Atomic layer deposition of Al 2 O 3 prevents NC aggregation and enables application in a polymer electrolyte membrane fuel cell (PEMFC) with a maximum r(H 2 O 2 ) of 2.26 mmol h -1 cm -2 and a current efficiency of 78.8% even at a high current density of 150 mA cm -2 . Catalyst stability enables an accumulated neutral H 2 O 2 concentration in 600 mL of 3.0 wt% (pH = 6.6).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

A glycoprotein B-neutralizing antibody structure at 2.8 Å uncovers a critical domain for herpesvirus fusion initiation

Members of the Herpesviridae, including the medically important alphaherpesvirus varicella-zoster virus (VZV), induce fusion of the virion envelope with cell membranes during entry, and between cells to form polykaryocytes in infected tissues. The conserved glycoproteins, gB, gH and gL, are the core functional proteins of the herpesvirus fusion complex. gB serves as the primary fusogen via its fusion loops, but functions for the remaining gB domains remain unexplained. As a pathway for biological discovery of domain function, our approach used structure-based analysis of the viral fusogen together with a neutralizing antibody. We report here a 2.8 Å cryogenic-electron microscopy structure of native gB recovered from VZV-infected cells, in complex with a human monoclonal antibody, 93k. This high-resolution structure guided targeted mutagenesis at the gB-93k interface, providing compelling evidence that a domain spatially distant from the gB fusion loops is critical for herpesvirus fusion, revealing a potential new target for antiviral therapies. Herpesvirus virions have an outer lipid membrane dotted with glycoproteins that enable fusion with cell membranes to initiate entry and establish infection. Here the authors elucidate the structural mechanism of a neutralizing antibody derived from a patient infected by the herpesvirus varicella-zoster virus and targeted to its fusogen, glycoprotein-B.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography

Single-domain Variable New Antigen Receptors (VNARs) from the immune system of sharks are the smallest naturally occurring binding domains found in nature. Possessing flexible paratopes that can recognize protein motifs inaccessible to classical antibodies, VNARs have yet to be exploited for the development of SARS-CoV-2 therapeutics. Here, we detail the identification of a series of VNARs from a VNAR phage display library screened against the SARS-CoV-2 receptor binding domain (RBD). The ability of the VNARs to neutralize pseudotype and authentic live SARS-CoV-2 virus rivalled or exceeded that of full-length immunoglobulins and other single-domain antibodies. Crystallographic analysis of two VNARs found that they recognized separate epitopes on the RBD and had distinctly different mechanisms of virus neutralization unique to VNARs. Structural and biochemical data suggest that VNARs would be effective therapeutic agents against emerging SARS-CoV-2 mutants, including the Delta variant, and coronaviruses across multiple phylogenetic lineages. This study highlights the utility of VNARs as effective therapeutics against coronaviruses and may serve as a critical milestone for nearing a paradigm shift of the greater biologic landscape.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Accurate determination of solvation free energies of neutral organic compounds from first principles

The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity

Despite rapid and ongoing vaccine and therapeutic development, SARS-CoV-2 continues to evolve and evade, presenting a need for next-generation diverse therapeutic modalities. Here we show that nurse sharks immunized with SARS-CoV-2 recombinant receptor binding domain (RBD), RBD-ferritin (RFN), or spike protein ferritin nanoparticle (SpFN) immunogens elicit a set of new antigen receptor antibody (IgNAR) molecules that target two non-overlapping conserved epitopes on the spike RBD. Representative shark antibody variable NAR-Fc chimeras (ShAbs) targeting either of the two epitopes mediate cell-effector functions, with high affinity to all SARS-CoV-2 viral variants of concern, including the divergent Omicron strains. The ShAbs potently cross-neutralize SARS-CoV-2 WA-1, Alpha, Beta, Delta, Omicron BA.1 and BA.5, and SARS-CoV-1 pseudoviruses, and confer protection against SARS-CoV-2 challenge in the K18-hACE2 transgenic mouse model. Structural definition of the RBD-ShAb01-ShAb02 complex enabled design and production of multi-specific nanobodies with enhanced neutralization capacity, and picomolar affinity to divergent sarbecovirus clade 1a, 1b and 2 RBD molecules. These shark nanobodies represent potent immunotherapeutics both for current use, and future sarbecovirus pandemic preparation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

A single nanobody neutralizes multiple epochally evolving human noroviruses by modulating capsid plasticity

Acute gastroenteritis caused by human noroviruses (HuNoVs) is a significant global health and economic burden and is without licensed vaccines or antiviral drugs. The GII.4 HuNoV causes most epidemics worldwide. This virus undergoes epochal evolution with periodic emergence of variants with new antigenic profiles and altered specificity for histo-blood group antigens (HBGA), the determinants of cell attachment and susceptibility, hampering the development of immunotherapeutics. Here, we show that a llama-derived nanobody M4 neutralizes multiple GII.4 variants with high potency in human intestinal enteroids. The crystal structure of M4 complexed with the protruding domain of the GII.4 capsid protein VP1 revealed a conserved epitope, away from the HBGA binding site, fully accessible only when VP1 transitions to a “raised” conformation in the capsid. Together with dynamic light scattering and electron microscopy of the GII.4 VLPs, our studies suggest a mechanism in which M4 accesses the epitope by altering the conformational dynamics of the capsid and triggering its disassembly to neutralize GII.4 infection.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Influence of the broadly neutralizing antibody VRC01 on HIV breakthrough virus populations in antibody-mediated prevention trials

In the antibody mediated prevention (AMP) trials, the broadly neutralizing antibody (bNAb) VRC01 demonstrated protective efficacy against susceptible HIV strains. To understand how VRC01 shaped breakthrough infections, deep sequencing was performed on 172 participants (>100,000 gag-Δpol and rev-env-Δnef sequences), at diagnosis and over time, in the placebo and treatment arms of the African (HVTN703/HPTN081; NCT02568215) and Americas/Europe (HVTN704/HPTN085; NCT02716675) cohorts. A high frequency of multilineage infections was detected (38%), including co-infection with both VRC01 sensitive and resistant viruses. This high frequency is largely accounted for by low-abundance lineages. Although VRC01 does not significantly affect the genetic transmission bottleneck compared to placebo, higher VRC01 doses trend towards greater VRC01 neutralization differences among co-infecting lineages. Two-thirds of multilineage infections showed evidence of recombination at the diagnostic timepoint. In the treatment group there is evidence of recombinant viruses preferentially inheriting resistance-associated mutations. This study provides critical insights into viral genetic and antigenic diversity that needs to be targeted to achieve protection, and highlights the role of recombination in facilitating escape.

59 BASIC BIOLOGICAL SCIENCES↗