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At least 343 records · Page 19

Structural Characterization of Disulfide-Linked p53-Derived Peptide Dimers

Disulfide bonds provide a convenient method for chemoselective alteration of peptide and protein structure and function. We previously reported that mild oxidation of a p53-derived bisthiol peptide (CTFANLWRLLAQNC) under dilute non-denaturing conditions led to unexpected disulfide-linked dimers as the exclusive product. The dimers were antiparallel, significantly α-helical, resistant to protease degradation, and easily reduced back to the original bisthiol peptide. Here, in this work, we examine the intrinsic factors influencing peptide dimerization using a combination of amino acid substitution, circular dichroism (CD) spectroscopy, and X-ray crystallography. CD analysis of peptide variants suggests critical roles for Leu6 and Leu10 in the formation of stable disulfide-linked dimers. The 1.0 Å resolution crystal structure of the peptide dimer supports these data, revealing a leucine-rich LxxLL dimer interface with canonical knobs-into-holes packing. Two levels of higher-order oligomerization are also observed in the crystal: an antiparallel “dimer of dimers” mediated by Phe3 and Trp7 residues in the asymmetric unit and a tetramer of dimers mediated by Trp7 and Leu10. In CD spectra of Trp-containing peptide variants, minima at 227 nm provide evidence for the dimer of dimers in dilute aqueous solution. Importantly, and in contrast to the original dimer model, the canonical leucine-rich core and robust dimerization of most peptide variants suggests a tunable molecular architecture to target various proteins and evaluate how folding and oligomerization impact various properties, such as cell permeability.

36 MATERIALS SCIENCE↗

Statistical analysis and degradation pathway modeling of photovoltaic minimodules with varied packaging strategies

Degradation pathway models constructed using network structural equation modeling (netSEM) are used to study degradation modes and pathways active in photovoltaic (PV) system variants in exposure conditions of high humidity and temperature. This data-driven modeling technique enables the exploration of simultaneous pairwise and multiple regression relationships between variables in which several degradation modes are active in specific variants and exposure conditions. Durable and degrading variants are identified from the netSEM degradation mechanisms and pathways, along with potential ways to mitigate these pathways. A combination of domain knowledge and netSEM modeling shows that corrosion is the primary cause of the power loss in these glass/backsheet PV minimodules. We show successful implementation of netSEM to elucidate the relationships between variables in PV systems and predict a specific service lifetime. The results from pairwise relationships and multiple regression show consistency. This work presents a greater opportunity to be expanded to other materials systems.

electrical measurements↗

Data for "Photoinduced Chemomimetic Biocatalysis for Enantioselective Intermolecular Radical Conjugate Addition"

Exploiting nature’s catalysts for non-natural transformations that are inaccessible to chemocatalysis is highly desirable but challenging. On the one hand, the widespread nicotinamide-dependent oxidoreductases have not been utilized for single-electron-transfer-induced bimolecular cross-couplings; on the other, the addition of catalytic asymmetric radical conjugate to terminal alkenes remains a challenge owing to strong racemic background reaction and unselective termination of prochiral radical species. Here we report a chemomimetic biocatalysitic approach for construction of alpha-carbonyl stereocentres via an unnatural intermolecular conjugate addition of N-(acyloxy)phthalimides-derived radicals with acceptor-substituted terminal alkenes, by combination of visible-light excitation and nicotinamide-dependent ketoreductases (KREDs). Based on protein crystal structure, we engineered KREDs via a semi-rational mutagenesis strategy to improve reaction outcomes with a small and high-quality variants library. Mechanistic investigations combining wet experiments, crystallographic studies and computational simulations demonstrate that the repurposed biocatalyst can suppress racemic background reaction and unselected side reactions, yielding enantioselectivity that is challenging to achieve by chemocatalysis.

Catalysis↗

RidgeAlloy: A high pressure die casting alloy that captures the approaching wave of automotive body sheet scrap

Oak Ridge National Laboratory (ORNL) has recently launched an effort to economically expand the North American aluminum supply chain by designing and developing a new family of Al-Mg-Si-Fe-Mn structural die cast aluminum alloys that can be made from up to 100% mixed 5xxx and 6xxx series automotive post-consumer sheet scrap and do not require heat treatment. The goal is to develop an alloy capable of capturing the approaching scrap wave of aluminum sheet intensive vehicles (in the 2030’s) into integrated structural high pressure die castings, rather than down-cycling these high-grade sheet alloys into non-structural castings. ORNL discovered a significant gap in the commercial thermodynamic databases that were unable to predict the trends of a key primary intermetallic phase as a function of composition. Experiments were performed to correct this gap and to create a unique, corrected quaternary database for Al-Mg-Si-Fe. High throughput computational methods, including solidification simulations, were used to identify a composition volume capable of avoiding this embrittling primary intermetallic phase, even at higher Fe + Si contents. Laboratory scale castings validated the thermodynamic and solidification predictions and resulted in lab-cast alloys with little primary intermetallic, and which met or exceeded structural casting properties requirements for yield strength and ductility. An accelerated demonstration of an HPDC automotive part was conducted in collaboration with two U.S. small businesses. Ingots made from 100% recycled 5xxx and 6xxx series scrap (plus Fe) were used to die cast one variant of this new family of Al-Mg-Si-Fe-Mn alloys (with high Si + Fe content) into a mid-sized HPDC structural-type automotive component. The HPDC alloy demonstration part showed good properties (especially ductility) and good castability for a complex component.

Plotkowski, Alex [ORNL] (ORCID:0000000154718681)↗

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Design principles for site-selective hydroxylation by a Rieske oxygenase

Rieske oxygenases exploit the reactivity of iron to perform chemically challenging C–H bond functionalization reactions. Thus far, only a handful of Rieske oxygenases have been structurally characterized and remarkably little information exists regarding how these enzymes use a common architecture and set of metallocenters to facilitate a diverse range of reactions. Herein, we detail how two Rieske oxygenases SxtT and GxtA use different protein regions to influence the site-selectivity of their catalyzed monohydroxylation reactions. We present high resolution crystal structures of SxtT and GxtA with the native β-saxitoxinol and saxitoxin substrates bound in addition to a Xenon-pressurized structure of GxtA that reveals the location of a substrate access tunnel to the active site. Ultimately, this structural information allowed for the identification of six residues distributed between three regions of SxtT that together control the selectivity of the C–H hydroxylation event. Substitution of these residues produces a SxtT variant that is fully adapted to exhibit the non-native site-selectivity and substrate scope of GxtA. Importantly, we also found that these selectivity regions are conserved in other structurally characterized Rieske oxygenases, providing a framework for predictively repurposing and manipulating Rieske oxygenases as biocatalysts.

59 BASIC BIOLOGICAL SCIENCES↗

Tensor network investigation of the double layer Kagome compound Ca 10 Cr 7 O 28

Quantum spin liquids are exotic quantum phases of matter that do not order even at zero temperature. While there are several toy models and simple Hamiltonians that could host a quantum spin liquid as their ground state, it is very rare to find actual, realistic materials that exhibit their properties. At the same time, the classical simulation of such instances of strongly correlated systems is intricate and reliable methods are scarce. Here, in this work, we investigate the quantum magnet Ca 10 Cr 7 O 28 that has recently been discovered to exhibit properties of a quantum spin liquid in inelastic neutron scattering experiments. This compound has a distorted bilayer Kagome lattice crystal structure consisting of Cr 5+ ions with spin- moments. Coincidentally, the lattice structure renders a tensor network algorithm in 2D applicable that can be seen as a new variant of a projected entangled simplex state algorithm in the thermodynamic limit. In this first numerical investigation of this material that takes into account genuine quantum correlations, good agreement with the experimental findings is found. Our study contributes to uplifting tensor networks from conceptual tools to methods to describe real two-dimensional quantum materials.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Quantitative SANS and multi-model analysis of spacer-dependent micellization of urea-based gemini surfactants

The micellization behavior of urea-based cationic gemini surfactants was investigated using small-angle neutron scattering (SANS) with multi-model form factor analysis. A homologous series of surfactants with urea group included in the hydrophobic tail and polymethylene spacers consisting of two to ten methylene units was analyzed using three form factor models: a core–shell ellipsoid and two variants of homogeneous ellipsoids. The results from all models show a consistent trend of the micelle structures, confirming that the spacer length critically influences micellar geometry, aggregation number, and hydration. The surfactant with four CH 2 groups in the spacer formed the largest micelles with the highest aggregation number, while longer spacers led to progressively smaller, more compact aggregates. The shell hydration—quantified as the volume fraction of heavy water within the hydrophilic region—decreased systematically with increasing spacer length due to enhanced hydrophobicity of the headgroup-spacer region. Intermicellar interactions, modeled as screened Coulomb interaction using the rescaled mean spherical approximation (RMSA), revealed the strongest electrostatic repulsion for the case of four methylene groups in the spacer, corresponding to the highest micellar charge and largest interparticle spacing. The observed spacer-dependent trends were robust across all modeling approaches, demonstrating that the spacer length serves as a key structural determinant of self-assembly in this type of urea-based gemini systems. These findings provide insight into the design of gemini surfactants with tailored aggregation behavior for applications in drug delivery, nanostructure templating, and solubilization technologies.

Core–shell ellipsoid model↗

Using hole injection layers for decreased metastability and higher performance in Cu(In,Ga)Se 2 devices

In this work, modifications to the buffer structure in Cu(In,Ga)Se 2 (CIGS) solar cells are examined in terms of power conversion efficiency and metastability. Varying amounts of thin hole-injecting layers are introduced at different locations in the CIGS/Zn(O,S) device structure. It is found that such layers simultaneously increase performance and decrease metastability. The most effective variant produces devices without metastability and with higher efficiency than the CdS-only controls. The most effective location for hole injection is found to be between the Zn(O,S) buffer and the transparent conductor. At this location, passivation of the CIGS surface is not a function of the hole injection layer, and thus a variety of materials with appropriate band-edge energies should achieve the same purpose.

36 MATERIALS SCIENCE↗

An African-Specific Variant of TP5 3 Reveals PADI4 as a Regulator of p53-Mediated Tumor Suppression

TP53 is the most frequently mutated gene in cancer, yet key target genes for p53-mediated tumor suppression remain unidentified. Here, we characterize a rare, African-specific germline variant of TP53 in the DNA-binding domain Tyr107His (Y107H). Nuclear magnetic resonance and crystal structures reveal that Y107H is structurally similar to wild-type p53. Consistent with this, we find that Y107H can suppress tumor colony formation and is impaired for the transactivation of only a small subset of p53 target genes; this includes the epigenetic modifier PADI4, which deiminates arginine to the nonnatural amino acid citrulline. Surprisingly, we show that Y107H mice develop spontaneous cancers and metastases and that Y107H shows impaired tumor suppression in two other models. We show that PADI4 is itself tumor suppressive and that it requires an intact immune system for tumor suppression. We identify a p53–PADI4 gene signature that is predictive of survival and the efficacy of immune-checkpoint inhibitors.

60 APPLIED LIFE SCIENCES↗

Consistency, Verification, and Validation of Turbulence Models for Reynolds-Averaged Navier-Stokes Applications

In current practice, it is often difficult to draw firm conclusions about turbulence model accuracy when performing multi-code CFD studies ostensibly using the same model because of inconsistencies in model formulation or implementation in different codes. This paper describes an effort to improve the consistency, verification, and validation of turbulence models within the aerospace community through a website database of verification and validation cases. Some of the variants of two widely-used turbulence models are described, and two independent computer codes (one structured and one unstructured) are used in conjunction with two specific versions of these models to demonstrate consistency with grid refinement for several representative problems. Naming conventions, implementation consistency, and thorough grid resolution studies are key factors necessary for success.

Rumsey, Christopher L.↗

Preemptive optimization of a clinical antibody for broad neutralization of SARS-CoV-2 variants and robustness against viral escape

Most previously authorized clinical antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have lost neutralizing activity to recent variants due to rapid viral evolution. To mitigate such escape, we preemptively enhance AZD3152, an antibody authorized for prophylaxis in immunocompromised individuals. Using deep mutational scanning (DMS) on the SARS-CoV-2 antigen, we identify AZD3152 vulnerabilities at antigen positions F456 and D420. Through two iterations of computational antibody design that integrates structure-based modeling, machine-learning, and experimental validation, we co-optimize AZD3152 against 24 contemporary and previous SARS-CoV-2 variants, as well as 20 potential future escape variants. Our top candidate, 3152-1142, restores full potency (100-fold improvement) against the more recently emerged XBB.1.5+F456L variant that escaped AZD3152, maintains potency against previous variants of concern, and shows no additional vulnerability as assessed by DMS. This preemptive mitigation demonstrates a generalizable approach for optimizing existing antibodies against potential future viral escape.

59 BASIC BIOLOGICAL SCIENCES↗

Structure and epitope of a neutralizing monoclonal antibody that targets the stem helix of β coronaviruses

Monoclonal antibodies that retain neutralizing activity against multiple coronavirus (CoV) lineages and variants of concern (VoC) must be developed to protect against future pandemics. These broadly neutralizing MAbs (BNMAbs) may be used as therapeutics and/or to assist in the rational design of vaccines that induce BNMAbs. 1249A8 is a BNMAb that targets the stem helix (SH) region of CoV spike (S) protein and neutralizes Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) original strain, delta, and omicron VoC, Severe Acute Respiratory Syndrome CoV (SARS-CoV), and Middle East Respiratory Syndrome CoV (MERS-CoV). To understand its mechanism of action, the crystal structure of 1249A8 bound to a MERS-CoV SH peptide was determined at 2.1 Å resolution. BNMAb 1249A8 mimics the SARS-CoV-2 S loop residues 743–749, which interacts with the N-terminal end of the SH helix in the S post-fusion conformation. The conformation of 1249A8-bound SH is distinct from the SH conformation observed in the post-fusion SARS-CoV-2 S structure, suggesting 1249A8 disrupts the secondary structure and refolding events required for CoV post-fusion S to initiate membrane fusion and ultimately infection. This study provides novel insights into the neutralization mechanisms of SH-targeting CoV BNMAbs that may inform vaccine development and the design of optimal BNMAb therapeutics.

60 APPLIED LIFE SCIENCES↗

Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes

Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs.

59 BASIC BIOLOGICAL SCIENCES↗

Down-Selection of Four Common Habitat Variants

The Common Habitat is a large habitat developed as an alternative architecture study, not part of the current NASA baseline, that uses the SLS core stage liquid oxygen tank as its primary structure. It has a gravity-independent internal architecture, such that identical units can be used on the lunar surface, Mars surface, and in microgravity. In developing the habitat, two key architectural questions emerged. Should the internal layout use a vertical or horizontal orientation of the tank? Should the crew size be four or eight? This led to the design of four variants: a four-crew horizontal, four-crew vertical, eight-crew horizontal, and eight-crew vertical. The four-crew variants use a shortened version of the tank while the eight-crew variants use the entire tank. The primary consideration applied for down-selection is the crew experience living and working in the habitat, inclusive of crew productivity, well-being, and survivability. Based on this consideration, a series of seven assessments were performed to compare the variants. This analysis was performed as an unfunded, volunteer activity leveraging civil servants across multiple field centers, most with expertise working in various Artemis teams. Additionally, the evaluation was limited to the use of CAD models, images, and spreadsheet data, with no resources available for mockups or Virtual Reality. A logistics analysis developed a standard logistics module and then estimated how much stowage could be carried onboard each Common Habitat and how many logistics modules are required by each variant for a given mission duration. It also considered the amounts of water to be stored in each variant. A functional analysis identified and compared the living and working functions across the habitats, ranking them relative to each other. A crew time assessment first estimated the total crew time, building a weekly crew timeline for both four and eight-person crews. It then allocated time to activities linked to living and working functions, comparing how much time was available for each function in each variant. A science productivity assessment developed a relative metric using crew time, science stowage, and assumed rates of experiment consumables use to analytically compare the four variants. It also comparatively ranked the habitats with respect to a number of subjective parameters and a workstation acceptability rating. A maintenance capacity assessment identified and compared eleven generic maintenance capabilities across the variants and also ranked them for their predicted ability to complete twelve fabrication, maintenance, and repair scenarios. A contingency responsiveness analysis examined twelve serious in-flight contingencies. For each scenario, the number of crew needed to respond were predicted and acceptability of various aspects of contingency response were evaluated, comparing the variants against each other. Finally, in a habitability assessment, 120 habitability characteristics reflecting 13 major categories were evaluated for each habitat. These results were compared to identify the most acceptable habitat in each category. Ultimately, the data favored the horizontal orientation over the vertical and an eight-person crew over four. Implications of selecting this variant are discussed, including specific architectural challenges that result from the use of the full tank.

Habitability↗

Rapid assessment of SARS-CoV-2–evolved variants using virus-like particles

Efforts to determine why new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants demonstrate improved fitness have been limited to analyzing mutations in the spike (S) protein with the use of S-pseudotyped particles. In this study, we show that SARS-CoV-2 virus-like particles (SC2-VLPs) can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and at multiple steps in the viral life cycle. In SC2-VLPs, four nucleocapsid (N) mutations found universally in more-transmissible variants independently increased messenger RNA delivery and expression ~10-fold, and in a reverse genetics model, the serine-202→arginine (S202R) and arginine-203→methionine (R203M) mutations each produced >50 times as much virus. SC2-VLPs provide a platform for rapid testing of viral variants outside of a biosafety level 3 setting and demonstrate N mutations and particle assembly to be mechanisms that could explain the increased spread of variants, including B.1.617.2 (Delta, which contains the R203M mutation).

60 APPLIED LIFE SCIENCES↗

The complexity of { 11 2 ¯ 1 } twin interface structure and energetics in HCP materials

Here, the quest for a deeper understanding of the mechanical properties of HCP alloys has been an ongoing effort. Due to the lack of a sufficient number of slip systems, twin nucleation and migration originate as a substantial plastic deformation mechanism in HCP metals. The paper uncovers the energetics and atomistic mechanism of the {$11\overline{2}1$} < $11\overline{2}6$ > which is one of the most prominent twin modes in HCP materials that has not been fully understood. In view of corrugated {$11\overline{2}1$} interfaces, the positioning of lattice/motif atoms needs to be clarified. First, we establish the initial twin boundary (TB) structure unambiguously via the lattice offsets resulting in volume invariancy and correct relative positioning of the twin variants. Secondly, the TB migration mechanism is determined from a crystallographic (zero net shuffle, $Σ\vec{s}$ = 0) and energetic standpoints (minimum energy path). The Generalized Planar Fault Energy (GPFE) curves are calculated for Ti, Hf, Mg, and Zr. Such GPFE curves for this twin mode are calculated for the first time, and point to unusually high unstable energies (300-850 mJ/m 2 ), and low migration barriers (<60 mJ/m 2 ) for twinning accompanied with large shuffle magnitudes, |$\vec{s}$|, comparable to the Burger’s vector (|$\vec{s}$| ≅ $b_e$ > 0.44Å)

36 MATERIALS SCIENCE↗

Modified Iterative Extended Hueckel. 1: Theory

Iterative Extended Huekel is modified by inclusion of explicit effective internuclear and electronic interactions. The one electron energies are shown to obey a variational principle because of the form of the effective electronic interactions. The modifications permit mimicking of aspects of valence bond theory with the additional feature that the energies associated with valence bond type structures are explicitly calculated. In turn, a hybrid molecular, orbital valence, bond scheme is introduced which incorporates variant total molecular electronic density distributions similar to the way that Iterative Extended Hueckel incorporates atoms.

Aronowitz, S.↗